Tom Schneider toms at ncifcrf.gov
Sun Jan 12 23:18:35 EST 1997

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.
: #>
: #>I also study it!
: #
: #The Kd value that you have listed for the minimal portion of "BPV-E2 
: #DNA binding domain" binding it's cognate site is very different from 
: #that which has been published.
: #
: #For instance, from J. Virol. 71:828-831 (1997) (a publication from
: #the Androphy lab), 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.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms at ncifcrf.gov

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