What is the SMALLEST DNA BINDING DOMAIN?

Dima Klenchin klenchin at facstaff.wisc.edu
Mon Jan 13 10:30:00 EST 1997


In article <5bcd2r$2gg8 at ncisun1-nf0.ncifcrf.gov>, toms at ncifcrf.gov (Tom Schneider) wrote:

#Dima Klenchin (klenchin at facstaff.wisc.edu) wrote:
#: In article <slrn5dg185.1n1.aiyar at ebv.oncology.wisc.edu>,
# aiyar at ebv.oncology.wisc.edu wrote:
#: #On Sat, 11 Jan 1997 11:52:26 EST, jstrassw at OPAL.TUFTS.EDU
#: # <jstrassw at OPAL.TUFTS.EDU> wrote:
#: #
#: #>Well, the Bovine Papillomavirus DNA binding domain (minimal) iosonlt 85 AA
#: #>although tit forms a dimer.  It has the aadvantage of many characterized
#: #>mutations, and an excellent crystal structure (1.2A) and  binds
#: #>sequence-specific to a palindropme at 10 -12 M.

#: #the Kd of the 87 a.a minimal DNA binding domain 
#: #for it's cognate site is listed as approximately 7.0 nM (i.e. 7 x 10e-9 M), 
#: #while a larger fragment, containing 127 a.a has a Kd of about 0.9 nM, 
#: #and even this is quite far from the picomolar affinity you have listed ....
#: 
#: Umm, I know nothing about DNA binding, but biology is not a quantitative 
#: science, so 3 orders of magnitude makes no difference (since nobody knows 
#: how to apply those numbers anyway). 
#
#It makes a big difference, and those numbers can be applied, using advanced
#molecular machine theory.  I'll present the results later in several new
#papers that are almost finished.  If you would like to prepare yourself for
#reading the new papers, read the ccmm, edmm and nano2 papers.  If THOSE don't
#make sense yet, read the earlier papers on binding site information theory
#and sequence logos.  All papers are available through my web site.

Of course they do. There are all sorts of different things one can do 
comparing numbers. However, going back to the obscured to me Bovine 
Papillomavirus DNA binding domain, I'd like to ask one Q. 
Will our understanding of the biology of this virus change to _any_ extent 
should someone prove that affinity is 1 pM instead of 1 nM (or vice 
versa)? I bet - no. Sure, it'll make a lot of difference to people 
studying what combination of aa in what milieu works best when binding 
to a given structure, but for biology of the virus... Nowhere in the viral 
lifecycle we can apply those numbers to derive new and meaningful 
information about this organism. 

Thanks for reply, Tom. Intersting WEB site. I'll try to read the papers. I 
sure liked the idea of "No Consensus Sequences!" cause they make less and 
less sense as we go along the unknowns. .  

- Dima





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