From owner-biophysics@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Jochen Gruber Newsgroups: bionet.biophysics,bionet.general,bionet.info-theory,bionet.microbiology,bionet.neuroscience,bionet.software Subject: online education in mathematics Date: 1 Sep 1998 17:30:51 -0700 Organization: VIMS Lines: 25 Sender: kristoff@net.bio.net Distribution: world Message-ID: <35EBE016.30FD7BFF@vims.net> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4361 bionet.general:30694 bionet.info-theory:6524 bionet.microbiology:14303 bionet.neuroscience:24294 bionet.software:21764 The Virtual Institute of Mathematical Sciences is now accepting students applications. We offer post-graduate online education in mathematics and quantitative sciences. Mathematics, Statistics, Numerical mathematics and programming, mathematical sciences, quantitative aspects of engineering and economics. Visit our site at http://www.vims.net Combining the advantages of distance education and traditional universities with virtual online class rooms. Studying from your home or your work place, meeting online with other students, teaching assistants and teachers. All our teachers hold regular positions at internationally recognized universities world-wide. In addition, working professionals show real world applications. We focus on graduates with the need to continue their education in quantitative sciences. Attention university faculty and professionals: we continously accept new teachers! From owner-biophysics@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsgate.duke.edu!not-for-mail From: wrankin@cerberus.ee.duke.edu (William T. Rankin) Newsgroups: bionet.biophysics Subject: Re: protein folding Date: 2 Sep 1998 10:20:46 -0400 Organization: Duke University, Durham, NC, USA Lines: 21 Message-ID: <6sjk7u$1q4$1@cerberus.ee.duke.edu> References: NNTP-Posting-Host: cerberus.ee.duke.edu In article , JJ Miranda wrote: >Hi all, > >This is a very subjective question. Which profs at which universities >are currently doing the leading work in protein folding? Theoretical or >experimental is fine. I just wanted to know what the current opinion in >the field was... > >Sincere regards, >JJ Miranda Not sure if this helps, but you may want to check out Dr. Klaus Schulten's Theoretical Biophysics Group at UIUC's Beckman: http://www.ks.uiuc.edu/ -bill -- bill rankin ...................................... philosopher/coffee-drinker wrankin@ee.duke.edu ........................................ doctoral wannabe duke university dept. of electrical engr ......... scientific computing group From owner-biophysics@net.bio.net Tue Sep 01 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!cyclone.news.idirect.com!island.idirect.com!newsin.agis.net!agis!newsfeeder.triton.net!news1.triton.net!not-for-mail From: 590@nlr579.com Newsgroups: bionet.biophysics Subject: NLREG - Nonlinear & linear statistical regression program - 34 0902172015 JCI Date: Wed, 2 Sep 98 17:20:25 Organization: Nonlinear Regression Software Lines: 55 Message-ID: <6skgb2$c38$1@news1.triton.net> NNTP-Posting-Host: ng.sandh.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit x-no-archive: yes ** Announcing NLREG -- Nonlinear Statistical Regression Program ** http://www.sandh.com/sherrod/nlreg.html NLREG is a powerful statistical analysis program for Windows 95 and NT that performs linear and nonlinear regression analysis and curve fitting. NLREG determines the values of parameters for an equation, whose form you specify, that cause the equation to best fit a set of data values. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions. NLREG features a full programming language with a syntax similar to C for specifying the function that is to be fitted to the data. This allows you to compute intermediate work variables, use conditionals, and even iterate in loops. With NLREG it is easy to construct piecewise functions that change form over different domains. NLREG performs true nonlinear regression, it does not transform the function into a linear form. As a result, it can handle functions that are impossible to linearize such as: Y = Amplitude*SIN(Freq*X+Phase) + A*EXP(X); Another advantage of handing the function in true nonlinear form is that the minimization of the sum of squared residual values (i.e., "least squares") is based on the true nonlinear value rather than some linearized transformation. In addition to computing the optimal values of the parameters, NLREG can generate plots of the data points and the fitted equation. In addition, it can plot the distribution of residual values. In addition to performing classic nonlinear regression, NLREG can be used to find the root or minimum value of a general nonlinear function. It can also be used in a special form where the independent variable is omitted; an interesting application of this is "circular regression" where a circle is fitted to a set of data points. NLREG is in use at hundreds of universities, laboratories, and government agencies around the world (including the U.S. Navy, Harvard, and Duke). NLREG has been validated using the NIST statistical reference datasets; the results are available on the NLREG web page. The price of NLREG is only $65 ($70 if outside the USA), which is far below the cost of comparable commercial regression programs. And you can download a shareware demonstration version of NLREG to try out before you decide to purchase it. To learn more about NLREG and download your free shareware version, visit the web site: http://www.sandh.com/sherrod/nlreg.html -- 34: bionet.biophysics 0902172015 -- From owner-biophysics@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.ox.ac.uk!quartz!carsten From: Carsten Liess Newsgroups: bionet.biophysics,ox.general Subject: Viscosity Date: Thu, 3 Sep 1998 17:15:18 +0100 Organization: Oxford Univerity Lines: 13 Message-ID: NNTP-Posting-Host: quartz.bioch.ox.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: news.ox.ac.uk 904839320 13536 163.1.215.1 (3 Sep 1998 16:15:20 GMT) X-Complaints-To: newsmaster@ox.ac.uk NNTP-Posting-Date: 3 Sep 1998 16:15:20 GMT X-Sender: carsten@quartz Dear all, does someone know how the viscosity of a solution depends on temperature and other solution-specific parameters? Also, how does the viscosity change if one has a known volume of a solution and adds a certain amount of water? Any thoughts or hints where I could find out about this gratefully appreciated. Thanks Carsten From owner-biophysics@net.bio.net Wed Sep 02 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.corridex.com!howland.erols.net!feed1.news.rcn.net!rcn!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: John Philo <"jphilo*NO SPAM12*"@earthlink.net> Newsgroups: bionet.biophysics,ox.general Subject: Re: Viscosity Date: Thu, 03 Sep 1998 14:06:22 -0700 Organization: Alliance Protein Laboratories Lines: 29 Message-ID: <35EF04CE.BB29DEE8@earthlink.net> References: NNTP-Posting-Host: 1cust2.tnt1.thousand-oaks.ca.da.uu.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To: Carsten Liess X-Posted-Path-Was: not-for-mail X-ELN-Date: Thu Sep 3 14:10:38 1998 X-Mailer: Mozilla 4.05 [en] (Win95; U) Carsten, The viscosity of water decreases strongly with temperature (about 2% per degree C). Data for the temperature dependence, and for the viscosities of solutions containing common salts, can be found in CRC Handbook of Chemistry and Physics. If you add water to solution you will simply dilute the solutes and end up with the viscosity appropriate to the new solute concentration. Carsten Liess wrote: > > Dear all, > > does someone know how the viscosity of a solution depends on temperature > and other solution-specific parameters? > Also, how does the viscosity change if one has a known volume of a > solution and adds a certain amount of water? > > Any thoughts or hints where I could find out about this gratefully > appreciated. Thanks > > Carsten -- John Philo, Alliance Protein Laboratories *** Remove "*NO SPAM12*" from return address before replying. *** From owner-biophysics@net.bio.net Thu Sep 03 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!192.26.210.166!sunqbc.risq.qc.ca!nntprelay.mathworks.com!newsfeed1.earthlink.net!nntp.earthlink.net!posted-from-earthlink!not-for-mail From: specpress@earthlink.net (SCIENCE-WEEK Editors) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: CURRENT SCIENCE TITLES: September 4, 1998 Date: Fri, 04 Sep 1998 00:46:39 GMT Organization: Science-Week Lines: 96 Message-ID: <6sndfk$fki$2@birch.prod.itd.earthlink.net> Reply-To: specpress@earthlink.net NNTP-Posting-Host: 1cust123.tnt47.chi5.da.uu.net X-Newsreader: Forte Free Agent 1.0.82 X-Posted-Path-Was: not-for-mail X-ELN-Date: Thu Sep 3 17:49:56 1998 Xref: biosci bionet.neuroscience:24304 bionet.biophysics:4366 bionet.cellbiol:10157 bionet.general:30709 CURRENT SCIENCE TITLES ---------------------- CST is a free weekly listing of selected current articles of broad and significant interest to the scientific community of researchers, educators, and policy makers. Each listing includes the subject of the article, lead author, author affiliation, and complete journal reference. The listing is extracted from the current issue of the publication SCIENCE-WEEK, and is delivered free each week via Email. To receive CURRENT SCIENCE TITLES free each week via Email, transmit EMAIL CST as the SUBJECT of an Email message to: CURRENT SCIENCE TITLES: September 4, 1998 -------------------------------------------------- 1. ON THE CHASM BETWEEN SCIENTISTS AND NON-SCIENTISTS QY: T. Tachibana, 2-18-12 Koishikawa, Bunkyo-ku, Tokyo 112 JP. (Science 7 Aug 98 281:778) (Science-Week 4 Sep 98) 2. CORPORATE PAYMENTS TO SCIENTISTS FOR LETTERS TO JOURNALS (Nature 13 Aug 98 394:609) (Science 14 Aug 98 281:895) (Science-Week 4 Sep 98) 3. ON PLANETARY NEBULA AND THE DEATH OF STARS QY: Sun Kwon, University of Calgary, CA. (Sky & Telescope October 1998) (Science-Week 4 Sep 98) 4. ON NEUTRON STARS AND THE FLUID PROPERTIES OF HOT ATOMIC NUCLEI QY: Vic Viola (American Scientist October 1998) (Science-Week 4 Sep 98) 5. MOLECULAR ARCHEOLOGY OF THE E. COLI GENOME QY: Howard Ochman (Proc. Natl. Acad. Sci. US 4 Aug 98 95:9413) (Science-Week 4 Sep 98) 6. MOLECULAR BIOLOGY OF MUSCLE: COUPLED CALCIUM ION CHANNELS QY: Andrew R. Marks (Science 7 Aug 98 281:818) (Science-Week 4 Sep 98) 7. CIRCADIAN OSCILLATORS: RESETTING BY TEMPERATURE CHANGES QY: Jay C. Dunlap (Science 7 Aug 98 281:825) (Science-Week 4 Sep 98) 8. BIOLOGY OF AGING: ON TELOMERES AND REPLICATIVE SENESCENCE QY: John M. Sedivy (Proc. Natl. Acad. Sci. US 4 Aug 98 95:9078) (Science-Week 4 Sep 98) 9. EMBRYOGENESIS: THE AREA CODE HYPOTHESIS UPDATED QY: William J. Dreyer (Proc. Natl. Acad. Sci. US 4 Aug 98 95:9072) (Science-Week 4 Sep 98) 10. ON ANTI-ANGIOGENIC GENE THERAPY QY: Judah Folkman, Children's Hospital, Boston MA 02115 US. (Proc. Natl. Acad. Sci. US 23 Jun 98 95:9064) (Science-Week 4 Sep 98) -------------------------------------------------- Detailed briefs and explicating material for all of the above articles are provided each week in the Email publication SCIENCE-WEEK. Information about SCIENCE-WEEK subscriptions is available at . Back issues of SCIENCE-WEEK are available free at the above website main page . -------------------------------------------------- Copyright (c) 1998 Science-Week/Spectrum Press Inc. All Rights Reserved --------------------------------------------- This publication may be freely copied or retransmitted provided it remains intact and without changes. No partial display, partial retransmission, or partial duplication in any medium, including BBS, Intranet, Internet Email, or website duplication, is permitted without the explicit consent of the rights holder. Please address all queries to . --------------------------------------------- From owner-biophysics@net.bio.net Fri Sep 04 23:00:00 1998 Path: biosci!daresbury!daresbury!server5.netnews.ja.net!server6.netnews.ja.net!nntp.news.xara.net!xara.net!insnet.net!uunet!uunet!in3.uu.net!server-b.cs.interbusiness.it!news.tin.it!not-for-mail From: excell@bware.it Newsgroups: bionet.biophysics Subject: Announce: how to SEND EMAIL AND NEWS from your GSM PHONE Date: 26 Aug 1998 10:49:16 GMT Organization: eXcell GSM/SMS gateway Lines: 27 Message-ID: <6s0p7c$ifv$5091@nslave1.tin.it> NNTP-Posting-Host: rub182.mi03.mi.interbusiness.it Mime-Version: 1.0 Content-Type: text/plain Your GSM phone is already connected to the Internet! Now you can send EMAIL and post to newsgroups directly from your GSM phone. Just write a short message (SMS) with the syntax: EMAIL user@host message and then send it to the "eXcell" phone number at +393388641732 If your phone does not have the @ character you can use the ! , like: EMAIL user!host message There are several options available, such as a personal signature, a personal email address configuration for getting back replies, personal mailing lists, anti-spamming, carbon copy, phone number anonymizer, etc.etc. The only cost for you is the SMS shipping; normally a few pennies. Our service is currently being used by the GSM users of 40 different countries all around the world, using more than 80 different GSM networks. And it will certainly work for you also, so give it a try! To know more about eXcell, and to get the complete user's guide, come and visit http://www.bware.it/excell ( no advertising banners ) Be an eXcellent GSM user! From owner-biophysics@net.bio.net Sun Sep 06 23:00:00 1998 Newsgroups: bionet.biophysics,bionet.molec-model Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!news.idt.net!nntp2.cerf.net!nntp3.cerf.net!news.msi.com!uucp From: "Jeffrey L. Nauss" Subject: Post-doc opening: molecular modeling of protein-DNA complexes X-Nntp-Posting-Host: 146.202.26.50 Content-Type: text/plain; charset=us-ascii Message-ID: <35F42E2F.31A8CDF7@usa.net> Sender: uucp@msi.com Reply-To: jnauss@usa.net Content-Transfer-Encoding: 7bit Organization: Molecular Simulations, Inc. Mime-Version: 1.0 Date: Mon, 7 Sep 1998 19:04:15 GMT X-Mailer: Mozilla 4.05 [en] (Win95; I) X-Disclaimer: _ Unless stated otherwise, everything in this message is personal opinion and nothing in it is an official statement of Molecular Simulations Inc. Lines: 25 Xref: biosci bionet.biophysics:4371 bionet.molec-model:2231 Molecular Simulations Inc. has an *immediate* opening for a post-doctoral scientist to investigate the dynamics of topoisomerase I, its complex with DNA, and possibly new drug candidates. The position will involve extensive use of a variety of software packages being developed here at MSI. This position will be in our San Diego office and will last until April 1999. If you know of anyone interested in this position, please have them forward their resume and CV to me at the address shown below. -- Jeffrey L. Nauss, PhD Phone: (619) 799-5555 Product Specialist, Simulations Fax: (619) 458-0136 Molecular Simulations Inc E-mail: jnauss@msi.com 9685 Scranton Road San Diego, CA 92121 -disclaimer- unless stated otherwise, everything in the above message is personal opinion and nothing in it is an official statement of molecular simulations inc. From owner-biophysics@net.bio.net Mon Sep 07 23:00:00 1998 Path: biosci!biosci!not-for-mail From: Y Xu Newsgroups: bionet.biophysics,pgh.jobs.offered Subject: Postdoc in NMR available (3 positions) Date: 8 Sep 1998 10:14:39 -0700 Organization: University of Pittsburgh Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <35EF0C9D.CD5BBBEB@imap.pitt.edu> NNTP-Posting-Host: net.bio.net --------------C058C7403440A99916EB66CF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Three postdoctoral positions (one as lab manager) available immediately to (1) determine the structures of functional channel peptides in membrane environment; (2) study the mechanisms underlying the actions of nonspecific drugs on these channels; OR (3) test therapeutic agents for treatment of neuronal injuries. Experience with NMR is preferred but not required. Salary competitive and long-term positions possible. Send CV and names of three references to Dr. Yan Xu, W-1358 Biomedical Science Tower, University of Pittsburgh, Pittsburgh, PA 15262, xu@smtp.anes.upmc.edu . Fax: (412) 648-9587. --------------C058C7403440A99916EB66CF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Three postdoctoral positions (one as lab manager) available immediately to (1) determine the structures of functional channel peptides in membrane environment; (2) study the mechanisms underlying the actions of nonspecific drugs on these channels; OR (3) test therapeutic agents for treatment of neuronal injuries.  Experience with NMR is preferred but not required.  Salary competitive and long-term positions possible.  Send CV and names of three references to Dr. Yan Xu, W-1358 Biomedical Science Tower, University of Pittsburgh, Pittsburgh, PA 15262, 
xu@smtp.anes.upmc.edu
.  Fax: (412) 648-9587. --------------C058C7403440A99916EB66CF-- From owner-biophysics@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!portc04.blue.aol.com!audrey01.news.aol.com!not-for-mail From: paraleepk@aol.com (Paralee PK) Newsgroups: bionet.biophysics Subject: 3-D structure of DNA Lines: 20 Message-ID: <1998090904052500.AAA18337@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 9 Sep 1998 04:05:25 GMT Organization: AOL http://www.aol.com I'm taking a molecular biology class. The professor gave us a problem set. He said we could ask anyone for help. I'm asking you! Here's the problem: You want to determine the 3-D structure of a 25 base pair oligonucleotide duplex. The sequence is: 5'TTTTTAAAAATTTTTGGGGGGGGGG3' 3'AAAAATTTTTAAAAACCCCCCCCCC5' A. Describe the kinds of secondary and tertiary DNA structues that youmight expect to find in the DNA. B. Propose a multi-approach experimental strategy for testing your hypotheses. Describe the kinds of information each approach would provide, andhow the approach could be used to confirm or discount your hypotheses. What could be the alternative outcomes and conclusions? I was considering making a flow chart of the approaches and possible outcomes. We've been talking about the various microscopies, NMR and crystallography. I'm assuming we would use those methodologies. Thanks. From owner-biophysics@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!btnet-peer!btnet!dispose.news.demon.net!demon!easynet-tele!easynet-uk!bunny.easynet.fr!easynet-fr!buggy.easynet.fr!not-for-mail From: philimar@easynet.fr (Philippe MARQUIS) Newsgroups: bionet.biophysics Subject: Software to print graph paper Date: Wed, 09 Sep 1998 20:02:07 GMT Organization: [Posted via] Easynet France Message-ID: <6t6mr8$ij2$12@buggy.easynet.fr> Reply-To: philimar@easynet.fr NNTP-Posting-Host: pop-metz-5.pops.easynet.fr X-Trace: buggy.easynet.fr 905371304 19042 195.114.93.5 (9 Sep 1998 20:01:44 GMT) X-Complaints-To: abuse@easynet.fr NNTP-Posting-Date: 9 Sep 1998 20:01:44 GMT X-Newsreader: Forte Free Agent 1.0.82 Lines: 36 The free software GRAPHPAP designed to print customized graph papers has known a big success. Thank you for all the comments and suggestions. It shows that despite the common belief that most graphing is done on-screen nowadays, many people still use ordinary paper graphs and that it is becoming increasingly difficult to find such stationery. The user feed-back has led to a new version 2.0, now available, always free on : http://perso.easynet.fr/~philimar/ Some bugs have been corrected and important new features added: 1) Scales: linear, logarithmic, quadratic and gaussian. 2) Coordinates: cartesian or polar. All the combinations are possible resulting in possibilities of quite esoteric formats. The quadratic scale is specially intended for immunochemistry teaching (plots of radial immunodiffusion assays). Polar coordinates have been required for diagrams of wave propagation and gaussian scale to check the distribution of cumulated frequencies. Submitting any new idea for the next version will be wellcome ----------------------------- Dr Philippe Marquis Centre hospitalier regional METZ - FRANCE e-mail : philimar@easynet.fr ---------------------------- From owner-biophysics@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!newsgate.cistron.nl!het.net!news.belnet.be!inf6serv.rug.ac.be!not-for-mail From: Wijnand Schepens Newsgroups: bionet.molec-model,bionet.biophysics,comp.programming,bionet.molbio.proteins,comp.graphics.visualization Subject: visualizing cluster of simple molecules Date: Wed, 09 Sep 1998 16:35:06 +0200 Organization: RUG Lines: 20 Message-ID: <35F69219.6C4B8549@rug.ac.be> NNTP-Posting-Host: lolita.rug.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5b1 [en] (Win95; I) X-Accept-Language: en Xref: biosci bionet.molec-model:2233 bionet.biophysics:4375 bionet.molbio.proteins:13269 Hi, I would like to visualize a cluster (set) of small (identical) molecules. I now the coordinates of every atom in every molecule. What I'm looking for is a simple way to see on the screen how it looks like. - Is there any freeware or shareware program (Windows or UNIX) that does this - What file-formats are appropriate for this goal and simple enough? I've tried to put the coordinates in a pdb-like format, and used rasmol to visualize it, but they expect proteins, and I don't need all that fancy stuff... Can anyone help me along? Wijnand Schepens From owner-biophysics@net.bio.net Tue Sep 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!not-for-mail From: Yu Wai Chen Newsgroups: bionet.biophysics Subject: Re: 3-D structure of DNA Date: Wed, 09 Sep 1998 10:49:10 +0100 Organization: MRC Centre for Protein Engineering Lines: 26 Message-ID: <35F64F16.485420EA@mrc-lmb.cam.ac.uk> References: <1998090904052500.AAA18337@ladder01.news.aol.com> NNTP-Posting-Host: i11.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX64 6.2 IP28) > You want to determine the 3-D structure of a 25 base pair oligonucleotide > duplex. The sequence is: > 5'TTTTTAAAAATTTTTGGGGGGGGGG3' > 3'AAAAATTTTTAAAAACCCCCCCCCC5' > > A. Describe the kinds of secondary and tertiary DNA structues that youmight > expect to find in the DNA. > B. Propose a multi-approach experimental strategy for testing your hypotheses. > Describe the kinds of information each approach would provide, andhow the > approach could be used to confirm or discount your hypotheses. What could be > the alternative outcomes and conclusions? > > I was considering making a flow chart of the approaches and possible outcomes. > We've been talking about the various microscopies, NMR and crystallography. > I'm assuming we would use those methodologies. For A, you need to thik about it yourself. This is the whole point of your exercise. For B, I bet NMR will tell you everything. Now you need to know why --- check your textbooks. -- =================================================================== Yu Wai CHEN, Ph.D. .................. email: ywc@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel: 44-(1223) 402148 MRC Centre, Cambridge CB2 2QH, U.K. fax: 44-(1223) 402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/people/wai.html From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!news-xfer.netaxs.com!newsread.com!not-for-mail From: "Tammy Patton" Newsgroups: bionet.biophysics Subject: science fair project Lines: 21 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: <6qHJ1.229$ee2.432903@newsread.com> Date: Wed, 9 Sep 1998 22:10:33 -0500 NNTP-Posting-Host: 205.228.194.206 X-Complaints-To: Abuse Role , We Care X-Trace: newsread.com 905396994 205.228.194.206 (Wed, 09 Sep 1998 23:09:54 EDT) NNTP-Posting-Date: Wed, 09 Sep 1998 23:09:54 EDT Organization: Telepath Systems (telepath.com) I am a high school biology teacher with a student interested in doing a science fair project dealing with the relationship between exercise and kidney stone prevention. He has had kidney stones himself and would like to make some simulated stones and subject them to agitation to simulate the motion of the body during exercise. He is also interested in the relationship between fluid intake and stone formation. If you have suggestions in terms of experimental design, we would REALLY appreciate your input. Thank you for any help you may be able to provide. Tammy Patton Moore High School 300 N Eastern Moore, OK 73160 (405)793-3111 (405)793-3140(FAX) From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!serra.unipi.it!news.caspur.it!newsfeeder.flashnet.it!news.flashnet.it!not-for-mail From: "public@itaca.com" Newsgroups: bionet.biophysics Subject: chacra Date: Thu, 10 Sep 1998 18:24:24 +0200 Organization: Customer of Flashnet S.p.A. - http://www.flashnet.it Lines: 5 Message-ID: <35F7FD38.5457A521@itaca.com> NNTP-Posting-Host: ip097.pool-07.flashnet.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.flashnet.it 905444836 18863 195.191.4.97 (10 Sep 1998 16:27:16 GMT) X-Complaints-To: abuse@flashnet.it NNTP-Posting-Date: 10 Sep 1998 16:27:16 GMT X-Mailer: Mozilla 4.04 [en] (Win95; I) I'm interested in biophysic of chacra. Could anyone send me material? Tanks From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: paraleepk@aol.com (Paralee PK) Newsgroups: bionet.biophysics Subject: Re: 3-D structure of DNA Lines: 14 Message-ID: <1998091011544600.HAA04285@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 10 Sep 1998 11:54:46 GMT Organization: AOL http://www.aol.com References: <35F64F16.485420EA@mrc-lmb.cam.ac.uk> Thanks for your lead. My professor seems to prefer NMR, he went over 2-D NOE quite intensively. Yes, I understand that I need to work out all the possible structures, ie- linear or circular (how long does an oligonucleotide have to be to circularize), cruciforms or loops, etc. ---then from all the possiblities design a test or tests that will select for the correct answer-- NMR can show which H's are affecting each other--within 5Angstroms, right? Would using a selective enzyme for single stranded DNA and then running a gel at least confirm that there are single strands of DNA and maybe even how many-- to narrow down the field before doing NMR? Thanks for your help! Paralee From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!nntp.cs.ubc.ca!newsfeed.direct.ca!news-xfer.netaxs.com!newsread.com!not-for-mail From: "Tammy Patton" Newsgroups: bionet.biophysics Subject: photoreactivation project Lines: 15 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: Date: Wed, 9 Sep 1998 22:28:21 -0500 NNTP-Posting-Host: 205.228.194.206 X-Complaints-To: Abuse Role , We Care X-Trace: newsread.com 905398062 205.228.194.206 (Wed, 09 Sep 1998 23:27:42 EDT) NNTP-Posting-Date: Wed, 09 Sep 1998 23:27:42 EDT Organization: Telepath Systems (telepath.com) I am a high school biology teacher looking for suggestions on a science fair project dealing with photoreactivation. Does anyone know what type of organism is most easily photoreactivated? We are wondering if this type of project would be easy to do in a high school setting. Appreciative of any help you may be able to provide, Tammy Patton Moore High School 300 N Eastern Moore. OK 73160 (405)793-3111 Fax(405)793-3140 From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newshub.northeast.verio.net!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!is.bbsrc.ac.uk!daresbury!not-for-mail From: "MTT E-mail Cimtar" Newsgroups: bionet.biophysics Subject: [026431012520113411972] UJ BEJEGYZES az MTT E-mail Cimtar rendszereben Date: 10 Sep 1998 21:43:04 +0100 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6t9dko$egs@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT Kedves felhasználó! Megtaláltuk az Ön e-mail címét az Interneten. Ha szeretné, hogy adatait az MTT E-mail Címtár rendszere tartalmazza, kérjük látogassa meg szerverünket a http://e_search.mtt.hu/ címen. Ott további adatokat adhat meg magáról, így könnyebben találják meg azok akik keresik. Ha nem akarja, hogy az MTT E-mail Címtár tartalmazza az Ön adatait, változtatás nélkül, egyszerűen küldje vissza ezt a levelet, és bejegyzése törölve lesz a rendszer adatbázisából. Amennyiben később mégis szeretné adatait a rendszer adatbázisában elhelyezni, látogasson meg minket a http://e_search.mtt.hu/ szerveren és kövesse az ott leírt lépéseket. Tisztelettel: MTT E-mail Címtár csoport -------- Betreff: NEUER EINTRAG in dem MTT E-Mail Verzeichnis Sehr geehrter Benutzer, wir haben Ihre E-Mail-Adresse im Internet gefunden. Wir laden Sie ein, die Internet-Seite http://e_search.mtt.hu/ zu besuchen, um den Eintrag mit Zusatzinformationen zu vervollständigen, damit Ihre Adresse leichter zu finden ist. Falls Sie den Eintrag löschen möchten, so bitten wir Sie lediglich diese Nachricht zu Antworten, ohne sie zu verändern. Wir bedanken uns für Ihre Zusammenarbeit und verbleiben mit freundlichen Grüßen Ihr MTT E-Mail-Verzeichnis Team -------- Subject: NEW ENTRY in the MTT e-mail directory Dear user, We have found your e-mail address on the internet. If you wish to be included in this directory, we kindly invite you to go to http://e_search.mtt.hu/ and enter some additional information about you so that you can be more easily found by those looking for you. If you do not wish to be included in this directory, simply reply to this message without changing it. Thank you very much. With kind regards, The MTT E-mail Directory Team From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!logbridge.uoregon.edu!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: 3-D structure of DNA Date: 10 Sep 1998 19:58:25 GMT Organization: University of Washington Lines: 31 Message-ID: <6t9b11$16iq$1@nntp4.u.washington.edu> References: <1998090904052500.AAA18337@ladder01.news.aol.com> <35F64F16.485420EA@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: homer18.u.washington.edu X-Trace: nntp4.u.washington.edu 905457505 39514 (None) 140.142.17.38 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto Yu Wai Chen writes: >> You want to determine the 3-D structure of a 25 base pair oligonucleotide >> duplex. The sequence is: >> 5'TTTTTAAAAATTTTTGGGGGGGGGG3' >> 3'AAAAATTTTTAAAAACCCCCCCCCC5' >> >> A. Describe the kinds of secondary and tertiary DNA structues that youmight >> expect to find in the DNA. >> B. Propose a multi-approach experimental strategy for testing your hypotheses. >> Describe the kinds of information each approach would provide, andhow the >> approach could be used to confirm or discount your hypotheses. What could be >> the alternative outcomes and conclusions? >> >> I was considering making a flow chart of the approaches and possible outcomes >> We've been talking about the various microscopies, NMR and crystallography. >> I'm assuming we would use those methodologies. >For A, you need to thik about it yourself. This is the whole point of >your exercise. For B, I bet NMR will tell you everything. Now you need >to know why --- check your textbooks. Isn't this too long for an NMR structure? 25 basepairs, non-self complementary? Does anyone know what is the longest duplex DNA for which a structure has been determined? Bryant Fujimoto fujimoto@u.washington.edu -- Bryant Fujimoto fujimoto@u.washington.edu From owner-biophysics@net.bio.net Wed Sep 09 23:00:00 1998 Path: biosci!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: David Eliezer Newsgroups: bionet.biophysics Subject: Structural Biology Postdoctoral Position Date: Thu, 10 Sep 1998 15:34:24 -0700 Organization: The Scripps Research Institute, La Jolla, CA Lines: 27 Message-ID: <35F853F0.FF04808F@scripps.edu> NNTP-Posting-Host: mime.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; U; IRIX 6.2 IP22) Postdoctoral Position: Structural transitions in cytoskeletal proteins. Department of Biochemistry, Cornell University Medical College A postdoctoral position is available to characterize structure and dynamics in native and partially folded forms of actin binding proteins using NMR. Specific goals address the biological function of conformational transitions and of partially folded proteins, the pathways for protein aggregation and amyloid formation, and the role of folding intermediates in directing the protein folding process. Resources include a new 4 channel 600 MHz spectrometer and newly renovated laboratory space. The New York City area boasts a vibrant structural biology community. Ideal candidates should have experience in protein biophysics or biochemistry, protein structure determination, and/or protein folding. Experience with protein expression and purification, modern triple-resonance NMR techniques and a general familiarity with software tools are also helpful. Interested applicants should send a C.V. and letters from two references to David Eliezer, Department of Molecular Biology/MB2, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037. Email inquiries are also welcome at Eliezer@Scripps.Edu. From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!portc01.blue.aol.com!audrey01.news.aol.com!not-for-mail From: paraleepk@aol.com (Paralee PK) Newsgroups: bionet.biophysics Subject: Re: 3-D structure of DNA Lines: 33 Message-ID: <1998091100373800.UAA26385@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 11 Sep 1998 00:37:38 GMT Organization: AOL http://www.aol.com References: <6t9b11$16iq$1@nntp4.u.washington.edu> Thank you for your advice. I did some reading today. Your clues provided me with some direction. I think I'll have some hypotheses by tommorow as far as the specific probable structures. Right now I'm pretty sure it: -isn't circular: need to have 80 bp minimum to circularize -isn't Z-DNA in any portion: need alternatine purine pyrimidine and supercoiling that can only occur in circular DNA -could be 3x helical, but that requires supercoiling/circularization which I'm assuming we don't have . . . the "breathing and fraying" of the A*T region wouldn't provide enough energy to make this happen would it? -could be bent 8.7 degrees for each dinucleotide, best seen if a long repeating strip were synthesized -could be slipping- my teacher said left slipping (because of backbone config.) is preffered, does that mean the 5' end slips to the left/ -is not forming cruciform: supercoiling required for energy needed, hairpin has to have 3-4 unpaired bases in it, 10 base pairs minimum are required Do these conclusions seem right? I based them mostly on what I read in Sinden's book-DNA Structure and Function. I'm tending to think of using: NMR-NOE Tm-Absorbance At first I wanted to use an enzymatic digest to select for single stranded DNA, but I don't think there is going to be much. I need to find out more about NMR-NOE. Glasel's book seems to be unavailable here. Any other resources? Paralee From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!daresbury!not-for-mail From: "MTT E-mail Cimtar" Newsgroups: bionet.biophysics Subject: <<026431012520113411972>> UJ BEJEGYZES az MTT E-mail Cimtar rendszereben Date: 11 Sep 1998 12:39:08 +0100 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6tb24s$j1o@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT Kedves felhasználó! Megtaláltuk az Ön e-mail címét az Interneten. Ha szeretné, hogy adatait az MTT E-mail Címtár rendszere tartalmazza, kérjük látogassa meg szerverünket a http://e_search.mtt.hu/ címen. Ott további adatokat adhat meg magáról, így könnyebben találják meg azok akik keresik. Ha nem akarja, hogy az MTT E-mail Címtár tartalmazza az Ön adatait, változtatás nélkül, egyszerűen küldje vissza ezt a levelet, és bejegyzése törölve lesz a rendszer adatbázisából. Amennyiben később mégis szeretné adatait a rendszer adatbázisában elhelyezni, látogasson meg minket a http://e_search.mtt.hu/ szerveren és kövesse az ott leírt lépéseket. Tisztelettel: MTT E-mail Címtár csoport -------- Betreff: NEUER EINTRAG in dem MTT E-Mail Verzeichnis Sehr geehrter Benutzer, wir haben Ihre E-Mail-Adresse im Internet gefunden. Wir laden Sie ein, die Internet-Seite http://e_search.mtt.hu/ zu besuchen, um den Eintrag mit Zusatzinformationen zu vervollständigen, damit Ihre Adresse leichter zu finden ist. Falls Sie den Eintrag löschen möchten, so bitten wir Sie lediglich diese Nachricht zu Antworten, ohne sie zu verändern. Wir bedanken uns für Ihre Zusammenarbeit und verbleiben mit freundlichen Grüßen Ihr MTT E-Mail-Verzeichnis Team -------- Subject: NEW ENTRY in the MTT e-mail directory Dear user, We have found your e-mail address on the internet. If you wish to be included in this directory, we kindly invite you to go to http://e_search.mtt.hu/ and enter some additional information about you so that you can be more easily found by those looking for you. If you do not wish to be included in this directory, simply reply to this message without changing it. Thank you very much. With kind regards, The MTT E-mail Directory Team From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: "MTT E-mail Cimtar" Newsgroups: bionet.biophysics Subject: [026431012520113411972] UJ BEJEGYZES az MTT E-mail Cimtar rendszereben Date: 11 Sep 1998 11:19:18 +0100 Lines: 60 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6tatf6$f3s@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7BIT Kedves felhasználó! Megtaláltuk az Ön e-mail címét az Interneten. Ha szeretné, hogy adatait az MTT E-mail Címtár rendszere tartalmazza, kérjük látogassa meg szerverünket a http://e_search.mtt.hu/ címen. Ott további adatokat adhat meg magáról, így könnyebben találják meg azok akik keresik. Ha nem akarja, hogy az MTT E-mail Címtár tartalmazza az Ön adatait, változtatás nélkül, egyszerűen küldje vissza ezt a levelet, és bejegyzése törölve lesz a rendszer adatbázisából. Amennyiben később mégis szeretné adatait a rendszer adatbázisában elhelyezni, látogasson meg minket a http://e_search.mtt.hu/ szerveren és kövesse az ott leírt lépéseket. Tisztelettel: MTT E-mail Címtár csoport -------- Betreff: NEUER EINTRAG in dem MTT E-Mail Verzeichnis Sehr geehrter Benutzer, wir haben Ihre E-Mail-Adresse im Internet gefunden. Wir laden Sie ein, die Internet-Seite http://e_search.mtt.hu/ zu besuchen, um den Eintrag mit Zusatzinformationen zu vervollständigen, damit Ihre Adresse leichter zu finden ist. Falls Sie den Eintrag löschen möchten, so bitten wir Sie lediglich diese Nachricht zu Antworten, ohne sie zu verändern. Wir bedanken uns für Ihre Zusammenarbeit und verbleiben mit freundlichen Grüßen Ihr MTT E-Mail-Verzeichnis Team -------- Subject: NEW ENTRY in the MTT e-mail directory Dear user, We have found your e-mail address on the internet. If you wish to be included in this directory, we kindly invite you to go to http://e_search.mtt.hu/ and enter some additional information about you so that you can be more easily found by those looking for you. If you do not wish to be included in this directory, simply reply to this message without changing it. Thank you very much. With kind regards, The MTT E-mail Directory Team From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!news.stanford.edu!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!not-for-mail From: Tom Chou Newsgroups: bionet.neuroscience,bionet.biophysics Subject: ion channel recordings on net? Date: Fri, 11 Sep 1998 15:28:55 +0100 Organization: DAMTP, University of Cambridge, UK. Lines: 16 Message-ID: <35F933A6.41C6@damtp.cam.ac.uk> NNTP-Posting-Host: decoy.amtp.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) Xref: biosci bionet.neuroscience:24350 bionet.biophysics:4388 Dear All, Can anyone tell me if they've seen any pictures (preferably .ps) of single (or few) ion channel recordings I can download (ie from homepages) or better yet, are there public files of ion channel conductance data? (conductance vs. time) I'd like to do some mathematical analysis on them as a signal processing exercise and it's not so important exactly what sample it is, although something with richer structure (multiple conductance states) would be fun.... Cheers, Tom From owner-biophysics@net.bio.net Thu Sep 10 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: Triple-stranded DNA Structure Date: 11 Sep 1998 08:36:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <35f928ae.0@news.netdirect.net.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4389 bionet.molec-model:2240 bionet.xtallography:4392 The formation and properties of triple-stranded DNA are now described in a substantial body of literature. However, I have been searching for early research reports identifying triple-stranded DNA and I have come upon a problem. I would be grateful to hear what thoughts others have had about it. Leslie et al.(J Mol Biol 143 (1980) 49-72) reported that a fibre of poly(dI).poly(dC) which gave sharp X-ray diffraction spots shortly after being drawn was unstable and transformed irreversibly after a few days into poly(dC).poly(dI).poly(dC+). This new molecule also gave sharp spots in its X-ray diffraction pattern, and this new pattern did not have any of the original spots. Therefore the conversion was complete, or substantially complete. Very similar results were reported for fibres of poly(dA).poly(dT) converting to poly(dT).poly(dA).poly(dT) (J Mol Biol 88 (1974) 509-521) and for the formation of poly(U).poly(A).poly(U) (Nature New Biology 244 (1973) 99-101). The problem is evident: How and where would the torque arise inside a solid fibre that would permit one double helix to rotate so as to unwind one strand and rewind it onto an adjacent triple helix having a different diameter and rotating at a different angular velocity ? Inside the fibre, individual molecules would have a random axial translation so only very rarely would two adjacent double helices have the same axial starting point. How would there be a very high conversion of double to triple stranded molecules when any rotation of adjacent double helices would normally find the free ends of one of them axially displaced down the fibre compared to its neighbour ? None of the original workers offered any explanation as to how this conversion might be possible, nor, indeed, remarked that there might be something to explain. Naturally I have given this problem some thought, but I have been driven towards a daunting conclusion. I shall be glad to share my thoughts with anyone who lets me know they are interested, or anyone who offers their thoughts on this problem. clived@ndirect.co.uk From owner-biophysics@net.bio.net Sat Sep 12 23:00:00 1998 Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!HEAnet!web3.tcd.ie!acer.gen.tcd.ie!tpwalsh From: tpwalsh@acer.gen.tcd.ie (Thomas Walsh) Newsgroups: bionet.molec-model,bionet.biophysics,comp.programming,bionet.molbio.proteins,comp.graphics.visualization Subject: Re: visualizing cluster of simple molecules Date: 9 Sep 1998 17:28:42 GMT Organization: Urmhumhan Lines: 13 Message-ID: <6t6dsa$1pg@web3.tcd.ie> References: <35F69219.6C4B8549@rug.ac.be> NNTP-Posting-Host: acer.gen.tcd.ie Xref: biosci bionet.molec-model:2245 bionet.biophysics:4393 bionet.molbio.proteins:13292 Wijnand Schepens wrote: >I would like to visualize a cluster (set) of small (identical) >molecules. >I now the coordinates of every atom in every molecule. What I'm looking >for is a simple way to see on the screen how it looks like. > >Can anyone help me along? I haven't used it but PREPI might do what you want: http://bonsai.lif.icnet.uk/people/suhail/prepi.html Tom Walsh From owner-biophysics@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!musc.edu!vakseri From: vakseri@musc.edu (Ilya Vakser) Newsgroups: bionet.biophysics Subject: Postdocs/Graduate Students in Docking Date: 14 Sep 1998 14:33:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: <35FD8A10.9F62C3CB@musc.edu> NNTP-Posting-Host: net.bio.net Applications are invited for postdoctoral and graduate student positions in my laboratory at the Medical University of South Carolina. The main subjects of the research in the laboratory are computational studies of molecular recognition and the development of docking methodology for protein complexes and computer-aided drug design. For more information, see the lab's web site at http://reco3.musc.edu. Programming skills in C are required. The positions are available immediately. To apply send or email a letter and CV with names of 3 referees. Ilya A. Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 171 Ashley Avenue Charleston, SC 29425 phone:(843)792-2471, fax:(843)792-2475 email: vakseri@musc.edu, http://reco3.musc.edu From owner-biophysics@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.ucdavis.edu!not-for-mail From: Chris Barry Newsgroups: bionet.biophysics Subject: File Format Date: Mon, 14 Sep 1998 14:44:16 -0700 Organization: University of California, Davis Lines: 4 Message-ID: <35FD8E30.41C6@krebs.ucdavis.edu> NNTP-Posting-Host: krebs.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04Gold (X11; I; IRIX 5.3 IP22) Does anyone out there know what program uses the format *.IMG to view an electron density map? Chris From owner-biophysics@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure Discussion Continued Date: 14 Sep 1998 10:56:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1007 Sender: daemon@net.bio.net Distribution: world Message-ID: <35fd48d9.0@news.netdirect.net.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4396 bionet.molec-model:2249 bionet.xtallography:4399 Bill further asks whether the side-by-side structure set out in my first attachment does not contradict the structures derived from the fibres. This is a key question and requires a full answer (if you'll indulge me a little.) There are several aspects to this. First, Crick had never seen any of Franklin's (high quality) DNA fibre diffraction patterns when he and Watson proposed their structure. Watson had seen a B-DNA pattern only very briefly and could not study it at leisure. Plectonaemic winding in DNA had already been proposed by Pauling & Corey early in 1953 and Watson & Crick seem to have adopted that idea. A R Stokes, a colleague and co-worker of Crick, had deduced an important geometric ratio for the classical helical cross (Prog. Biophys. & Biophys. Chem. 5 (1955) 140-167, page 163) (see attachment) such that, for the angle from the vertical (delta), tan delta = helical pitch / (helical circumference). In Franklin's famous B-DNA diffraction pattern (see attachment), delta = 40 degrees approximately, and, as the pitch is known to be 33.4 Angstroms from the layer lines, we deduce that the major diffractors lie on a helix of diameter of about 12 to 13 Angstroms. This is close to Franklin's deduction of a diameter of 11 Angstroms from her Pattersons. I now have seventeen published DNA fibre diffraction studies in which the researchers make it explicitly clear that they chose a unit cell which would be large enough to accommodate a double helical diameter of some 19-23 Angstroms even though their patterns of systematic absences in the reflections would have allowed them to choose a smaller unit cell (into which the double helix could not be fitted.) I also have references to unpublished studies in 3 or 4 PhD theses where a larger unit cell was chosen than the raw diffraction data actually required. I should be very glad to forward the list of references to anyone interested. If you choose the smaller unit cell allowed by the dffraction pattern and recalculate the helical diameter (a simple geometric exercise, of course), you get diameters in the range 11.2 to 13.6 Angstroms. A really fascinating study in conventional chemistry is that of James & Mazia (Biochim.Biophys.Acta 10 (1953) 367-370). They discovered that 1 mg of dry calf thymus DNA could be spread in a monolayer to cover 0.28 square metres. They didn't notice that from just this result alone we can directly estimate the minor axis diameter of the duplex as 11.7 Angstroms. I would be very glad if people would like to calculate the diameter for themselves and compare their sums with mine. (James & Mazia measured the major axis diameter, that is the height of the spread film in a separate experiment as 21.6 Angstroms. Therefore their results lead us to a duplex with an elliptical section.) The new model for DNA structure leads to the presence of a "front" and a "rear" face with great implications for protein-DNA recognition, including the way such DNA would wind onto nucleosomal cores, for example. What problems would people see with this account so far, please ? 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MU]?7U^;7U]?7U]?7U]?7U]?7U]?7U]?7Y-?7U]?7U]?7U]?7YM?7U]?7U]?7 MU]?8U]?7U]?7U]?MV-CBU]?7U]?7U]?FU]? MU]?7U]?7U]?7[]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7[]?B MU]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?SXM?7U]?7U]?7U]?7 MU]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7U]?7 =U]?7U]?7U]?7U]?7U]?7U]?7U]?7LHD``%2C```` ` end From owner-biophysics@net.bio.net Sun Sep 13 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: The Structure of Duplex DNA Date: 14 Sep 1998 10:54:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <35fd48dc.0@news.netdirect.net.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4395 bionet.molec-model:2248 bionet.xtallography:4398 Eric, You are right, and it is timely, to raise the topological papers by Crick, Wang & Bauer (J Mol Biol 129 (1979) 449-461), and Bauer, Crick & White (Scientific American 243 (1980) 100-113). Their treatments did not apply to every side-by-side model, however : "..This proves that the linking number is not equal to zero (at least for the great majority of those, i.e., side-by-side, molecules.), and also only to such side-by-side models "...in which the two ...chains do not coil around each other ...but instead lie side by side over most of their length, having only a few helical turns." Their treatment only applies to side-by-side models, like that of Rodley et al., for which there is a net winding because an equal number of right and left turns do not get you back to an equivalent repeat point in space because of the D chirality of asymmetric carbon in all the pentoses. The model I have come upon has exactly and identically zero plectonaemic turns in its relaxed state over any length of duplex and is therefore not covered and constrained by the two papers just cited. Thermodynamics has always been a delight to me, though I find it difficult! Chemical energy is dissipated in all directions; that is, it is not a vector, but torque is a vector. Therefore chemical energy would seem to be unable to either wind or unwind two plectonaemic strands where no breakage of covalent bonds takes place. My solution to this conundrum is to say that neither winding nor unwinding does actually take place ! But tell me - let me tease you a little - what do you make of the results of Kabata et al. (SCIENCE 262 (1993) 1561-1563) who found that RNA polymerase slides along its DNA duplex substrate and does not follow a helical path ? An absolutely crucial test of the new model offers itself, though we need someone to carry it out. Drew & Travers (J Mol Biol 186 (1985) 773-790) have constructed a 169 bp circular, covalently closed length of duplex DNA. With this length of DNA there can only be a very limited number of topoisomers present if the ring closure, of itself, could introduce only a very few superhelical turns. That is, all the 169 bp molecules would share a range of superhelical turns between about -1 and +1. Therefore in suitably mild denaturing conditions, in the absence of any strand breakage, the 169 bp sequence would be largely separable into complementary covalently closed single-stranded DNA circles interlinked at very few places according to the new model. Thus the most direct route to distinguishing between the DNA double helix and the new model is based on topology. The complementary strands in that 169 bp sequence may actually be linked by 0, or perhaps ± 1 superhelical turns due to the algebra of the enzymic closure reaction used on the 169 bp linear duplex, and the denatured covalently closed circular strands could be decorated with a suitable protein and then be examined under AFM to determine their linking number. Therefore, if the 169 bp circular DNA is denatured under mild conditions, perhaps using aqueous urea, it could then be decorated with the single-strand DNA binding protein, the product of gene 32 from phage T4 (Scanning Microscopy 9 (1995) 705-727), so as to be rendered easily visible under AFM, and the actual numbers of crossovers then counted. According to the double helix model, LK will lie in the range 16 to 18, or so, while the new model predicts LK is -1, 0 or +1. A very similar experiment could be carried out with the small circular DNAs described by Bates & Maxwell (EMBO J 8 (1989) 1861-1866), where, for the smallest, the double helix model predicts LK = 9, and the new model predicts LK = -2. Is there any research group with the interest and ability to conduct this experiment ? clive delmonte clived@ndirect.co.uk From owner-biophysics@net.bio.net Sun Sep 13 23:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: Triple-stranded DNA Discussion on Structure Date: Mon, 14 Sep 1998 14:56:16 +0100 Lines: 1178 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.117 Message-ID: <35fd14f7.0@news.netdirect.net.uk> X-Trace: 14 Sep 1998 14:07:03 GMT, 195.7.225.117 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!btnet-peer!btnet!demeter.clara.net!194.112.50.17.MISMATCH!news.clara.net!peer1.news.dircon.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.117 Xref: biosci bionet.biophysics:4394 bionet.molec-model:2247 bionet.xtallography:4397 Let me thank Eric Fairfield, Kandala Chary and Bill Ross for their helpful, initial comments made in response to my request on 11th September for suggestions as to how the problem of triple strand formation inside fibres might be resolved. Kandala suggests that: "In poly(dI).poly(dC) and poly(dA).poly(dT) sequences dI and dA strands have a propencity to accept the third strand on the major groove side. And in poly(dI).poly(dC) and poly(dA).poly(dT) mixtures, before they are drawn into fibres, the duplexes are in dynamic equilibrium with monomeric strands. Thus, when one forms fibers, the need to unwind a duplex is not necessary. There are sufficient monomeric strands which hug to the duplexes, thus forming stable irreversible triplexes. I hope this will answer your question." These are very interesting points but it seems to me that there may be some difficulties with them. The dynamic equilibrium existing between single strands and duplexes could be seen to invite a very similar point about how exactly a duplex unwinds in solution during denaturation. Where does the torque come from ? I have never seen this question addressed. The unwinding situation in solution is very similar in biophysical terms to that found in fibres during triple strand formation when one duplex also has to "unwind", it seems to me. Moreover, in solution, the duplex is folded into 3 dimensions, compared to being linear in fibres, and unwinding might be even harder than in fibres. As I recall, the major groove does not exist on one side of a duplex, but follows a helical path around the duplex axis. If a third strand is to join the first two by lying in the major groove, it would have to be wound onto the original duplex, I believe. The initial fibre X-ray diffraction patterns were characteristic of those ascribed to duplexes and distinct from single strand diffraction patterns (from poly(rC) and from poly(rA), for example). Therefore single strands would seem to have been absent initially, but were produced in forming the triplex plus a residual single strand over a period of some days after the young fibre had been drawn. Bill suggests that: "Not knowing much about fiber diffraction, it's easy enough to speculate that somehow the original duplex was somehow not really a duplex, but assuming it was, I wonder if you are thinking about bond breaking, maybe some sort of autocatalytic mechanism." Again, I am grateful for these very interesting suggestions. Even if the initial duplexes were not really duplexes, they would seem to have wound around each other to form the final triplex (assuming that winding around was involved in triplex formation !) I think that here lies actually the germ of the answer. The initial duplexes were not duplexes in the sense that the strands were wound around each other, and the final triplex structures did not involve any strands winding around each other either. There was no unwinding and no winding either. This would then become the explanation of denaturation. The duplexes are not composed of two strands wound around each other, but two helical strands running antiparallel alongside each other. During denaturation the two helical strands could then move apart in a linear direction. In triplex formation in a fibre, one strand moves in a linear manner from its initial partner to an adjacent duplex. Probably the helical sugar-phosphate chains would move hardly at all, but the bases might rotate to reach their new partners. I wonder if you recall the paper by Kabata et al. (SCIENCE 262 (1993) 1561-1563) ? They found that single molecules of RNA polymerase were sliding along tethered molecules of duplex DNA. The polymerase did not describe a helical locus at all. The DNA was immobilised and could not rotate and nor did the polymerase rotate either. If duplex DNA consisted of two chains wound around each other, how would the polymerase "read" the message on the alternate half turns of the duplex which lay on the other side away from the polymerase ? Would that not require two reading mechanisms, one each to be used on alternating half turns ? This would hardly be conducive to high quality transduction of the message contained in the base sequence. Kabata et al. did not address this question. If the DNA actually consisted of two antiparallel helical chains running alongside each other, the RNA polymerase could remain on the same face of the duplex and read the whole message. Attached to this note should be a diagram of the structure of duplex B-DNA, if I understand the scanner software, which I believe can account for all the experimental results with DNA which are known to me and would be very glad to consider with you what you think its limitations might be. Each sugar-phosphate helix would have the same diameter as the width of a Watson-Crick base pair, about 11 Angstroms, and the same pitch as a Watson-Crick B form double helix, about 34 Angstroms. Aaron Klug told Robert Olby in "The Path to the Double Helix", page 373, that Rosalind Franklin had been working with her Pattersons on separate helices of diameter 11 Angstroms, which would have been before she could have known about Watson-Crick base pairs (whose width is necessarily close to 11 also in order to make the geometry work). You may know Max Delbruck (Watson's tutor) wrote to Watson in 1953: "These (DNA strands) would have to be untwiddled to separate the threads....In any event, one must postulate that the DNA opens up in some manner, both for replication and for doing its business otherwise. In the structure you describe this opening up is opposed both by the two hydrogen bonds per nucleotide, and by the interlocking of the helices, and it becomes a very important consideration to find a way out of this dilemma, or to think of a modification of the structure that does not involve interlocking." Delbrück's prescience stands out across 40 years and more. I have been actively scouring the X-ray and NMR literature to bring together those many experimental results which would seem to support the suggested side-by-side model. 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