From owner-proteins@hgmp.mrc.ac.uk  Sat Apr  1 22:09:10 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 47F5817A4E; Sat,  1 Apr 2000 22:09:10 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA13932
	for <proteins-list@hgmp.mrc.ac.uk>; Sat, 1 Apr 2000 22:09:08 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA19523
	for proteins-list@hgmp.mrc.ac.uk; Sat, 1 Apr 2000 22:09:07 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: 01142000@theheadoffice.com
X-Newsgroups: bionet.molbio.proteins
Subject: Work From Home In Your Sweats!
Date: 1 Apr 2000 22:09:07 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 39
Message-ID: <200004012107.XAA15598@tikal.hef.kun.nl>
X-Trace: niobium.hgmp.mrc.ac.uk 954623347 19521 193.62.192.80 (1 Apr 2000 21:09:07 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from tikal.hef.kun.nl (root@tikal.hef.kun.nl [131.174.192.96])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id WAA13790
	for <proteins@net.bio.net>; Sat, 1 Apr 2000 22:09:05 +0100 (BST)
X-Received: from unknown (phoenix-ip-2-138.dynamic.ziplink.net [209.206.49.138]) by tikal.hef.kun.nl with SMTP (8.8.6 (PHNE_17135)/8.7.1) id XAA15598; Sat, 1 Apr 2000 23:07:45 +0200 (METDST)
X-To: klfldfjk@mail.com
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk



This Is NOT Multi Level Marketing

LOOKING FOR GEMS!

It's So Simple To Earn $2,000 - $5,000 Per Week Nowadays...
We're searching for only 10 elite individuals with the work ethic necessary to generate a cash-flow for themselves of $2,000 - $5,000 per week, and to increase that to over $20,000 per month, in as little as four to six months.

And you know what? If you really have a burning desire and commitment, we guarantee you that you'll reach this explosive income!

Can you read a short script to our qualified leads, and then turn the
interested prospects over to our electronic sales medium? (you will not be required to do any selling.)

Do you have the self-discipline to ignore the TV
for a couple of hours per day?

Are you looking for a legitimate home-based business opportunity, that is not multi-level marketing or a chain-letter scheme?

If you would like to build an amazing income that will grow lightning-fast and have you profit $1,000.00 every time only one prospect makes a purchase, then this is for you! You can build the business under our guidance and support without having to attend meetings or sell people things they don't need.

Call NOW our TOLL FREE, PRE-RECORDED Message: 1-800-320-9895 Ext. 7866

We market a real product, that pays real commissions to you,$1,000.00 per sale, just for making the initial contacts. With our turn-key lead
generation systems you'll always talk to people who actually WANT to talk to you.

You have nothing to lose, there's no risk involved, nor is there any
obligation whatsoever, and you may be qualified to earn thousands of extra dollars per month! So call now!

The call is FREE, and there is absolutely no obligation, So what have you got to lose?

Call Toll Free 1-800-320-9895 Ext. 7866

P.S. You literally have a once-in-a-lifetime opportunity to GET INVOLVED NOW!

Don't let this one go by. You have absolutely nothing to lose! This could be the most fascinating and profitable business of your life!

Please, serious inquiries only.
---


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr  3 07:27:00 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 5D75617A8D; Mon,  3 Apr 2000 07:26:59 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA23945
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 3 Apr 2000 07:26:57 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA21326
	for proteins-list@hgmp.mrc.ac.uk; Mon, 3 Apr 2000 07:26:55 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Christina Philipp <philipp@mpiz-koeln.mpg.de>
X-Newsgroups: bionet.molbio.proteins
Subject: Expression of a 300kDa protein possible?
Date: Mon, 03 Apr 2000 08:27:21 +0200
Organization: MPI fuer Zuechtungsforschung, Koeln
Lines: 13
Message-ID: <8c9djd$2jpi$1@gwdu67.gwdg.de>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: gwdu67.gwdg.de 954743213 85810 195.37.46.55 (3 Apr 2000 06:26:53 GMT)
X-Complaints-To: news@gwdg.de
X-Mailer: Mozilla 4.6 [en] (WinNT; I)
X-Accept-Language: de
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hello Ng,

until now, I tried two methods to express my protein:
1. TNT T7 Quick Coupled Transcription/Translation System (Promega).
The luciferase control worked well, but I did not see my desired
protein.
2. A "normal" expression (T7 promoter, induction with 1mM IPTG) in E.
coli HMS174(DE3).

Has anyone ever had success with the expression of such a large
protein?
Thank you for your help.
Christina


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr  3 08:43:34 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 9BCBB17A8D; Mon,  3 Apr 2000 08:43:33 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA26928
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 3 Apr 2000 08:43:31 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA22127
	for proteins-list@hgmp.mrc.ac.uk; Mon, 3 Apr 2000 08:43:30 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Richard P. Grant" <rgrant@netscape.net>
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Expression of a 300kDa protein possible?
Date: Mon, 03 Apr 2000 08:43:30 +0100
Organization: MRC LMB
Lines: 25
Message-ID: <rgrant-5FD1EF.08433003042000@nntp-serv.cam.ac.uk>
References: <8c9djd$2jpi$1@gwdu67.gwdg.de>
User-Agent: MT-NewsWatcher/3.0 (PPC)
X-No-Archive: yes
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

In article <8c9djd$2jpi$1@gwdu67.gwdg.de>, Christina Philipp 
<philipp@mpiz-koeln.mpg.de> wrote:

> Hello Ng,
> 
> until now, I tried two methods to express my protein:
> 1. TNT T7 Quick Coupled Transcription/Translation System (Promega).
> The luciferase control worked well, but I did not see my desired
> protein.
> 2. A "normal" expression (T7 promoter, induction with 1mM IPTG) in E.
> coli HMS174(DE3).
> 
> Has anyone ever had success with the expression of such a large
> protein?


I successfully expressed a 220 kDa protein once, it required 1 % glucose 
and 1 mM Mg2+ adding to the 2xTY (I kept getting premature termination 
of translation) . . .  it may help you.

-- 
Richard P. Grant MAD Phil          http://www.gerbil.org.uk/
Please reply to rpg 'at' mrc-lmb.cam.ac.uk

'There's a fine line between genius and just farting around'


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr  3 13:17:04 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1056017A84; Mon,  3 Apr 2000 13:17:02 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA24107;
	Mon, 3 Apr 2000 13:16:51 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA25738;
	Mon, 3 Apr 2000 13:16:50 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Richard P. Grant" <rgrant@netscape.net>
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: 2ndry structure prediction
Date: Mon, 03 Apr 2000 13:16:49 +0100
Organization: MRC LMB
Lines: 16
Message-ID: <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>
User-Agent: MT-NewsWatcher/3.0 (PPC)
X-No-Archive: yes
To: bio-software@hgmp.mrc.ac.uk, proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hi peeps,

Please excuse the x-post.  Which secondary structure prediction method 
is generally reckoned the 'best' these days.  I know about 
http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any 
other pointers.

Cheers,

Richard

-- 
Richard P. Grant MAD Phil          http://www.gerbil.org.uk/
Please reply to rpg 'at' mrc-lmb.cam.ac.uk

'There's a fine line between genius and just farting around'


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr  3 15:25:59 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1753E17AA6; Mon,  3 Apr 2000 15:25:58 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA08040;
	Mon, 3 Apr 2000 15:25:57 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA27281;
	Mon, 3 Apr 2000 15:25:55 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: letondal@nefertiti.pasteur.fr (Catherine  Letondal)
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: Re: 2ndry structure prediction
Date: 3 Apr 2000 14:25:46 GMT
Organization: Institut Pasteur, Paris
Lines: 16
Message-ID: <8ca9la$vv7$1@desdemone.pasteur.fr>
References: <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>
Reply-To: letondal@nefertiti.pasteur.fr (Catherine  Letondal)
X-Trace: desdemone.pasteur.fr 954771946 32743 157.99.64.20 (3 Apr 2000 14:25:46 GMT)
X-Complaints-To: usenet@pasteur.fr
X-Newsreader: mxrn 6.18-31
To: bio-software@hgmp.mrc.ac.uk, proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


In article <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>, "Richard P. Grant" <rgrant@netscape.net> writes:
>Hi peeps,
>
>Please excuse the x-post.  Which secondary structure prediction method 
>is generally reckoned the 'best' these days.  I know about 
>http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any 
>other pointers.

Try:
http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&query=second&bio=structural+biology

(BioNetbook: http://www.pasteur.fr/recherche/BNB/bnb-en.html)

-- 
Catherine Letondal -- Pasteur Institute Computing Center


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr  4 08:55:26 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 25FB517A58; Tue,  4 Apr 2000 08:55:24 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA13488;
	Tue, 4 Apr 2000 08:55:23 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA18511;
	Tue, 4 Apr 2000 08:55:22 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Richard P. Grant" <rgrant@netscape.net>
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: Re: 2ndry structure prediction
Date: Tue, 04 Apr 2000 08:55:23 +0100
Organization: MRC LMB
Lines: 16
Message-ID: <rgrant-80E868.08552304042000@nntp-serv.cam.ac.uk>
References: <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk> <8ca9la$vv7$1@desdemone.pasteur.fr>
User-Agent: MT-NewsWatcher/3.0 (PPC)
X-No-Archive: yes
To: bio-software@hgmp.mrc.ac.uk, proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


Hi again,

http://globin.bio.warwick.ac.uk/psipred/

looks pretty good, gave good results on a known structure too.

Thanks everyone.

R

-- 
Richard P. Grant MAD Phil          http://www.gerbil.org.uk/
Please reply to rpg 'at' mrc-lmb.cam.ac.uk

'There's a fine line between genius and just farting around'


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr  4 13:25:41 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 43DB117AE3; Tue,  4 Apr 2000 13:25:39 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA13810
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 4 Apr 2000 13:25:37 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA22115
	for proteins-list@hgmp.mrc.ac.uk; Tue, 4 Apr 2000 13:25:35 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Paul <pd1@mole.bio.cam.ac.uk>
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Expression of a 300kDa protein possible?
Date: Tue, 04 Apr 2000 13:29:37 +0100
Organization: Virology
Lines: 54
Message-ID: <38E9E031.8B831D12@mole.bio.cam.ac.uk>
References: <8c9djd$2jpi$1@gwdu67.gwdg.de>
Reply-To: pd1@mole.bio.cam.ac.uk
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 4.7 (Macintosh; I; PPC)
X-Accept-Language: en,pdf
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk



Christina Philipp wrote:

> Hello Ng,
>
> until now, I tried two methods to express my protein:
> 1. TNT T7 Quick Coupled Transcription/Translation System (Promega).
> The luciferase control worked well, but I did not see my desired
> protein.

You don't say what you did get with the IVT: a smear of shorter products
or
nothing at all?  (The latter would indicate a problem with the construct

rather than retic struggling to make such a large protein).

The largest protein I've made/seen made in retic is up around the 250
kDa mark,
(albeit with quite a lot of shorter crap too), so 300 should be
possible.

There are a few things you can do to improve your chances:

1) Do the TNT at 37, not 30 (as the protocol used to sugggest)

2) Play with the Mg2+ concentration: easier (and a lot cheaper) to do
this if you
buy ordinary retic from Promega and make your own "home-made" TNT kit by
adding
NTPs, T7 (GIBCO enzyme works well) and Mg according to the protocol of
Craig, NAR 20, 4987 (1992). Optimal incorporation of 35S-met doesn't
equate
with optimal translation quality, and it does seem to vary according to
the template.

3) Transcribe capped RNA separately and titrate into plain retic: too
much
RNA often leads to increased amounts of internal initiation/premature
termination.

I've never tired this, but people tell me that titrating KCl can also
help translation
quality.

Hope this is useful.

Paul Digard

Division of Virology
Department of Pathology
University of Cambridge




From owner-proteins@hgmp.mrc.ac.uk  Tue Apr  4 14:50:55 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 8FEE317B0A; Tue,  4 Apr 2000 14:50:54 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA25993
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 4 Apr 2000 14:50:52 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA23129
	for proteins-list@hgmp.mrc.ac.uk; Tue, 4 Apr 2000 14:50:50 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Edith <djianaNOdjSPAM@hotmail.com.invalid>
Subject: Recovering activity in fusion protein?
X-Newsgroups: bionet.molbio.proteins
Message-ID: <089f08e0.e4006b01@usw-ex0109-069.remarq.com>
Lines: 8
Bytes: 324
X-Originating-Host: 132.204.195.68
Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here
X-Wren-Trace: eICljYyV0pjTxJ6BhM6AqZqchIiEjczYhoOCw9jHy47d1pTP35nAwNrZ
Date: Tue, 04 Apr 2000 06:38:53 -0700
X-Complaints-To: wrenabuse@remarq.com
X-Trace: WReNphoon2 954855952 10.0.2.69 (Tue, 04 Apr 2000 06:45:52 PDT)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hi everybody.
I'm looking for means to recover a cabbage methyl-
transferase activity in E. coli lysate, after indution of
expression with IPTG.
Thanks in advance.


* Sent from AltaVista http://www.altavista.com Where you can also find related Web Pages, Images, Audios, Videos, News, and Shopping.  Smart is Beautiful


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr  4 17:09:39 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id EE30F17B51; Tue,  4 Apr 2000 17:09:36 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA15343
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 4 Apr 2000 17:09:33 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA24933
	for proteins-list@hgmp.mrc.ac.uk; Tue, 4 Apr 2000 17:09:32 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Richard P. Grant" <rgrant@netscape.net>
X-Newsgroups: bionet.molbio.proteins
Subject: cancel <rgrant-5FD1EF.08433003042000@nntp-serv.cam.ac.uk>
Control: cancel <rgrant-5FD1EF.08433003042000@nntp-serv.cam.ac.uk>
Date: Tue, 04 Apr 2000 17:09:32 +0100
Organization: MRC LMB
Lines: 2
Message-ID: <rgrant-1A1C05.17093204042000@mac309-4.mrc-lmb.cam.ac.uk>
User-Agent: MT-NewsWatcher/3.0 (PPC)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Article <rgrant-5FD1EF.08433003042000@nntp-serv.cam.ac.uk> cancelled by rgrant@netscape.net



From owner-proteins@hgmp.mrc.ac.uk  Wed Apr  5 10:52:56 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 13EFF17A75; Wed,  5 Apr 2000 10:52:54 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA18478;
	Wed, 5 Apr 2000 10:52:51 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA16276;
	Wed, 5 Apr 2000 10:52:50 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Nicolas Le Novere <nl223@cus.cam.ac.uk>
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: Re: 2ndry structure prediction
Date: Wed, 05 Apr 2000 09:43:16 +0100
Organization: university of Cambridge
Lines: 37
Message-ID: <38EAFCA4.29F3E6AB@cus.cam.ac.uk>
References: <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.2.13 i686)
X-Accept-Language: en
To: bio-software@hgmp.mrc.ac.uk, proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

"Richard P. Grant" wrote:

> Please excuse the x-post.  Which secondary structure prediction method
> is generally reckoned the 'best' these days.  I know about
> http://www.EMBL-Heidelberg.DE/predictprotein/  would appreciate any
> other pointers.

see http://www.pasteur.fr/recherche/unites/neubiomol/ secstrpr.html
for pointers, references and a little discussion.

Important: use SEVERAL programs, based on DIFFERENT approaches 
See the result of JPRED with PHD+DSC+NNSSP+PREDATOR

Currently the best are:

->statistical information (GOR, hydrophobicity etc ...)
	DSC - It is not maintained anymore, because its son, PROF
is launched. However nothing is published. You can find DSC on the
pasteur website. Q3 ~ 70-72

->nearest-neighbor (~similarity with protein of know structures)
	NNSSP    Q3 ~ 68-72

->neural-networks
	JNET
	PSIPRED - it is a sort of reimplementation of PHD, with a 
currated alignment as input, and a better training. Q3 up to 76%

->hmm
	SAM99, aimed to be a fold-recognition program, can provide
good secondary structure predictions.

--
Dr Nicolas Le Novère                   e-mail: nl223@cus.cam.ac.uk 
Dpt Zoology, Univ Cambridge, Downing street, Cambridge CB2 3EJ, UK

tel: +44 1223 336623                          fax: +44 1223 336676


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr  5 16:21:47 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E1ADC17ABC; Wed,  5 Apr 2000 16:21:46 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA02719
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 5 Apr 2000 16:21:43 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA20580
	for proteins-list@hgmp.mrc.ac.uk; Wed, 5 Apr 2000 16:21:42 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Toninho <nhaniNOnhSPAM@fcav.unesp.br.invalid>
Subject: Protein expression in Yeast
X-Newsgroups: bionet.molbio.proteins
Message-ID: <0e54ac28.4018289a@usw-ex0109-068.remarq.com>
Lines: 6
Bytes: 233
X-Originating-Host: 200.145.127.9
Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here
X-Wren-Trace: eLSRubih5qzn+qi9v/2Vu6Wmsv+kvvGxofa5pf3y/aT146Dg9KXz7fbs
Date: Wed, 05 Apr 2000 08:09:45 -0700
X-Complaints-To: wrenabuse@remarq.com
X-Trace: WReNphoon2 954947807 10.0.2.68 (Wed, 05 Apr 2000 08:16:47 PDT)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Is there a tip and/or hint to obtain transformants using a
11 Kb plasmid?



* Sent from AltaVista http://www.altavista.com Where you can also find related Web Pages, Images, Audios, Videos, News, and Shopping.  Smart is Beautiful


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr  6 05:00:24 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 8D65D17A72; Thu,  6 Apr 2000 05:00:23 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id FAA07370
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 6 Apr 2000 05:00:21 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id FAA08229
	for proteins-list@hgmp.mrc.ac.uk; Thu, 6 Apr 2000 05:00:20 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: k-yap@bs.aist-nara.ac.jp (yunkiam)
X-Newsgroups: bionet.molbio.proteins
Subject: fusion protein expression
Date: 6 Apr 2000 05:00:20 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 25
Message-ID: <38EC0BDF.A9AE6185@bs.aist-nara.ac.jp>
Mime-Version: 1.0
Content-Type: text/plain; charset=iso-2022-jp
Content-Transfer-Encoding: 7bit
X-Trace: niobium.hgmp.mrc.ac.uk 954993620 8227 193.62.192.80 (6 Apr 2000 04:00:20 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from bs.aist-nara.ac.jp (enterprise.aist-nara.ac.jp [163.221.80.21])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id FAA07362
	for <proteins@net.bio.net>; Thu, 6 Apr 2000 05:00:17 +0100 (BST)
X-Received: (qmail 5687 invoked from network); 6 Apr 2000 13:00:14 +0900
X-Received: from ryo1219.aist-nara.ac.jp (HELO bs.aist-nara.ac.jp) (163.221.150.60)
  by bsmailgate.aist-nara.ac.jp with SMTP; 6 Apr 2000 13:00:14 +0900
X-Mailer: Mozilla 4.7 [ja] (Win95; I)
X-Accept-Language: ja
X-To: proteins@hgmp.mrc.ac.uk
X-CC: k-yap@bs.aist-nara.ac.jp
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Dear netters,

I am a PhD student in Japan.  I am facing some problems in expressing my
fusion proteins (both GST-fusions and His-tag fusions) in soluble
fractions; therefore I decided to use  the TNT-coupled recticulocyte
system to synthesis the desired proteins.

I need to use these fusion proteins for the following assay:

(i) protein interaction - pull down assay
(ii) in-vitro kinase assay

My questions are:

(i) how to purify the translated product from the TNT- coupled
recticulocyte system?
(ii) Are there any references for the above assays (pull down assay &
in-vitro kinase assay) using both in-vitro translated fusion proteins?

Your help are kindly appreciated. Thank you.

sincerely,
YK

---


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr  6 16:40:59 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id B8D7117AA6; Thu,  6 Apr 2000 16:40:58 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA23532
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 6 Apr 2000 16:40:56 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA17629
	for proteins-list@hgmp.mrc.ac.uk; Thu, 6 Apr 2000 16:40:55 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "-" <leadinginfo@adelphia.net>
X-Newsgroups: bionet.molbio.proteins
Subject: Obtaining Proteins
Lines: 6
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2314.1300
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300
Message-ID: <ae2H4.5$UW.156797@news2.news.adelphia.net>
Date: Thu, 06 Apr 2000 15:40:54 GMT
X-Complaints-To: abuse@adelphia.net
X-Trace: news2.news.adelphia.net 955035654 24.48.37.78 (Thu, 06 Apr 2000 11:40:54 EDT)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Is there anyone that can point me in the right direction on obtaining the
proteins beta-Catenin and Lef-1?  I need these to do some research with.

Thanks.




From owner-proteins@hgmp.mrc.ac.uk  Thu Apr  6 21:01:26 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1FB0217A94; Thu,  6 Apr 2000 21:01:23 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA13218
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 6 Apr 2000 21:01:20 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA20751
	for proteins-list@hgmp.mrc.ac.uk; Thu, 6 Apr 2000 21:01:18 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Neil McKenna" <nmckenna@ottawa.com>
X-Newsgroups: bionet.molbio.proteins
Subject: "Sticky" FLAG epitopes?
Date: Thu, 6 Apr 2000 15:53:04 -0400
Organization: University of Ottawa, Ottawa, Canada
Lines: 14
Message-ID: <8ciqbf$h32$1@mercury.cc.uottawa.ca>
Reply-To: "Neil McKenna" <nmckenna@ottawa.com>
Mime-Version: 1.0
Content-Type: Text/Plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2615.200
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hello,

I am currently using two FLAG-tagged proteins to test for their interaction
properties. It was recently brought to my attention that FLAG tags can be
sticky -- I am wondering now whether the two FLAG tags may increase the
interaction of my two proteins. Does anyone out there have any experience
with this happening? I'm planning on running a control with a separate
epitope, but I'd still like to hear if anyone has any experience with two
FLAG peptides interacting.

Thanks
Neil




From owner-proteins@hgmp.mrc.ac.uk  Fri Apr  7 09:19:32 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E6A6917A74; Fri,  7 Apr 2000 09:19:29 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA10874
	for <proteins-list@hgmp.mrc.ac.uk>; Fri, 7 Apr 2000 09:19:26 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA08105
	for proteins-list@hgmp.mrc.ac.uk; Fri, 7 Apr 2000 09:19:25 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38ED9A0A.398E543E@nospam.gmx.ch>
Date: Fri, 07 Apr 2000 10:19:24 +0200
From: "M. Hertel" <hippocampus@nospam.gmx.ch>
Organization: ETH-Zuerich
X-Mailer: Mozilla 4.51 (Macintosh; I; PPC)
X-Accept-Language: en
MIME-Version: 1.0
X-Newsgroups: bionet.molbio.proteins
Subject: recipe for a Prestained Protein Marker?
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit
X-Trace: 7 Apr 2000 10:19:20 +0100, knockout.ethz.ch
Lines: 10
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hello,
We are looking for a recipe for a self made PRESTAINED protein marker,
or a way to prestain an unstained protein weight  standard,
Anybody out there with a good solution? The commercially available
products are quit expensive, and we will need a lot in the next time for
a student course.
Thanks for Your ideas
Moritz




From owner-proteins@hgmp.mrc.ac.uk  Fri Apr  7 11:31:34 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3EB3B17A58; Fri,  7 Apr 2000 11:31:31 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA25612
	for <proteins-list@hgmp.mrc.ac.uk>; Fri, 7 Apr 2000 11:30:07 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA09743
	for proteins-list@hgmp.mrc.ac.uk; Fri, 7 Apr 2000 11:30:06 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Petri Kursula <pkursula@cc.oulu.fi>
X-Newsgroups: bionet.molbio.proteins
Subject: Workshop/Mini-Conference
Date: Fri, 7 Apr 2000 13:27:25 +0300
Organization: University of Oulu
Lines: 9
Message-ID: <Pine.GSO.4.21.0004071326560.19373-100000@sun3.oulu.fi>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Trace: ousrvr3.oulu.fi 955103249 7397 130.231.240.13 (7 Apr 2000 10:27:29 GMT)
X-Complaints-To: news@news.oulu.fi
X-Sender: pkursula@sun3.oulu.fi
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Workshop/Mini-Conference Proteins: From Structures to Properties with
Biocomputing Approaches to be held at the University of Oulu in Finland,
June 4-6, 2000.

http://www.biochem.oulu.fi/tutkimus/Biocomputing/WorkshopBiocomputing/

Registration is open as from February 1, 2000. Dead line is April 15,
2000.



From owner-proteins@hgmp.mrc.ac.uk  Sun Apr  9 19:10:54 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id A365417AA4; Sun,  9 Apr 2000 19:10:52 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA09443
	for <proteins-list@hgmp.mrc.ac.uk>; Sun, 9 Apr 2000 19:10:47 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA07102
	for proteins-list@hgmp.mrc.ac.uk; Sun, 9 Apr 2000 19:10:46 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "SciMedWeb" <hoevel@geocities.com>
X-Newsgroups: bionet.molbio.proteins
Subject: Markers of breast cancer
Date: Sun, 9 Apr 2000 20:00:03 +0200
Organization: Planet Internet NV
Lines: 5
Message-ID: <8cqetb$oq8$5@news.planetinternet.be>
X-Trace: news.planetinternet.be 955301611 25416 195.207.174.97 (9 Apr 2000 17:33:31 GMT)
X-Complaints-To: abuse@planetinternet.be
X-Newsreader: Microsoft Outlook Express 4.71.1712.3
X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

A selection of molecular markers of breast cancer:
http://www.geocities.com/m.lacroix/marqueurs/lismark.htm





From owner-proteins@hgmp.mrc.ac.uk  Sun Apr  9 21:34:29 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 49FA717AAE; Sun,  9 Apr 2000 21:34:28 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA15741
	for <proteins-list@hgmp.mrc.ac.uk>; Sun, 9 Apr 2000 21:34:25 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA17302
	for proteins-list@hgmp.mrc.ac.uk; Sun, 9 Apr 2000 21:34:23 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38F0E935.E68EAC09@mac.com>
From: IMKoRnNuts <IMKoRnNuts@mac.com>
Reply-To: IMKoRnNuts@mac.com
X-Mailer: Mozilla 4.72C-AtHome0403 (Macintosh; I; PPC)
X-Accept-Language: en,pdf
MIME-Version: 1.0
X-Newsgroups: bionet.molbio.proteins
Subject: Research project, please help...
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit
Lines: 4
Date: Sun, 09 Apr 2000 20:33:47 GMT
X-Complaints-To: abuse@home.net
X-Trace: news1.frmt1.sfba.home.com 955312427 24.1.89.6 (Sun, 09 Apr 2000 13:33:47 PDT)
Organization: @Home Network
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I am a 17 year old high school student doing a research project for my
chemistry class. My assignment is to apply chemistry to weight lifting
and muscle production. Any help is appreciated.



From owner-proteins@hgmp.mrc.ac.uk  Mon Apr 10 18:36:34 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id F133F17AE6; Mon, 10 Apr 2000 18:36:32 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA04014
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 10 Apr 2000 18:36:30 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA03323
	for proteins-list@hgmp.mrc.ac.uk; Mon, 10 Apr 2000 18:36:25 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "mdl24" <mdl24@cam.ac.uk>
X-Newsgroups: bionet.molbio.proteins,sci.physics
Subject: Protein Folding
Date: Mon, 10 Apr 2000 18:40:36 +0100
Organization: Customer of Planet Online
Lines: 13
Message-ID: <8ct3en$d5$1@news7.svr.pol.co.uk>
X-Trace: news7.svr.pol.co.uk 955388183 421 62.136.172.206 (10 Apr 2000 17:36:23 GMT)
X-Complaints-To: abuse@theplanet.net
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2314.1300
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hello,

In Roger Penrose's book, The Emperor's New Mind, it is asserted that certain
types of crystal formation may include non-local quantum effects. It occured
to me that perhaps quantum effects are involved in protein folding - it is
impossible for a protein to try every possible conformation sequentially so
perhaps several different conformations are attempted in paralell.

Is this at all possible?

Magnus




From owner-proteins@hgmp.mrc.ac.uk  Mon Apr 10 21:23:04 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id CA7A017A7B; Mon, 10 Apr 2000 21:23:03 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA18994
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 10 Apr 2000 21:23:00 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id VAA13965
	for proteins-list@hgmp.mrc.ac.uk; Mon, 10 Apr 2000 21:22:58 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: erg@panix.com (Edward Green)
X-Newsgroups: bionet.molbio.proteins,sci.physics
Subject: Re: Protein Folding
Date: 10 Apr 2000 20:22:57 GMT
Organization: Public Access Networks Corp.
Lines: 26
Message-ID: <8ctd71$ndo$1@news.panix.com>
References: <8ct3en$d5$1@news7.svr.pol.co.uk>
X-Trace: news.panix.com 955398177 23992 166.84.0.227 (10 Apr 2000 20:22:57 GMT)
X-Complaints-To: abuse@panix.com
X-Newsreader: trn 4.0-test72 (19 April 1999)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

In article <8ct3en$d5$1@news7.svr.pol.co.uk>, mdl24 <mdl24@cam.ac.uk> wrote:
>Hello,
>
>In Roger Penrose's book, The Emperor's New Mind, it is asserted that certain
>types of crystal formation may include non-local quantum effects. It occured
>to me that perhaps quantum effects are involved in protein folding - it is
>impossible for a protein to try every possible conformation sequentially so
>perhaps several different conformations are attempted in paralell.
>
>Is this at all possible?

It sounds way cool, but why fish for the obscure before there is a
reason to doubt that protein folding may be understood as a result of
classical kinetics operating on a ball and stick molecule, the way we
often understand chemical reactions.

I think you may err in supposing that a folding protein molecule
"tries out every conformation".  It's not solving a traveling salesman
problem; it's simply choosing a locally best route.

[I see you have added some heavy duty special purpose bio group, where
there may be people who really know about protein folding...  so I
shall shortly find out, a poor generalist from sci.physics, if I know
the first thing about protein folding.  You do realize this type of
cross- posting opens an interdimensional portal, through which
sci.physics cranks may invest your universe?]


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 11 00:54:27 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6CCFF17A7C; Tue, 11 Apr 2000 00:54:26 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA16456
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 11 Apr 2000 00:54:24 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA16433
	for proteins-list@hgmp.mrc.ac.uk; Tue, 11 Apr 2000 00:54:22 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: stu@cse.ucsc.edu (Spencer Tu)
X-Newsgroups: bionet.molbio.proteins
Subject: ANNOUNCE: UCSC SAM-T99 alignment tuneup web site
Date: 10 Apr 2000 23:54:18 GMT
Organization: UC Santa Cruz CS/CE
Lines: 17
Message-ID: <8ctpja$luv@darkstar.ucsc.edu>
Summary: UCSC SAM-T99 alignment tuneup web site
Keywords: SAM-T99, SAM, HMM, multiple alignment
X-Newsreader: TIN [UNIX 1.3 950824BETA PL0]
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

The SAM-T99 alignment tuneup page is now available in beta release at

http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html

Services offered by the site include:

   1) creating a multiple alignment from unaligned sequences
   2) tuning up an existing multiple alignment
   3) adding new unaligned sequences to an existing alignment

A license for the full SAM software package may be obtained at

http://www.cse.ucsc.edu/research/compbio/sam.html


Spencer Tu
stu@cse.ucsc.edu


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 11 06:03:20 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 6971017AF5; Tue, 11 Apr 2000 06:03:18 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id GAA06180
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 11 Apr 2000 06:03:14 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id GAA19919
	for proteins-list@hgmp.mrc.ac.uk; Tue, 11 Apr 2000 06:03:12 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Mika Yehezkeli" <mika@labonweb.com>
X-Newsgroups: bionet.molbio.proteins
Subject: novel gene discovery platform
Date: Tue, 11 Apr 2000 06:47:57 +0200
Organization: NetVision Israel	
Lines: 24
Message-ID: <8cuat5$3ta$1@news.netvision.net.il>
X-Trace: news.netvision.net.il 955428581 4010 194.90.227.251 (11 Apr 2000 04:49:41 GMT)
X-Complaints-To: abuse@netvision.net.il
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2314.1300
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

LabOnWeb introduces a novel gene discovery platform. Elongate
partial EST/cDNA sequences to full length genes, analyze them
and get SAGE expression information at http://www.labonweb.com.


LabOnWeb combines state-of-the-art algorithms with proprietary
databases to provide the most comprehensive and accurate gene
discovery platform. Powered by Compugen (www.cgen.com),
a worldwide leader in gene discovery, the LabOnWeb research engine
includes:

* InstantRACE sequence elongation and primer design
* SAGE™ based expression profiles
* Comprehensive homology search  and complete genomic analysis


LabOnWeb's novel gene discovery platform elongates partial
EST/cDNA sequences to full length genes, analyzes them and
and provides SAGE expression information.


-Mika Yehezkeli, LabOnWeb.com




From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 11 09:27:15 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id CE6D517A8C; Tue, 11 Apr 2000 09:27:14 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA17458
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 11 Apr 2000 09:27:12 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA22353
	for proteins-list@hgmp.mrc.ac.uk; Tue, 11 Apr 2000 09:27:10 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Frank Fuerst <fant.1@gmx.net>
X-Newsgroups: bionet.molbio.proteins,sci.physics
Subject: Re: Protein Folding
Date: Tue, 11 Apr 2000 10:37:47 +0200
Lines: 43
Message-ID: <8cunkt$6t4fb$1@fu-berlin.de>
References: <8ct3en$d5$1@news7.svr.pol.co.uk> <8ctd71$ndo$1@news.panix.com>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: fu-berlin.de 955441629 7246315 141.89.207.60 (16 49 955)
X-Mailer: Mozilla 4.51 [de]C-CCK-MCD QXW03200  (WinNT; I)
X-Accept-Language: de,en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Edward Green wrote:

> >perhaps quantum effects are involved in protein folding - it is
> >impossible for a protein to try every possible conformation sequentially so
> >perhaps several different conformations are attempted in paralell.
> >
> >Is this at all possible?
> 
> It sounds way cool, but why fish for the obscure before there is a
> reason to doubt that protein folding may be understood as a result of
> classical kinetics operating on a ball and stick molecule, the way we
> often understand chemical reactions.
> 
> I think you may err in supposing that a folding protein molecule
> "tries out every conformation".  It's not solving a traveling salesman
> problem; it's simply choosing a locally best route.
> 
> [I see you have added some heavy duty special purpose bio group, where
> there may be people who really know about protein folding... 

You're quite right. When one tries to visualize the multi-dimensional
conformational space of a protein using a two dimensional model, the
third dimension beeing the potential energy [1], on gets potential
energy surfaces with the form of a "funnel". This means that the
folding process means in general just going downhill (or diffusing in
flat valleys and terraces)[2].
Thus, the protein doesn't have to try every possible conformation.
Once that, by a statistical search, a small subset of favourable,
near-in-sequence interactions is established, these interactions are
stable and are kept throughout the rest of the folding process. The
rest of the polypeptide chain finds its native conformation either by
stepwise addition of further stable interactions to that nucleus, or
(in the case of long chains) by forming of several independent nuclei.

Bye,
Frank

[1] to be exactly: the internal free energy, i.e. the Gibbs free
energy with all contributions except chain entropy
[2] things get a little more difficult when we also look at chain
entropy
-- 
PhD student, department of physical biochemistry, Potsdam university


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 11 18:11:09 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2492217AB1; Tue, 11 Apr 2000 18:11:06 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA09245
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 11 Apr 2000 18:11:05 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA02735
	for proteins-list@hgmp.mrc.ac.uk; Tue, 11 Apr 2000 18:11:03 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Jon" <jonathan.gilthorpe@kcl.ac.uk>
X-Newsgroups: bionet.molbio.proteins
Subject: 293-EBNA cell line
Date: Tue, 11 Apr 2000 18:06:31 -0500
Organization: King's College London
Lines: 19
Message-ID: <8cvlsb$gfg$1@willow.cc.kcl.ac.uk>
X-Trace: willow.cc.kcl.ac.uk 955472587 16880 159.92.52.56 (11 Apr 2000 17:03:07 GMT)
X-Complaints-To: abuse@news.kcl.ac.uk
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2314.1300
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Does anyone in the UK (preferably London) have any 293-EBNA cells (human
embyonic kidney cells expressing EBNA-1). I have been trying to obtain them
from Invitrogen to no avail.

Regards

--
Jon

Dr Jon Gilthorpe
Department of Developmental Neurobology
King's College London
New Hunt's House
Guy's Campus
London SE1 9RT

jonathan.gilthorpe@kcl.ac.uk




From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 11 19:39:56 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 9722017A75; Tue, 11 Apr 2000 19:39:55 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA16919
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 11 Apr 2000 19:39:52 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id TAA03820
	for proteins-list@hgmp.mrc.ac.uk; Tue, 11 Apr 2000 19:39:51 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: John Kuszewski <johnk@speck.niddk.nih.gov>
X-Newsgroups: bionet.molbio.proteins,sci.physics
Subject: Re: Protein Folding
Date: Mon, 10 Apr 2000 16:25:47 -0400
Organization: National Institutes of Health
Lines: 35
Message-ID: <38F238CB.189D6C66@speck.niddk.nih.gov>
References: <8ct3en$d5$1@news7.svr.pol.co.uk>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

mdl24 wrote:
> 
> Hello,
> 
> In Roger Penrose's book, The Emperor's New Mind, it is asserted that certain
> types of crystal formation may include non-local quantum effects. It occured
> to me that perhaps quantum effects are involved in protein folding - it is
> impossible for a protein to try every possible conformation sequentially so
> perhaps several different conformations are attempted in paralell.
> 
> Is this at all possible?

No.  Quantum entanglement of states of something as big as a protein
would
be destroyed very quickly at physiological temperature.  

All the recent evidence is that folding happens quickly because
of either the magic of folding funnels (ie., many parallel folding 
pathways that tend to converge into the same region of conformational
space) or the magic of enzymes (ie., chaperonins).  No need for 
all that tedious mucking about in quantum mechanics.

-- 
				_____________
				|        ___/_
				|        |/  /
				--  /\  //  /--
Dr. John Kuszewski		||  ||  /  /||
johnk@speck.niddk.nih.gov	||  || /  / ||
				||  ||/  /  ||
				||  |/  /|  ||      
				||  /  /||  ||
My parents went to Zaire	\/ /  / ||  \/
and all I got			 |/__/|      |
was this lousy retrovirus.	   /_________|


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 03:35:25 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3D47517A68; Wed, 12 Apr 2000 03:35:25 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA27236
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 03:35:23 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA17863
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 03:35:21 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Luis Velasquez <velasqu7@pilot.msu.edu>
X-Newsgroups: bionet.molbio.proteins
Subject: mannitol dehydrogenase
Date: Tue, 11 Apr 2000 22:37:32 -0400
Organization: Michigan State University
Lines: 3
Message-ID: <38F3E16B.F70F1624@pilot.msu.edu>
Reply-To: velasqu7@pilot.msu.edu
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-AUTHid: velasqu7
X-Mailer: Mozilla 4.5 [en] (Win98; U)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I am looking for a method to detect mannitol dehydrogenase using
acrylamide electrophoresis.  Is there a specific staining I could use?



From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 07:27:49 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 40BE417A68; Wed, 12 Apr 2000 07:27:49 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id HAA13160
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 07:27:47 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id HAA20536
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 07:27:46 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38F3B4EF.D9059D80@mac.com>
From: IMKoRnNuts <IMKoRnNuts@mac.com>
Reply-To: IMKoRnNuts@mac.com
X-Mailer: Mozilla 4.72C-AtHome0403 (Macintosh; I; PPC)
X-Accept-Language: en,pdf
MIME-Version: 1.0
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Research project, please help...
References: <38F0E935.E68EAC09@mac.com>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit
Lines: 5
Date: Wed, 12 Apr 2000 06:27:30 GMT
X-Complaints-To: abuse@home.net
X-Trace: news1.frmt1.sfba.home.com 955520850 24.1.89.6 (Tue, 11 Apr 2000 23:27:30 PDT)
Organization: @Home Network
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I am a 17 year old high school student doing a research project for my
chemistry class. My assignment is to apply chemistry to weight lifting
and muscle production. Any help is appreciated.




From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 10:30:10 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3824B17A68; Wed, 12 Apr 2000 10:30:08 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA24388
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 10:30:06 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA22844
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 10:30:05 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Petri Kursula <pkursula@sun3.oulu.fi>
X-Newsgroups: bionet.molbio.proteins
Subject: similarities/identities from an alignment?
Date: Wed, 12 Apr 2000 12:26:33 +0300
Organization: University of Oulu
Lines: 9
Message-ID: <Pine.GSO.4.21.0004121225130.14611-100000@sun3.oulu.fi>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Trace: ousrvr3.oulu.fi 955531596 23021 130.231.240.13 (12 Apr 2000 09:26:36 GMT)
X-Complaints-To: news@news.oulu.fi
X-Sender: pkursula@sun3.oulu.fi
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hi,

I would like to get a table of identities/similarities between each
sequence in a multiple sequence alignment. Any pointers to servers or
programs automatically doing this would be appreciated.

Pete




From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 12:44:23 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 7B26317A91; Wed, 12 Apr 2000 12:44:22 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id MAA07931
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 12:44:20 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA24576
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 12:44:18 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Simon Andrews <simon.andrews@bbsrc.ac.uk>
X-Newsgroups: bionet.molbio.proteins
Subject: Re: similarities/identities from an alignment?
Date: Wed, 12 Apr 2000 12:40:50 +0100
Organization: BBSRC Biotechnology and Biological Sciences Research Council
Lines: 21
Message-ID: <38F460C2.475D69D7@bbsrc.ac.uk>
References: <Pine.GSO.4.21.0004121225130.14611-100000@sun3.oulu.fi>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 4.5 [en] (WinNT; I)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Petri Kursula wrote:
> 
> Hi,
> 
> I would like to get a table of identities/similarities between each
> sequence in a multiple sequence alignment. Any pointers to servers or
> programs automatically doing this would be appreciated.
> 
> Pete

You can do this using the program GeneDoc, which is freeware.  This
produces shaded graphics from multiple sequence alignments, and will
also tabulate percentage identity / similarity.

You can download it from;

http://www.cris.com/~Ketchup/genedoc.shtml

HTH

Simon.


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 13:31:58 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id AA7A717AAD; Wed, 12 Apr 2000 13:31:57 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA12345;
	Wed, 12 Apr 2000 13:31:54 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA25213;
	Wed, 12 Apr 2000 13:31:53 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Klemens Raithel <klemens@biophysik.biologie.uni-mainz.de>
X-Newsgroups: sci.chem,sci.physics,bionet.molbio.proteins,bionet.molbio.methds-reagnts,z-netz.wissenschaft.chemie,jogu.physik,bionet.biophysics
Subject: Searching for a dependency of the maximum gas saturation in different viscous solutions
Date: Wed, 12 Apr 2000 14:31:41 +0200
Organization: Johannes Gutenberg-Universitaet Mainz, Germany
Lines: 9
Message-ID: <38F46CAC.34ABFBB6@biophysik.biologie.uni-mainz.de>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: bambi.zdv.Uni-Mainz.DE 955542710 7206 134.93.248.79 (12 Apr 2000 12:31:50 GMT)
X-Complaints-To: usenet@mail.uni-mainz.de
X-Mailer: Mozilla 4.06 [en] (Win95; I)
To: biophys@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk,
	proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


I was wondering, if there exists a dependency between the maximum
saturation of a gas (oxygen) and the viscosity of the solution caused by
a high concentrated cosolvent (e.g. sucrose, 3M).

Is there something known about this problem in the world of science?

Klemens Raithel



From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 14:22:28 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id A225317A61; Wed, 12 Apr 2000 14:22:23 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA17519
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 14:22:10 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA25894
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 14:22:09 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Frank Fuerst <fant.1@gmx.net>
X-Newsgroups: bionet.molbio.proteins,sci.physics
Subject: Re: Protein Folding
Date: Wed, 12 Apr 2000 10:26:59 +0200
Lines: 38
Message-ID: <8d1bch$6gmg5$1@fu-berlin.de>
References: <8ct3en$d5$1@news7.svr.pol.co.uk> <38F238CB.189D6C66@speck.niddk.nih.gov>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: fu-berlin.de 955527377 6838789 141.89.207.60 (16 49 955)
X-Mailer: Mozilla 4.51 [de]C-CCK-MCD QXW03200  (WinNT; I)
X-Accept-Language: de,en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

John Kuszewski wrote:
 
> All the recent evidence is that folding happens quickly because
> of either [...folding funnels...] or the magic of enzymes 
> (ie., chaperonins).  

To my knowledge, chaperones do not act on folding kinetics in the
sense of the original posting, i.e. by helping the protein "solve" the
Levinthal paradox [1]. What they do is
a) prevent partially folded proteins from aggregation by binding them
and keeping them soluble
b) helping them out of kinetic traps, that means of kinetically
stable, but misfolded conformations, by partially unfolding them using
"mechanical" force driven by ATP.

Of course this changes the observed refolding kinetics - e.g. in the
case of firefly luciferase the refolding reaction in vitro takes
longer than overnight in a purified sample, but in the precense of
eucaryotic cell lysate (reticulozytes or wheat germ) it takes about 10
minutes. But this is not because the protein needs to try less
conformations, but rather because the protein gets stuck in a kinetic
trap and some unidentified chaperone helps it out (Herbst et al.,
Biochemistry _37_(18), 6586ff and references therein).


> No need for
> all that tedious mucking about in quantum mechanics.

Of course.

Bye, Frank

[1] Levinthal paradox: (over)simplified calculation that sampling all
possible conformations of a protein would take more time than the
lifetime of the universe.
-- 
Die Verwendung von mehreren Ausrufezeichen macht die Aussage nicht
ausrufender sondern ausufernder. [Michael Bauer in dnq]


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 15:07:30 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id D41FB17A6C; Wed, 12 Apr 2000 15:07:28 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA22420
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 15:07:24 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA26446
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 15:07:23 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Frank Fuerst <fant.1@gmx.net>
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Research project, please help...
Date: Wed, 12 Apr 2000 16:18:04 +0200
Lines: 21
Message-ID: <8d1vup$72jjj$1@fu-berlin.de>
References: <38F0E935.E68EAC09@mac.com> <38F3B4EF.D9059D80@mac.com>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: fu-berlin.de 955548441 7425651 141.89.207.60 (16 49 955)
X-Mailer: Mozilla 4.51 [de]C-CCK-MCD QXW03200  (WinNT; I)
X-Accept-Language: de,en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

IMKoRnNuts wrote:
> 
> I am a 17 year old high school student doing a research project for my
> chemistry class. My assignment is to apply chemistry to weight lifting
> and muscle production. Any help is appreciated.

No need to post this twice. We've read it.

But this is usenet, not your automatic homework-machine.

If you ask specific questions, you'll probably get specific answers (but
better read your textbook before asking). If you cry for "any help", you'll
probably get nothing.

Yours, Frank

P.S. If your textbook doesn't help, try any biochemistry book from the next
universities library.
-- 
Die Verwendung von mehreren Ausrufezeichen macht die Aussage nicht
ausrufender sondern ausufernder. [Michael Bauer in dnq]


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 15:56:38 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 287FE17B31; Wed, 12 Apr 2000 15:56:34 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA02700;
	Wed, 12 Apr 2000 15:56:31 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA27240;
	Wed, 12 Apr 2000 15:56:30 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38F48E9B.21679BDE@hate.spam.net>
From: Uncle Al <UncleAl0@hate.spam.net>
Organization: The Noble Krell
X-Mailer: Mozilla 4.61 [en]C-AtHome0407  (Win98; U)
X-Accept-Language: en
MIME-Version: 1.0
X-Newsgroups: sci.chem,sci.physics,bionet.molbio.proteins,bionet.molbio.methds-reagnts,z-netz.wissenschaft.chemie,jogu.physik,bionet.biophysics
Subject: Re: Searching for a dependency of the maximum gas saturation in 
 different viscous solutions
References: <38F46CAC.34ABFBB6@biophysik.biologie.uni-mainz.de>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Lines: 22
Date: Wed, 12 Apr 2000 14:56:16 GMT
X-Complaints-To: abuse@home.net
X-Trace: news1.alsv1.occa.home.com 955551376 24.16.181.181 (Wed, 12 Apr 2000 07:56:16 PDT)
To: biophys@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk,
	proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk



Klemens Raithel wrote:
> 
> I was wondering, if there exists a dependency between the maximum
> saturation of a gas (oxygen) and the viscosity of the solution caused by
> a high concentrated cosolvent (e.g. sucrose, 3M).
> 
> Is there something known about this problem in the world of science?

It's hard to see how thermodynamics depends on viscosity rather than
concentration and identity of the solute.  A very small concentration
of high MW polyacrylamide will give you a very viscous aqueous
solution.  It's still mostly water.

-- 
Uncle Al
http://www.mazepath.com/uncleal/
http://www.ultra.net.au/~wisby/uncleal/
http://www.guyy.demon.co.uk/uncleal/
 (Toxic URLs! Unsafe for children and most mammals)
"Quis custodiet ipsos custodes?"  The Net!


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 16:39:47 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id CBD2E17B39; Wed, 12 Apr 2000 16:39:42 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA07648;
	Wed, 12 Apr 2000 16:39:35 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA27746;
	Wed, 12 Apr 2000 16:39:34 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Klemens Raithel <klemens@biophysik.biologie.uni-mainz.de>
X-Newsgroups: sci.chem,sci.physics,bionet.molbio.proteins,bionet.molbio.methds-reagnts,z-netz.wissenschaft.chemie,jogu.physik,bionet.biophysics
Subject: Re: Searching for a dependency of the maximum gas saturation in 
	 different viscous solutions
Date: Wed, 12 Apr 2000 17:39:20 +0200
Organization: Johannes Gutenberg-Universitaet Mainz, Germany
Lines: 27
Message-ID: <38F498A7.B43FBAD5@biophysik.biologie.uni-mainz.de>
References: <38F46CAC.34ABFBB6@biophysik.biologie.uni-mainz.de> <38F48E9B.21679BDE@hate.spam.net>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: bambi.zdv.Uni-Mainz.DE 955553970 12226 134.93.248.79 (12 Apr 2000 15:39:30 GMT)
X-Complaints-To: usenet@mail.uni-mainz.de
To: Uncle Al <UncleAl0@hate.spam.net>
X-Mailer: Mozilla 4.06 [en] (Win95; I)
To: biophys@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk,
	proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk



Uncle Al wrote:

> Klemens Raithel wrote:
> >
> > I was wondering, if there exists a dependency between the maximum
> > saturation of a gas (oxygen) and the viscosity of the solution caused by
> > a high concentrated cosolvent (e.g. sucrose, 3M).
> >
> > Is there something known about this problem in the world of science?
>
> It's hard to see how thermodynamics depends on viscosity rather than
> concentration and identity of the solute.  A very small concentration
> of high MW polyacrylamide will give you a very viscous aqueous
> solution.  It's still mostly water.

Hi Uncle Al,

I am not searching for a viscous solution mostly consisting of water.
I am trying to find a relationship between different viscous solutions and
their capacity to solve gas (to the maximum saturation).
Does a physical formula or chemical rule exist for THIS problem???
Thanks,

Klemens Raithel



From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 17:23:26 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 1E00A17A6D; Wed, 12 Apr 2000 17:23:24 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA12978;
	Wed, 12 Apr 2000 17:23:18 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA28410;
	Wed, 12 Apr 2000 17:23:16 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Mitchell Isaacs" <misaacs@student.usyd.edu.au>
X-Newsgroups: sci.chem,sci.physics,bionet.molbio.proteins,bionet.molbio.methds-reagnts,z-netz.wissenschaft.chemie,bionet.biophysics
Subject: Re: Searching for a dependency of the maximum gas saturation in  different viscous solutions
Date: Thu, 13 Apr 2000 02:21:30 +1000
Organization: The University of Sydney, Australia
Lines: 51
Message-ID: <8d27tg$fj3$1@metro.ucc.usyd.edu.au>
References: <38F46CAC.34ABFBB6@biophysik.biologie.uni-mainz.de> <38F48E9B.21679BDE@hate.spam.net> <38F498A7.B43FBAD5@biophysik.biologie.uni-mainz.de>
X-Trace: metro.ucc.usyd.edu.au 955556592 15971 10.0.99.197 (12 Apr 2000 16:23:12 GMT)
X-Complaints-To: usenet@news.usyd.edu.au
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2919.6600
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600
To: biophys@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk,
	proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

It is my understanding that a solution can theoretically dissolve the same
amount of gas regardless of viscosity (if that is the only variable).

However, as can be learnt from vulcanology, viscosity may affect the
apparent solubility. Granitic, or high silica magmas are very viscous, and
have a much higher gas content (4-6%) than basaltic magmas which are lower
in silica (~1% gas).

This is due largely to the viscosity, and the fact that the viscous magmas
do not release the gas nearly as readily.

I would assume that the opposite effect can also be noticed, in that gases
will dissolve slower in a viscous solution, possibly to the extent that the
same concentration may not be reached in a practical time frame.

Cheers,
Mitchell


"Klemens Raithel" <klemens@biophysik.biologie.uni-mainz.de> wrote in message
news:38F498A7.B43FBAD5@biophysik.biologie.uni-mainz.de...
>
>
> Uncle Al wrote:
>
> > Klemens Raithel wrote:
> > >
> > > I was wondering, if there exists a dependency between the maximum
> > > saturation of a gas (oxygen) and the viscosity of the solution caused
by
> > > a high concentrated cosolvent (e.g. sucrose, 3M).
> > >
> > > Is there something known about this problem in the world of science?
> >
> > It's hard to see how thermodynamics depends on viscosity rather than
> > concentration and identity of the solute.  A very small concentration
> > of high MW polyacrylamide will give you a very viscous aqueous
> > solution.  It's still mostly water.
>
> Hi Uncle Al,
>
> I am not searching for a viscous solution mostly consisting of water.
> I am trying to find a relationship between different viscous solutions and
> their capacity to solve gas (to the maximum saturation).
> Does a physical formula or chemical rule exist for THIS problem???
> Thanks,
>
> Klemens Raithel
>




From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 12 23:15:18 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E56F317AB3; Wed, 12 Apr 2000 23:15:16 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA23857
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 12 Apr 2000 23:15:10 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id XAA11317
	for proteins-list@hgmp.mrc.ac.uk; Wed, 12 Apr 2000 23:15:08 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: bpoirier@dres.dnd.ca (Bob Poirier)
X-Newsgroups: bionet.molbio.proteins
Subject: Capillary Electrophoresis user group
Date: Wed, 12 Apr 2000 22:01:49 GMT
Organization: DRES
Lines: 1
Message-ID: <bpoirier.10.38F4F24D@dres.dnd.ca>
X-Newsreader: Trumpet for Windows [Version 1.0 Rev B]
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Is anyone aware of a user group for CE?


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 13 00:22:35 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id C7ACA17AB3; Thu, 13 Apr 2000 00:22:33 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id AAA27211;
	Thu, 13 Apr 2000 00:22:30 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id AAA11981;
	Thu, 13 Apr 2000 00:22:29 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "Mitchell Isaacs" <misaacs@student.usyd.edu.au>
X-Newsgroups: sci.chem,sci.physics,bionet.molbio.proteins,bionet.molbio.methds-reagnts,z-netz.wissenschaft.chemie,bionet.biophysics
Subject: Re: Searching for a dependency of the maximum gas saturation in  different viscous solutions
Date: Thu, 13 Apr 2000 09:20:45 +1000
Organization: The University of Sydney, Australia
Lines: 87
Message-ID: <8d30fj$2bt$1@metro.ucc.usyd.edu.au>
References: <38F46CAC.34ABFBB6@biophysik.biologie.uni-mainz.de> <38F48E9B.21679BDE@hate.spam.net> <38F498A7.B43FBAD5@biophysik.biologie.uni-mainz.de> <8d27tg$fj3$1@metro.ucc.usyd.edu.au>
X-Trace: metro.ucc.usyd.edu.au 955581747 2429 10.0.99.197 (12 Apr 2000 23:22:27 GMT)
X-Complaints-To: usenet@news.usyd.edu.au
X-Priority: 3
X-MSMail-Priority: Normal
X-Newsreader: Microsoft Outlook Express 5.00.2919.6600
X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600
To: biophys@hgmp.mrc.ac.uk, methods@hgmp.mrc.ac.uk,
	proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Fowarded message from Wolfgang Schechinger

----- Original Message -----
From: "Wolfgang Schechinger" <Wolfgang.Schechinger@med.uni-tuebingen.de>
To: "Mitchell Isaacs" <misaacs@student.usyd.edu.au>
Sent: Thursday, 13 April 2000 10:03
Subject: Re: Searching for a dependency of the maximum gas saturation in


> Given an unlimited amount of time (means we are looking at
> thermodynamic, not kinetical properties):
>
> 1) I would look at the gas like it was a undissociated chemical, e.g.
> glucose.
>
> 2) If the amount of substance causing the viscosity is vanishingly
> low, the solubility of the gas actually should not be different.
>
> 3) If there is a significant amount of substance causing the
> viscosity (say 5%) and this substance is inert, I would assume the
> solubility as much as 95% of the solvent's capacity. Since there is
> 95% of the solvent in this case. Best would be considering molarities
> in this case.
>
> 4) However, if the substance is changing the solvent's structure,
> the solute is intercalating or there is sme kind of a chemical
> reaction (like iodine in starch containing solutions or if KI is
> present),  the solubility of the gas would be totally different and
> only a complex model (or practical measurements) would make a good
> approach
>
> Just some ideas,
>
> Wolfgang
>
>
> > It is my understanding that a solution can theoretically dissolve
> > the same amount of gas regardless of viscosity (if that is the only
> > variable).
> >
> > However, as can be learnt from vulcanology, viscosity may affect the
> > apparent solubility. Granitic, or high silica magmas are very
> > viscous, and have a much higher gas content (4-6%) than basaltic
> > magmas which are lower in silica (~1% gas).
> >
> > This is due largely to the viscosity, and the fact that the viscous
> > magmas do not release the gas nearly as readily.
> >
> > I would assume that the opposite effect can also be noticed, in that
> > gases will dissolve slower in a viscous solution, possibly to the
> > extent that the same concentration may not be reached in a practical
> > time frame.
> >
> > Cheers,
> > Mitchell
> >
> >
> > "Klemens Raithel" <klemens@biophysik.biologie.uni-mainz.de> wrote in
> > message news:38F498A7.B43FBAD5@biophysik.biologie.uni-mainz.de... >
> > > > Uncle Al wrote: > > > Klemens Raithel wrote: > > > > > > I was
> > wondering, if there exists a dependency between the maximum > > >
> > saturation of a gas (oxygen) and the viscosity of the solution
> > caused by > > > a high concentrated cosolvent (e.g. sucrose, 3M). >
> > > > > > > Is there something known about this problem in the world
> > of science? > > > > It's hard to see how thermodynamics depends on
> > viscosity rather than > > concentration and identity of the solute.
> > A very small concentration > > of high MW polyacrylamide will give
> > you a very viscous aqueous > > solution.  It's still mostly water. >
> > > Hi Uncle Al, > > I am not searching for a viscous solution mostly
> > consisting of water. > I am trying to find a relationship between
> > different viscous solutions and > their capacity to solve gas (to
> > the maximum saturation). > Does a physical formula or chemical rule
> > exist for THIS problem??? > Thanks, > > Klemens Raithel >
> >
> >
> -----
> This message is encrypted. Use your brain to decode it.
> -----
> Dr. Wolfgang Schechinger, Dept. of Pathobiochemistry
> University of Tuebingen, Germany
> email: wolfgang.schechinger@med.uni-tuebingen.de
> wwWait: http://www.medizin.uni-tuebingen.de/~wgschech/start.htm
> -----
> usual disclaimers apply
> -----




From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 13 01:25:50 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 17C8717B4F; Thu, 13 Apr 2000 01:25:49 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA01234
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 13 Apr 2000 01:25:46 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA12675
	for proteins-list@hgmp.mrc.ac.uk; Thu, 13 Apr 2000 01:25:45 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38F4B199.4BEF483B@mac.com>
From: IMKoRnNuts <IMKoRnNuts@mac.com>
Reply-To: IMKoRnNuts@mac.com
X-Mailer: Mozilla 4.72C-AtHome0403 (Macintosh; I; PPC)
X-Accept-Language: en,pdf
MIME-Version: 1.0
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Research project, please help...
References: <38F0E935.E68EAC09@mac.com> <38F3B4EF.D9059D80@mac.com> <8d1vup$72jjj$1@fu-berlin.de>
Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353"
Content-Transfer-Encoding: 7bit
Lines: 41
Date: Thu, 13 Apr 2000 00:25:33 GMT
X-Complaints-To: abuse@home.net
X-Trace: news1.frmt1.sfba.home.com 955585533 24.1.89.6 (Wed, 12 Apr 2000 17:25:33 PDT)
Organization: @Home Network
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

No this isn't my automatic homework machine. But when I found everything I can
at the two local and the school libraries, interviewed the school weight
lifting teacher and school trainer, searched the internet for two months, and
still haven't found enough, then I have to look for other sources. The nearest
college is over an hour away and I just don't have that kind of time. Posting
on newsgroups was suggested to me by MY CHEMISTRY TEACHER, so that is what I
am doing. Actually it has been quite successful.

If you want a specific questions, fine.

1. What is the difference between protein synthesis and protein breakdown?
2. What is the function of ATP?
3. Can you explain the effects of insulin on muscle?

P.S. This is a pick-your-own-topic-and-apply-chemistry-to-it assignment, so my
textbook isn't going to help.

Frank Fuerst wrote:

> IMKoRnNuts wrote:
> >
> > I am a 17 year old high school student doing a research project for my
> > chemistry class. My assignment is to apply chemistry to weight lifting
> > and muscle production. Any help is appreciated.
>
> No need to post this twice. We've read it.
>
> But this is usenet, not your automatic homework-machine.
>
> If you ask specific questions, you'll probably get specific answers (but
> better read your textbook before asking). If you cry for "any help", you'll
> probably get nothing.
>
> Yours, Frank
>
> P.S. If your textbook doesn't help, try any biochemistry book from the next
> universities library.
> --
> Die Verwendung von mehreren Ausrufezeichen macht die Aussage nicht
> ausrufender sondern ausufernder. [Michael Bauer in dnq]



From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 13 10:17:31 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 0165517A63; Thu, 13 Apr 2000 10:17:29 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA07250
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 13 Apr 2000 10:17:27 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA21624
	for proteins-list@hgmp.mrc.ac.uk; Thu, 13 Apr 2000 10:17:26 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Frank Fuerst <fant.1@gmx.net>
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Research project, please help...
Date: Thu, 13 Apr 2000 11:28:06 +0200
Lines: 26
Message-ID: <8d43b3$78p2f$1@fu-berlin.de>
References: <38F0E935.E68EAC09@mac.com> <38F3B4EF.D9059D80@mac.com> <8d1vup$72jjj$1@fu-berlin.de> <38F4B199.4BEF483B@mac.com>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: fu-berlin.de 955617443 7627855 141.89.207.60 (16 49 955)
X-Mailer: Mozilla 4.51 [de]C-CCK-MCD QXW03200  (WinNT; I)
X-Accept-Language: de,en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

IMKoRnNuts wrote:
> 
> 1. What is the difference between protein synthesis and protein breakdown?

The enzymes involved are totally different. Protein synthesis takes
place on the ribozome, a complex organelle consisting of RNA and
proteins. The polypeptide chain is synthesized from one end to the
other, adding on amino acid after the other according to the
information on the messenger-RNA. 

Protein degradation works totally different. The proteins selected are
transported to a different kind of organelles (or perhaps some are
degraded in the cytoplasm/periplasm, I don't know) and there they are
cut in pieces by proteases - there is no information (from RNA)
involved, but the process is regulated in a complex way (which
proteins are degraded, where is this done, ...)

> 2. What is the function of ATP?

Principally ATP is the short-term "energy currency" in a cell. For
protein synthesis, a lot of ATP is needed.

I think you should really consult some biochemistry textbook.

HTH
Frank


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 13 16:40:48 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 3124717A87; Thu, 13 Apr 2000 16:40:47 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA20366
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 13 Apr 2000 16:40:43 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA29924
	for proteins-list@hgmp.mrc.ac.uk; Thu, 13 Apr 2000 16:40:42 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: pirmail@NBRF.Georgetown.Edu (pirmail)
X-Newsgroups: bionet.molbio.proteins
Subject: Release 64.00, PIR-International Protein Sequence Database
Date: 13 Apr 2000 16:40:40 +0100
Organization: National Biomedical Research Foundation
Lines: 60
Message-ID: <38F5E9EE.C314C43A@nbrf.georgetown.edu>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Trace: niobium.hgmp.mrc.ac.uk 955640442 29922 193.62.192.80 (13 Apr 2000 15:40:42 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from nbrf.georgetown.edu (nbrf.georgetown.edu [141.161.237.70])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA20334
	for <proteins@net.bio.net>; Thu, 13 Apr 2000 16:40:34 +0100 (BST)
X-Received: from nbrf1.nbrfnet.georgetown.edu by NBRF.Georgetown.Edu
 (PMDF V5.2-31 #34596) with ESMTP id <01JO6PBC1L5S96VKW9@NBRF.Georgetown.Edu>
 for proteins@net.bio.net; Thu, 13 Apr 2000 11:39:04 -0400 (EDT)
X-Received: from NBRF1/SpoolDir by nbrf1.nbrfnet.georgetown.edu (Mercury 1.47)
 ; Thu, 13 Apr 2000 11:39:11 -0500
X-Received: from SpoolDir by NBRF1 (Mercury 1.47); Thu, 13 Apr 2000 11:38:42 -0500
X-Received: from nbrf.georgetown.edu (141.161.237.192)
 by nbrf1.nbrfnet.georgetown.edu (Mercury 1.47) with ESMTP; Thu,
 13 Apr 2000 11:38:42 -0500
X-To: proteins@hgmp.mrc.ac.uk
X-Mailer: Mozilla 4.7 [en] (Win98; U)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

==============================================================
  ANNOUNCING RELEASE 64 OF THE PIR PROTEIN SEQUENCE DATABASE
                           and
    NEW FEATURES AND ANALYSIS TOOLS ON THE PIR WEB SITE

                http://pir.georgetown.edu/
==============================================================
RELEASE 64.00 OF THE PIR-PSD
   - Contains 178,050 entries and is available by ftp at
   - ftp://nbrfa.georgetown.edu/pir and
   - ftp://nbrf.georgetown.edu/pir

PIR-PSD ENTRIES ON THE WEB SITE HAVE COMPLETE LINKS TO:
   - KEGG, BRENDA, and metabolic pathways and enzyme databases
   - The Protein Databank of Protein Structures (PDB)
   - Clusters of Orthologous Groups (COGs) at NCBI

NEW PROTEIN SEARCH AND ANALYSIS TOOLS ON THE WEB INCLUDE:
(see Bioinformatics 16, 2000)

1. Domain Search
Searches for sequence similarity with domains annotated by
PIR-International.
The results are presented in a table and graphical bars format.

2. Global and Domain Search
Simultaneously searches the PIR-PSD and the PIR Domain Databases.
Results are presented in table and graphical format.

3. Integrated Environment for Sequence Analysis (IESA)
This program provides an integrated environment for protein sequence
analysis
using all the tools on the Web Site. You can:
- Browse PIR-International Protein Sequence Database.
- Display database statistics in graph and table format.
- Display annotations in a table format.
- Find Links to PDB, COG, KEGG, BRENDA, WIT and PIR-ASDB.
- Search text fields.
- Search specialized genomes, e.g. Homo sapiens, Mus musculus,
  S. cerevisiae and E. coli.
- Use the integrated sequence analysis tool including:
      - BLAST and FASTA searches,
      - Pattern Matching,
      - Domain Search
      - Global and Domain Search
 - Multiple alignments with feature display.
 - Annotation Similarity Search

NEW PROTEIN DATABASE AVAILABLE:

The PIR Annotation And Similarity Database (PIR-ASDB):
This is a precompiled database of FASTA scores and alignments for the
entire PIR-International
Protein Sequence Database and includes both annotation and
classification information.
The database is accessible directly, or from within the PIR Integrated
Environment for
Sequence Analysis (IESA).

---


From owner-proteins@hgmp.mrc.ac.uk  Fri Apr 14 01:49:42 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 222DA17A43; Fri, 14 Apr 2000 01:49:40 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA12994
	for <proteins-list@hgmp.mrc.ac.uk>; Fri, 14 Apr 2000 01:49:38 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA15261
	for proteins-list@hgmp.mrc.ac.uk; Fri, 14 Apr 2000 01:49:36 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: pathos@freerealtime.com (pathos)
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Research project, please help...
Date: Thu, 13 Apr 2000 20:48:43 -0400
Organization: none
Lines: 29
Message-ID: <pathos-1304002048430001@pelli.pathology.pitt.edu>
References: <38F0E935.E68EAC09@mac.com> <38F3B4EF.D9059D80@mac.com> <8d1vup$72jjj$1@fu-berlin.de> <38F4B199.4BEF483B@mac.com>
X-Newsreader: MT-NewsWatcher 2.4.4
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

In article <38F4B199.4BEF483B@mac.com>, IMKoRnNuts@mac.com wrote:

> 1. What is the difference between protein synthesis and protein breakdown?

Protein synthesis is what makes you grow.  for that matter, protein
synthesis is required for all cells to grow.  If you inhibit the protein
synthesis, then the cell and the higher organism dies.
Protein breakdown occurs in the lysosome of every normal cell in your
body.  It also occurs in the pathologic states.

> 2. What is the function of ATP?

It is what makes the world go round as far as your body is concerned.  It
is the primary energy molecule in the body.  Sugar and proteins and fat
are broken down to create this molecule.

> 3. Can you explain the effects of insulin on muscle?

Insulin upregulates specific sugar transoport molecules in the cell
membrane.  i think that they are GLUT# and GLUT4


Why don't you go back to the libray and check out a book on biochemistry. 
Chapters if not volumes of books have been written on these topics

-- 
Peter Pediaditakis
University of Pittsburgh
Dept. of Pathology


From owner-proteins@hgmp.mrc.ac.uk  Fri Apr 14 13:56:54 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2597417AD3; Fri, 14 Apr 2000 13:56:51 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08709
	for <proteins-list@hgmp.mrc.ac.uk>; Fri, 14 Apr 2000 13:56:48 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA24072
	for proteins-list@hgmp.mrc.ac.uk; Fri, 14 Apr 2000 13:56:46 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: fridaymorning1@fnmail.com
X-Newsgroups: bionet.molbio.proteins
Subject: SPRING SPECIAL - BULK E-MAILING CAN WORK FOR YOU.
Date: 14 Apr 2000 13:56:44 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 31
Message-ID: <200004141256.NAA08650@hgmp.mrc.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 955717005 24066 193.62.192.80 (14 Apr 2000 12:56:45 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from cpsinternet.compuscape.com (srvr.pey.clarkson.edu [128.153.30.46])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08650
	for <proteins@net.bio.net>; Fri, 14 Apr 2000 13:56:39 +0100 (BST)
X-Received: from 5Qc7oC08y (ip201.modesto.ca.pub-ip.psi.net [38.28.4.201]) by cpsinternet.compuscape.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21)
	id 27VN0KR8; Fri, 14 Apr 2000 08:14:15 -0400
X-Reply-to: fridaymorning1@fnmail.com
X-TO: fridaymorning1@fnmail.com
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I am sorry if this ad as offended you.  Please go to removeall@china.com to be removed.

We offer some of the best bulk e-mail prices on the Internet.  Bulk e-mail can get you the best exposure on the net. What makes this kind of advertising so effective is the fact that you go to the potential customer. Not like search engines or print ads that the potential customer has to do all the searching.  Dollar for dollar bulk e-mailing is also the most economical.

What we offer:

*General AOL Lists or other ISPs 
$200.00 for 1-million e-mails sent. 
$400.00 for 3-million e-mails sent. 
$600.00 for 5-million e-mails sent. 
$800.00 for 7-million e-mails sent. 
$1000.00 for 10-million e-mails sent. 

WE ALSO HAVE LARGER PACKAGES!


*Targeted Lists: 
$400.00 for 1-million e-mails sent. 
$700.00 for 2-million e-mails sent. 
$1,000.00 for 3-million e-mails sent.

SPRING special, order within 2 days and get 1 free million general names sent.  Order within 5 working days and get 500,000-SALE ENDS JUNE 1.  SO RESERVE YOUR SPOT TODAY!!!

Call for bigger packages!

We can also send some form of verification, so why not give us a call and see what it is that we can do for you.  call anytime 209-669-0176, we are in California. METHOD OF PAYMENT , CASHIERS CHECK MONEY ORDER OR BANK WIRE.




---


From owner-proteins@hgmp.mrc.ac.uk  Sat Apr 15 15:56:51 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 76F4517AA8; Sat, 15 Apr 2000 15:56:50 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA00483
	for <proteins-list@hgmp.mrc.ac.uk>; Sat, 15 Apr 2000 15:56:47 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA21336
	for proteins-list@hgmp.mrc.ac.uk; Sat, 15 Apr 2000 15:56:45 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: fridaymorning1@fnmail.com
X-Newsgroups: bionet.molbio.proteins
Subject: SPRING SPECIAL - BULK E-MAILING CAN WORK FOR YOU.
Date: 15 Apr 2000 15:56:44 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 31
Message-ID: <200004151456.PAA00476@hgmp.mrc.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 955810605 21333 193.62.192.80 (15 Apr 2000 14:56:45 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from cpsinternet.compuscape.com (srvr.pey.clarkson.edu [128.153.30.46])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA00476
	for <proteins@net.bio.net>; Sat, 15 Apr 2000 15:56:41 +0100 (BST)
X-Received: from 5Qc7oC08y (ip201.modesto.ca.pub-ip.psi.net [38.28.4.201]) by cpsinternet.compuscape.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21)
	id 27VN0KR8; Fri, 14 Apr 2000 08:14:15 -0400
X-Reply-to: fridaymorning1@fnmail.com
X-TO: fridaymorning1@fnmail.com
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I am sorry if this ad as offended you.  Please go to removeall@china.com to be removed.

We offer some of the best bulk e-mail prices on the Internet.  Bulk e-mail can get you the best exposure on the net. What makes this kind of advertising so effective is the fact that you go to the potential customer. Not like search engines or print ads that the potential customer has to do all the searching.  Dollar for dollar bulk e-mailing is also the most economical.

What we offer:

*General AOL Lists or other ISPs 
$200.00 for 1-million e-mails sent. 
$400.00 for 3-million e-mails sent. 
$600.00 for 5-million e-mails sent. 
$800.00 for 7-million e-mails sent. 
$1000.00 for 10-million e-mails sent. 

WE ALSO HAVE LARGER PACKAGES!


*Targeted Lists: 
$400.00 for 1-million e-mails sent. 
$700.00 for 2-million e-mails sent. 
$1,000.00 for 3-million e-mails sent.

SPRING special, order within 2 days and get 1 free million general names sent.  Order within 5 working days and get 500,000-SALE ENDS JUNE 1.  SO RESERVE YOUR SPOT TODAY!!!

Call for bigger packages!

We can also send some form of verification, so why not give us a call and see what it is that we can do for you.  call anytime 209-669-0176, we are in California. METHOD OF PAYMENT , CASHIERS CHECK MONEY ORDER OR BANK WIRE.




---


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr 17 03:41:09 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 51EF717A5B; Mon, 17 Apr 2000 03:41:08 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA13244;
	Mon, 17 Apr 2000 03:41:06 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id DAA04026;
	Mon, 17 Apr 2000 03:41:04 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: karplus@cse.ucsc.edu (Kevin Karplus)
X-Newsgroups: bionet.molbio.proteins,bionet.software
Subject: Re: 2ndry structure prediction
Date: 17 Apr 2000 02:40:58 GMT
Organization: University of California, Santa Cruz
Lines: 19
Message-ID: <8ddtjq$3lh@darkstar.ucsc.edu>
References: <rgrant-1CDB0A.13164903042000@nntp-serv.cam.ac.uk>
Reply-To: karplus@ce.ucsc.edu (Kevin Karplus)
To: bio-software@hgmp.mrc.ac.uk, proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


The best 2ry structure predictor at CASP3 was clearly Jones's PSIPRED:
	http://globin.bio.warwick.ac.uk/psipred/

A close second was our predictor, which was not then on the web.
We have since improved our predictor considerably and put it on the web.
We hope to beat PSIPRED at CASP4 with the predictor at
	http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html
Currently, this predictor is about 77-78% correct, and does a good job
of knowing when it is inaccurate.

(We have some more experimental secondary-structure predictors that we
hope will be working by the time CASP4 starts also---we have even
bigger hopes for them.)
-- 
Kevin Karplus 	karplus@cse.ucsc.edu	http://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
Anything below this line is junk added by others without my approval.


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr 17 04:13:15 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 9A59017A72; Mon, 17 Apr 2000 04:13:14 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id EAA14693
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 17 Apr 2000 04:13:12 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id EAA04541
	for proteins-list@hgmp.mrc.ac.uk; Mon, 17 Apr 2000 04:13:11 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: wangqm@nic.bmi.ac.cn (Zhang Bo)
X-Newsgroups: bionet.molbio.proteins
Subject: how to find the genome DNA
Date: 17 Apr 2000 04:13:11 +0100
Organization: AMMS
Lines: 14
Message-ID: <38FA818F.601EC493@nic.bmi.ac.cn>
Mime-Version: 1.0
Content-Type: text/plain; charset=gb2312
Content-Transfer-Encoding: 7bit
X-Trace: niobium.hgmp.mrc.ac.uk 955941191 4539 193.62.192.80 (17 Apr 2000 03:13:11 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from nic.bmi.ac.cn ([202.38.153.248])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id EAA14686
	for <proteins@hgmp.mrc.ac.uk>; Mon, 17 Apr 2000 04:13:06 +0100 (BST)
X-Received: from nic.bmi.ac.cn (ZHANG [202.38.152.84]) by nic.bmi.ac.cn with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0)
	id 2HV5PZVS; Mon, 17 Apr 2000 11:19:45 +0800
X-Mailer: Mozilla 4.51 [zh-cn] (Win98; I)
X-Accept-Language: zh-CN,zh-TW,zh
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Dear Netters:
As the genomic DNA sequencing proceeding, more data are available. But I
am a greenhand,who can tell me how to retrieve the genomic DNA sequence
that I want.
Thanks a lot.

--
Zhang Bo
Taiping Road 48#
Beijing,100850
P.R.China


---


From owner-proteins@hgmp.mrc.ac.uk  Mon Apr 17 16:21:04 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 32BBE17AC2; Mon, 17 Apr 2000 16:21:02 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA17810
	for <proteins-list@hgmp.mrc.ac.uk>; Mon, 17 Apr 2000 16:20:58 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA14511
	for proteins-list@hgmp.mrc.ac.uk; Mon, 17 Apr 2000 16:20:56 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: jpeters@ipoe.uni-kiel.de (Janna Peters)
X-Newsgroups: bionet.molbio.proteins
Subject: Protein Precipitation Method
Date: 17 Apr 2000 16:20:55 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 13
Message-ID: <l03102800b520ead8a263@[134.245.180.156]>
Mime-Version: 1.0
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: 8bit
X-Trace: niobium.hgmp.mrc.ac.uk 955984856 14508 193.62.192.80 (17 Apr 2000 15:20:56 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from ipoe.uni-kiel.de (root@polaris.ipoe.uni-kiel.de [134.245.180.251])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA17793
	for <proteins@net.bio.net>; Mon, 17 Apr 2000 16:20:52 +0100 (BST)
X-Received: from [134.245.180.156] (brachiura.ipoe.uni-kiel.de [134.245.180.156])
	by ipoe.uni-kiel.de (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) with ESMTP id QAA15751
	for <proteins@net.bio.net>; Mon, 17 Apr 2000 16:18:27 -0700
X-Sender: jpeters@polaris.ipoe.uni-kiel.de
X-To: proteins@hgmp.mrc.ac.uk
X-MIME-Autoconverted: from quoted-printable to 8bit by hgmp.mrc.ac.uk id QAA17794
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I want to determine the protein and lipid content of zooplankton from the
same sample. I will extract the lipid with Dichlormethane:Methanol (2:1)
and now I am looking for an adequate protein precipitation method, which I
can combine with the lipid-extraktion without serious influence on the
lipid content.
Has anyone experience with determination of lipid and protein from the same
sample? Maybe the Method of Wessel and Függe 1984 (Analyt. biochem. 138,
141-143) could be useful with some changes?
I would be very thankful for any kind of advice!!!! Thank you in advance.
Janna Peters


---


From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 18 16:12:25 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id C610617A66; Tue, 18 Apr 2000 16:12:24 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA02564
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 18 Apr 2000 16:12:22 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA10915
	for proteins-list@hgmp.mrc.ac.uk; Tue, 18 Apr 2000 16:12:20 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: "P.J. Shaw" <pjs14@le.ac.uk>
X-Newsgroups: bionet.molbio.proteins
Subject: his-tag protein problem
Date: Tue, 18 Apr 2000 16:07:04 +0100
Organization: University of Leicester, UK
Lines: 11
Message-ID: <Pine.SGI.3.96.1000418160131.1591657A-100000@harrier>
Mime-Version: 1.0
Content-Type: TEXT/PLAIN; charset=US-ASCII
X-Trace: rook.le.ac.uk 956070431 638911 143.210.8.56 (18 Apr 2000 15:07:11 GMT)
X-Complaints-To: usenet@le.ac.uk
X-Sender: pjs14@harrier
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

I have purified a C-terminal His-tagged peptide on a His-bind 900
cartridge from Novagen. When I run it on SDS-PAGE, it runs at twice the
expected MW. I guess it's a dimer via a single S-S since there's a single
Cys residue. Is there a reducing agent stronger than DTT/B-ME which will
unzip it to monomers? 

Phil Shaw
Dept. of Genetics
Uni of Leicester, UK
pjs14@le.ac.uk



From owner-proteins@hgmp.mrc.ac.uk  Tue Apr 18 23:34:55 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id E7C3017AF2; Tue, 18 Apr 2000 23:34:54 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA17737
	for <proteins-list@hgmp.mrc.ac.uk>; Tue, 18 Apr 2000 23:34:53 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id XAA24903
	for proteins-list@hgmp.mrc.ac.uk; Tue, 18 Apr 2000 23:34:51 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: phone4u@grifonline.it
X-Newsgroups: bionet.molbio.proteins
Subject: Take The Call By April 21st, It's FREE!!!                             (freetalking)
Date: 18 Apr 2000 23:34:50 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 251
Message-ID: <200004182234.XAA17717@hgmp.mrc.ac.uk>
X-Trace: niobium.hgmp.mrc.ac.uk 956097291 24901 193.62.192.80 (18 Apr 2000 22:34:51 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from aurora.dspl.com.au (aurora.dspl.com.au [203.18.35.254])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA17717
	for <proteins@net.bio.net>; Tue, 18 Apr 2000 23:34:42 +0100 (BST)
X-Received: from douglas ([203.18.35.225]) by aurora.dspl.com.au with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3)
	id 2FY3JFTA; Wed, 19 Apr 2000 08:29:52 +1000
X-Reply-To: phone4u@grifonline.it
X-To: phone4u@grifonline.it
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

        ______________________________________________
        «¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤
        ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
       Guaranteed -- Best FREE Cell Phone Offer On The Planet!!!
        ______________________________________________
        «¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤»§«¤»¥«¤
        ¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯

  => Get the 1st and ONLY FREE PCS Digital Cell Phone with:

  => NO Long Distance and NO Roaming Charges.

  => Call anytime you want.

  => Now Available on the Net for a Limited Time.

    ####   FIRST 2500 NEW APPS GET A FREE  ####
   #####   PCS "Dual-Band " Digital Cell Phone.   #####

  You get 7.5 cents a minute !!!

  You SAVE over $125.00 !!!

  Don't miss out on using the best NATIONWIDE DIGITAL PCS NETWORK!!!

  * You can safely order your new service.
  * Guaranteed through one of the largest & proven providers who is..
  * Listed with the Consumer Protection Agency of America.

  After you read everything in this e-mail, you can call
  1-888-248-1136 to verify what we say is true.

  Your "Free" Digital Phone includes the following:
  => Your choice of a NEW Samsung or Qualcomm Thin Phone
  => You pay No Activation Fee.
  => You Risk Nothing.

  Order Now and You Get:
  + FREE Long Distance and Roaming.
  + FREE Caller ID.
  + FREE Call Waiting.
  + FREE Call Forwarding.
  + FREE Three Way Calling
  + FREE VoiceMail.
  + FREE Paging. [Get rid of your pager bill.]
  + FREE Home Charger.

  + PLUS, You Get The First Incoming Minute FREE.

  Your NEW phone is...
  => Slim and Lightweight -- just 6 oz.
  => Easy to use.

  You will enjoy...
  * CALLING PLAN AS LOW AS 7.5 CENTS PER MINUTE.
  * Crystal Clear Sound.
  * CDMA technology protects your calls against eavesdropping.
  *  Voice Activated Dialing and Voice Memo with the Samsung model.
  *  The best and largest digital carrier in the USA.

  You get FREE Delivery by UPS within just 10-15 working days of
  approval.

  * * * 30 Day Satisfaction Guarantee * * *

  Just fill out the form below and fax it to us.  One of our
  professional Cell Phone experts will promptly call you to complete
  the setup process.

  **** When they call you, ask for the 7.5 cents per minute offer !!!

  Bad credit is NO PROBLEM.
  You'll be notified if a deposit is needed to activate your new
  service.

  TO ORDER your FREE CELL PHONE, just print the form below. Then
  fax it to the number below. You should have your new Cell Phone within
  10-15 business days after your service is set up.

  Is there any question that this is an incredible opportunity?

  Apply now for the best wireless phone service for the new millennium
  and get your new "FREE" PCS digital Cell Phone.

  Sound too good to be true?  We're going to make this an easy decision
  for you to FAX YOUR APPLICATION TODAY...

  FREE BONUS #1
  Fax your application before Friday, April 21st and you get a
  certificate for THREE EXCITING DAYS and TWO FUN FILLED NIGHTS
  in a mini-suite at a major LAS VEGAS casino hotel or you can choose
  one of 19 other resort destinations including Branson and Cancun.

  FREE BONUS #2
  Fax your application in the next 72 hours and you get a certificate
  for over $500 in Casino Benefits to use with your vacation to
  Reno/Lake Tahoe or Las Vegas. Anaheim and Orlando Fun Books
  are also available that offer discount entertainment and meals.

  This vacation package alone will save you more than $700.00 !!!

  ** So what's the catch?  Company's are scrambling for new customers.
  They're taking risks like never before to get new business. The hotels
  know that once you have experienced their services, you'll want to
  come back.  It's a great way for them to advertise.

  FREE BONUS #3
  Fax your application before Friday, April 21st and you'll receive
  a brochure to get a Continental Advantage credit card with an
  immediate $4,000 line of credit  "PLUS"  an instant $100
  Merchandise Certificate to use just like CASH!!!

  You simply can't lose!!!

  DON'T WAIT to get started ...FAX YOUR APPLICATION NOW!!!

  PS. There are a limited number of vacation certificates that will be
  given out on a first-come, first-serve bases to those who fax their
  application by midnight Friday, April 21st.

  Go Ahead And Fax Your Application Now!

  Thank you for reading this e-mail,


  Opt-In Marketing Concepts
  Copyright 2000, All Rights Reserved



                                 - - - - - - - CUT HERE - - - - - - -

           * * * WARNING, DO NOT MODIFY THIS APPLICATION * * *

  Fax Order Center:  (312) 803-9668

  Please TYPE or PRINT CLEARLY.  Fax ONLY this application.
  APPLICATION MUST BE COMPLETED or IT WILL NOT BE PROCESSED.
  No blank fields.     (04BW)

  [Sorry, no coverage currently available to residents of MT, MS, NC,
  SC, AK]

  "VERY CLEARLY" Print or Type

  [       ]   My application is being faxed 'before'  April 21st, please
  send the three bonus packages as outlined above.  You must
  initialize the box to the left to receive them.

  YOUR E-MAIL ADDRESS: _________________________________

  NAME
  First:__________________ M.I. ____ Last:__________________________

  USA
  Address ______________________________________ Apt# ___________

  City _______________________________ ST ________ Zip _________

  County _______________________ [NEEDED TO FIND YOUR COVERAGE AREA]

  SS# ________________________ Date Of Birth ______/_____/___________

  DL# __________________________ Exp. Date _____/_____/_______

  Home Ph# (___)_______________ [NO PAGER NUMBERS]

  Work Ph# (____)_____________ Ext# ______ [NO PAGER NUMBERS]

  Best Time To Call _________________________ Time Zone: _____________

  YOUR Business or EMPLOYER Information:  (04BW)

  Check one: ____ Self Employed  ____ Employee

  If Self Employed, please enter your Business License # ______________
  or Sales Tax ID #_____________

  Company or Employer NAME:
________________________________________________

  Address: ______________________________________

  City:_______________________________ST:________ Zip:_________

  Phone #:______________________

  Check the phone you want:
  ___ Sanyo 3000   ___ Qualcomm Thin Phone

  Available Calling Plans:
                            =>  120  Anytime minutes per month!!!
                            =>  500  Anytime minutes per month!!!
                            =>  700  Anytime minutes per month!!!
                            =>  1,000  Anytime minutes per month!!!
                            =>  1,500  Anytime minutes per month!!!
                            =>  2000  Anytime minutes per month!!!

  Best of all, every plan exclusive to this offer, allows you the
  freedom to upgrade or downgrade at any time!!!

  One of our professional Cell Phone experts will promptly call you to
  help you choose the plan that best fits your needs.

  [       ]   My application is being faxed 'before' April 21st, please
  send the three bonus packages as outlined above.  You must
  initialize the box to the left to receive them.

  Signature: ______________________________ Date: ____/____/_______

  NO UP-FRONT MONEY -- your first bill comes within 30 days from receipt
  of phone.
  [2 year Air Time contract, O.A.C.]     (04BW)

  Authorization for credit check and contract approved by my signature.

  Check your application status by calling:  1-888-248-1136

  Fax Order Center:  (312) 803-9668

           * * * WARNING, DO NOT MODIFY THIS APPLICATION * * *

                                 - - - - - - - CUT HERE - - - - - - -


  IMPORTANT NOTE:  An independent marketing company will be
  processing your free bonus's and not the cell phone provider or the
  company sending this email.  So don't forget to initialize the box
  above to receive them.


        =-=-=-=-=-=-=-=-=-=-REMOVE INSTRUCTIONS-=-=-=-=-=-=-=-=
  Please follow the instructions below to be removed from our in-house
  mailing list. We will immediately take action to remove you from
  future mailings.

  Access the website below and enter your e-mail address.
  If this service page has been shut down, it is because someone
  complained about this service. If this is the case, we are sorry for
  the inconvenience.

  http://sede.aecoc.es%647key=removeremoveindex=ixbtl730iq%403522794361/
  ~joeb/remove/21268.htm

  We are making an effort to keep the Internet spam-free. Your address
  can also be permanently deleted from this database by sending and email
  to thankyou15@bigfoot.com



---


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 19 02:46:10 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 2211617A61; Wed, 19 Apr 2000 02:46:09 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id CAA28387
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 19 Apr 2000 02:46:08 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id CAA27230
	for proteins-list@hgmp.mrc.ac.uk; Wed, 19 Apr 2000 02:46:06 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: xiaocy@sparc2.hunnu.edu.cn ("xiaocy")
X-Newsgroups: bionet.molbio.proteins
Subject: Databse searching
Date: 19 Apr 2000 02:46:05 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 44
Message-ID: <000701bfa9a0$e5abdb50$3c7ac5ca@esquire-lc>
Mime-Version: 1.0
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0004_01BFA9E3.F37E3C30"
X-Trace: niobium.hgmp.mrc.ac.uk 956108765 27228 193.62.192.80 (19 Apr 2000 01:46:05 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from sparc2.hunnu.edu.cn (sparc2.hunnu.edu.cn [202.197.120.2])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id CAA28379
	for <proteins@net.bio.net>; Wed, 19 Apr 2000 02:45:59 +0100 (BST)
X-Received: (qmail 22070 invoked from network); 19 Apr 2000 01:40:11 -0000
X-Received: from unknown (HELO esquire-lc) (202.197.122.60)
  by sparc2.hunnu.edu.cn with SMTP; 19 Apr 2000 01:40:11 -0000
X-To: <proteins@hgmp.mrc.ac.uk>
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 4.72.3110.5
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

This is a multi-part message in MIME format.

------=_NextPart_000_0004_01BFA9E3.F37E3C30
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hello reader
I am working on database searching with MALDI-TOF-MS data.I have used =
such as PeptIdent,Peptidesearch,Mascot, ProFound,MS-Fit software to =
search database, but I find the result not satisficated.I can not make =
sure the prompt protein.Can anyone recommond a better software and how =
to get it?My adress is lee_wu@21cn.com Your help are kindly appreciated. =
Thank you

------=_NextPart_000_0004_01BFA9E3.F37E3C30
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD W3 HTML//EN">
<HTML>
<HEAD>

<META content=3Dtext/html;charset=3Diso-8859-1 =
http-equiv=3DContent-Type>
<META content=3D'"MSHTML 4.72.3110.7"' name=3DGENERATOR>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT color=3D#000000 size=3D1>Hello reader</FONT></DIV>
<DIV><FONT color=3D#000000 size=3D1>I am working on database searching =
with=20
MALDI-TOF-MS data.I have used such as PeptIdent,Peptidesearch,Mascot,=20
ProFound,MS-Fit software to search database, but I find the result not=20
satisficated.I can not make sure the prompt protein.Can anyone recommond =
a=20
better software and how to get it?My adress is <A=20
href=3D"mailto:lee_wu@21cn.com">lee_wu@21cn.com</A> Your help are kindly =

appreciated. Thank you</FONT></DIV></BODY></HTML>

------=_NextPart_000_0004_01BFA9E3.F37E3C30--

---


From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 19 20:37:02 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 5FF3217AE6; Wed, 19 Apr 2000 20:37:00 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA29248
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 19 Apr 2000 20:36:58 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA10780
	for proteins-list@hgmp.mrc.ac.uk; Wed, 19 Apr 2000 20:36:57 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: s691461@condor.mbcr.bcm.tmc.edu (Anton D Solovyov)
X-Newsgroups: bionet.molbio.proteins
Subject: Looking for dsbA DNA
Date: 19 Apr 2000 19:31:35 GMT
Organization: The Baylor College of Medicine
Lines: 16
Message-ID: <8dl1in$puc@gazette.bcm.tmc.edu>
X-Newsreader: TIN [UNIX 1.3 950824BETA PL0]
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hi all,

I was wondering if someone could help me to find the E.coli protein dsbA.
The sequence that we have has mutations that introduce the unwanted
restriction sites (BamHI and BglII) (it still encodes the same a.a.
sequence). Instead of performing the mutagenesis maybe some kind soul can
share their plasmid encoding wild-type dsbA with us?

Thank you in advance!

Anton Solovyov
Graduate Research Assistant
Departemt of Biochemistry and Molecular Biology
Baylor College of Medicine
Houston TX 77030



From owner-proteins@hgmp.mrc.ac.uk  Wed Apr 19 23:16:18 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 89CF817A6A; Wed, 19 Apr 2000 23:16:17 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id XAA24868
	for <proteins-list@hgmp.mrc.ac.uk>; Wed, 19 Apr 2000 23:16:14 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id XAA21445
	for proteins-list@hgmp.mrc.ac.uk; Wed, 19 Apr 2000 23:16:12 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Daniel <05757NO05SPAM@upch.edu.pe.invalid>
Subject: Protein Exposed Surface
X-Newsgroups: bionet.molbio.proteins
Message-ID: <25d0e1ac.054020ad@usw-ex0109-070.remarq.com>
Lines: 17
Bytes: 633
X-Originating-Host: 200.48.64.11
Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here
X-Wren-Trace: eC4LIyI7fDZ9Pm9xfjkPMiw+NmUuLnt2Oydhf3dqeTp5Zjh7bj9q
Date: Wed, 19 Apr 2000 15:01:46 -0700
X-Complaints-To: wrenabuse@remarq.com
X-Trace: WReNphoon3 956183007 10.0.2.70 (Wed, 19 Apr 2000 15:23:27 PDT)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

PLease!
I have a 3D model of my protein, and I need to calculate
the solvent exposed surface...per aminoacid.

I know about algorithms based on the simulation of a probe
scanning around all the protein structure.  Even the WebLab
Viewer does this, but it only draws the surface, it does
not give any numerical result.

Is there any downloadable program or Internet service able
to do this?

(I work in Perú, there is no one here to ask about this,
please help me)


* Sent from AltaVista http://www.altavista.com Where you can also find related Web Pages, Images, Audios, Videos, News, and Shopping.  Smart is Beautiful


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 01:39:12 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 08A4817B0A; Thu, 20 Apr 2000 01:39:11 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA02400
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 01:39:10 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id BAA22923
	for proteins-list@hgmp.mrc.ac.uk; Thu, 20 Apr 2000 01:39:09 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
Message-ID: <38FE51C5.D73EA901@freeuk.com>
From: ChenHA <hzhen@freeuk.com>
X-Mailer: Mozilla 4.7 [en] (Win95; I)
X-Accept-Language: en
MIME-Version: 1.0
X-Newsgroups: bionet.molbio.proteins
Subject: Re: Protein Exposed Surface
References: <25d0e1ac.054020ad@usw-ex0109-070.remarq.com>
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Lines: 17
Date: Thu, 20 Apr 2000 01:39:33 +0100
X-Complaints-To: abuse@freeuk.net
X-Trace: nnrp4.clara.net 956191147 212.126.154.211 (Thu, 20 Apr 2000 01:39:07 BST)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


Daniel wrote:
> 
> PLease!
> I have a 3D model of my protein, and I need to calculate
> the solvent exposed surface...per aminoacid.
> 
> I know about algorithms based on the simulation of a probe
> scanning around all the protein structure.  Even the WebLab
> Viewer does this, but it only draws the surface, it does
> not give any numerical result.
> 
> Is there any downloadable program or Internet service able
> to do this?

Try Naccess at 
http://sjh.bi.umist.ac.uk/naccess.html


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 13:50:26 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id DDF6017B5D; Thu, 20 Apr 2000 13:50:17 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA01090
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 13:50:11 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA01970
	for proteins-list@hgmp.mrc.ac.uk; Thu, 20 Apr 2000 13:50:09 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: Gary Coulton <g.coulton@ic.ac.uk>
X-Newsgroups: bionet.molbio.proteins
Subject: Cell Biology & Imaging Tools for the New Century
Date: Thu, 20 Apr 2000 13:36:00 +0100
Organization: Imperial College
Lines: 78
Message-ID: <38FEF9AF.F091B18E@ic.ac.uk>
Mime-Version: 1.0
Content-Type: multipart/alternative;
 boundary="------------2AC7B4AC371F11269A04546A"
X-Mailer: Mozilla 4.61 [en] (Win95; I)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk


--------------2AC7B4AC371F11269A04546A
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

             Announcing the 11th International Congress of
              Histochmistry and Cytochemistry (ICHC 2000)

          "Cell Biology and Imaging tools for the New Century"

   Come to the beautiful Medieval City of York in England and enjoy 27
  scientific sessions aimed at the very latest development in  imaging
techniques for Cell Biology, Pathology, Plant sciences and Environmental
                              toxicology.

                               Latest News

Roger Tsien is awarded the Pearse Prize for Histochemistry. The Pearse
Prize is the highest award in the UK for contributions made in the field
of Histochemistry.
Richard Hauglund awarded the Histochemical Journal Lecture.
Morris Karnovsky to give the David Glick Lecture
Fred Bosman to give the Piet Van Duijn Lecture.
                   Over a 100 other leading speakers.

  ****Sign-up for the accompanying Molecular Morphology Techniques Wet
                              workshop****.

Register for the week or choose from our daily rates.

Student Bursaries still available, apply right away.

Abstract deadline May 15th 2000. In order to enter the book of
abstracts.

For details on on-line registration, bursaries abstract submission and
excursions in York see the ICHC 2000 web-site
http://www.med.ic.ac.uk/external/ichc_2000



--------------2AC7B4AC371F11269A04546A
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>

<center><b><u><font size=+2>Announcing the 11th International Congress
of</font></u></b>
<br><b><u><font size=+2>Histochmistry and Cytochemistry (ICHC 2000)</font></u></b><b><u></u></b>
<p><b><font size=+1>"Cell Biology and Imaging tools for the New Century"</font></b><b></b>
<p><b>Come to the beautiful Medieval City of York in England and enjoy
27 scientific sessions aimed at the very latest development in&nbsp; imaging
techniques for Cell Biology, Pathology, Plant sciences and Environmental
toxicology.</b>
<p><b><font face="Arial,Helvetica">Latest News</font></b></center>

<p><b>Roger Tsien</b> is awarded the Pearse Prize for Histochemistry. The
Pearse Prize is the highest award in the UK for contributions made in the
field of Histochemistry.
<br><b>Richard Hauglund</b> awarded the Histochemical Journal Lecture.
<br><b>Morris Karnovsky</b> to give the David Glick Lecture
<br><b>Fred Bosman</b> to give the Piet Van Duijn Lecture.
<center><b>Over a 100 other leading speakers.</b>
<p><u>****Sign-up for the accompanying Molecular Morphology Techniques
Wet workshop****</u>.</center>

<p>Register for the week or choose from our daily rates.
<p>Student Bursaries still available, apply right away.
<p>Abstract deadline May 15th 2000. In order to enter the book of abstracts.
<p>For details on on-line registration, bursaries abstract submission and
excursions in York see the ICHC 2000 web-site <A HREF="http://www.med.ic.ac.uk/external/ichc_2000">http://www.med.ic.ac.uk/external/ichc_2000</A>
<br>&nbsp;
<br>&nbsp;</html>

--------------2AC7B4AC371F11269A04546A--



From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 15:45:11 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id A351F17AC9; Thu, 20 Apr 2000 15:45:10 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA14702
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 15:45:08 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA03442
	for proteins-list@hgmp.mrc.ac.uk; Thu, 20 Apr 2000 15:45:06 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: koen peeters <kopee@gengenp.rug.ac.be>
X-Newsgroups: bionet.molbio.proteins
Subject: glycosylation
Date: Thu, 20 Apr 2000 16:41:42 +0200
Organization: University of Ghent, Belgium
Lines: 27
Message-ID: <38FF1726.851F266C@gengenp.rug.ac.be>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Mailer: Mozilla 4.7 [en] (Win98; I)
X-Accept-Language: en
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk





Dear,

I'd like to study glycosylation of certain plant proteins.
I'm mainly interested in the presence of xylose and fucose residus
of secreted proteins.

Could anyone provide me with info on wich techniques I could use
for answering my question?
Are there commercial available antibodies against xylose/fucose residus?

Thanks in advance,

Koen


-- 
==================================================================
Koen Peeters 
DEPARTMENT OF GENETICS                         Fax:32 (0)9 2645349
UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
Vlaams Instituut voor Biotechnologie                           VIB
mailto:kopee@gengenp.rug.ac.be             http://spider.rug.ac.be
==================================================================


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 18:12:47 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id B305817B51; Thu, 20 Apr 2000 18:12:46 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA00021
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 18:12:44 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id SAA05406
	for proteins-list@hgmp.mrc.ac.uk; Thu, 20 Apr 2000 18:12:43 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
From: DOCTORHIM@aol.com
X-Newsgroups: bionet.molbio.proteins
Subject: Re: glycosylation
Date: 20 Apr 2000 18:12:41 +0100
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
Lines: 3
Message-ID: <4b.2cdc11f.263092ad@aol.com>
Mime-Version: 1.0
Content-Type: text/plain; charset="US-ASCII"
Content-Transfer-Encoding: 7bit
X-Trace: niobium.hgmp.mrc.ac.uk 956250762 5403 193.62.192.80 (20 Apr 2000 17:12:42 GMT)
X-Complaints-To: news@net.bio.net
X-Received: from imo-d10.mx.aol.com (imo-d10.mx.aol.com [205.188.157.42])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA00011
	for <proteins@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 18:12:39 +0100 (BST)
X-Received: from DOCTORHIM@aol.com
	by imo-d10.mx.aol.com (mail_out_v26.7.) id w.4b.2cdc11f (3957);
	Thu, 20 Apr 2000 13:04:45 -0400 (EDT)
X-To: kopee@gengenp.rug.ac.be, proteins@hgmp.mrc.ac.uk
X-Mailer: AOL 4.0 for Mac - Post-GM sub 146
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

You can get a xylosidase that will remove the beta 1-2 xylose.  Prozyme 
(www.prozyme.com) is the only company that sells this enzyme.
---


From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 20:18:02 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 77D3B17A85; Thu, 20 Apr 2000 20:18:01 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA11145
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 20:17:59 +0100 (BST)
Received: (from news@localhost)
	by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id UAA06908
	for proteins-list@hgmp.mrc.ac.uk; Thu, 20 Apr 2000 20:17:58 +0100 (BST)
X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to <news> using -f
X-Originating-Host: 130.37.84.107
Organization: http://www.remarq.com: The World's Usenet/Discussions Start Here
Subject: Re: how to find the genome DNA
Lines: 20
From: rogier <stugerNOstSPAM@cellbiology.uni-frankfurt.de.invalid>
X-Newsgroups: bionet.molbio.proteins
Message-ID: <161d8bad.f23df688@usw-ex0103-086.remarq.com>
References: <38FA818F.601EC493@nic.bmi.ac.cn>
Bytes: 739
X-Wren-Trace: eE9qQkNaHVccHE9STQpcZl5ZU0ZIQgBVRURZAlNVX0JGWw5ASglPU1cAT08BXg8IABAUDgBEYX5/eA==
Date: Thu, 20 Apr 2000 12:13:04 -0700
X-Complaints-To: wrenabuse@remarq.com
X-Trace: WReNphoon3 956258593 10.0.2.86 (Thu, 20 Apr 2000 12:23:13 PDT)
To: proteins@hgmp.mrc.ac.uk
Sender: owner-proteins@hgmp.mrc.ac.uk
Precedence: bulk

Hi Zhang,
start by running a GenBank search for [organism] + [genename or
chromosome or keywords]. Or do a BLAST search and see what
genomic sequences pop up.

Good places to start:
NCBI: http://www.ncbi.nlm.nih.gov
GenBank: http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
Blast: http://www.ncbi.nlm.nih.gov/BLAST

Good luck,
Rogier
http://zap.to/rogier
_______________________________________
get a free laserpointer for signing up and earn cash for writing
reviews on biology kits and reagents:
http://www.biowire.com/bw_jsp/gate_top.jsp?add=1&referrer=rogier

* Sent from RemarQ http://www.remarq.com The Internet's Discussion Network *
The fastest and easiest way to search and participate in Usenet - Free!



From owner-proteins@hgmp.mrc.ac.uk  Thu Apr 20 20:27:18 2000
Return-Path: <owner-proteins@hgmp.mrc.ac.uk>
Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110)
	id 9381F17AAF; Thu, 20 Apr 2000 20:27:17 +0100 (BST)
Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41])
	by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA12005
	for <proteins-list@hgmp.mrc.ac.uk>; Thu, 20 Apr 2000 20:27:15