Help with Prot.-DNA interactions

m griep mgriep at unlinfo.unl.edu
Sat May 14 11:11:53 EST 1994


remeans at husc9.harvard.edu (Robert Means) writes:

>Subject: Help with Prot.-DNA interactions
>Newsgroups: bionet.molbio.proteins
>Summary: 
>Keywords: 

>Hello,
>	I have a problem that I'm hoping that some of you can help me 
>with, thus saving me a great deal of legwork in an unfamiliar subject. 
>While looking at something completely different, we engineered a purine 
>to pyrimidine change into a stretch of DNA that is involved with 
>interactions with a certain protein. (sorry to be so circumspect)
>At any point, we weren't sure what section of this protein was 
>interacting with the DNA and to make a long story short, we are getting a 
>compensatory mutation in the protein which causes a Val to Ile change. 
>While this change is fairly conservative, I was wondering if anybody out 
>there could make any suggestions about what this change might mean. 
>Amoung DNA-protein interactions, are there any noted preferences for a 
>Val over Ile when interacting with a purine, or vise-versa? Even if no 
>one out there can give me a dirrect answer could somebody give a 
>suggestion as to how I could screen a large number of DNA-interacting 
>proteins for possible clues as to what is going on.

>						Thanks in advance,
>							Bob Means

>New England Regional Primate Research Center...Where the primates have 
>better living conditions than the grad. students.

>"Why don't activists ever picket for better living conditions for 
>me?"--any impoverished grad student


     A simple interpretation would involve steric factors.
In going from purine to pyrimidine, you have decreased
the size of the nucleotide (assuming this is a ssDNA
binding protein).  In going from val to ile, you are 
making a compensatory increase to fill a potential void.
--
Mark Griep
Department of Chemistry      ____   ____      __________________
Center for Biotechnology    |    | /    |    |                  \_
University of Nebraska      |    |/     |    |                    \



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