Help with Prot.-DNA interactions

Steven Brenner seb1005 at
Sat May 14 13:58:12 EST 1994

Your result is very curious, but the lack of information you provide
makes diagnosis even more difficult than it should be.  In order to be
of any help, we need to know:

	1) What is the DNA sequence
	2) Is it dsDNA or ssDNA.  If it is ds, then your purine->pyrimidine
	   transversion also made a pyrimidine->purine on the other strand
	3) What type of dna-binding protein is it?  HTH, Zn Finger, Other?

Of course, it would be best if you could just tell us more of the

In any case, since both Val and Ile are hydrophobic they're really
only able to make recognition contacts in the major groove with T and
C--neither of which (of course) is a purine.  For more information,
you might wish to look at   Suzuki, M. "A Framework for the DNA-protein
code of the probe helix in transcription factors: the chemical and
stereochemical rules", _Structure_ (1994) 2:317-326.


mgriep at (m griep) writes:
>remeans at (Robert Means) writes:

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

>>	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      ____   ____      __________________
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Steven E. Brenner                    | S.E.Brenner at 
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