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From: wrp@biochsn.acc.Virginia.EDU (William R. Pearson)
Newsgroups: bionet.molbio.proteins
Subject: Re: protein design using computational methods
Keywords: protein folding, computational methods, molecular dynamics
Message-ID: <1991May17.121858.12141@murdoch.acc.Virginia.EDU>
Date: 17 May 91 12:18:58 GMT
References: <719@mixcom.COM> <2158@fcs280s.ncifcrf.gov> <1991May17.005953.12252@beaver.cs.washington.edu>
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In article <1991May17.005953.12252@beaver.cs.washington.edu> pauld@stowe.cs.washington.edu (Paul Barton-Davis) writes:
>
>On the other hand, there are a number of well known cases (I've been
>out of research in this area for 4 years, so your guess at names is as
>good as mine) of:
>
>	1) proteins of very similar sequence folding into
>		rather different conformations, even at the secondary
>		level (helices and sheets)
>
>	2) proteins of quite different sequence folding into
>		rather similar conformations.	
>

	I do not believe that there are any "well-known cases" of proteins
of very similar sequence (>50% identity) folding into different
conformations. I would be very interested in evidence to the contrary.
Often, when X-ray structure people mention very different structures,
they are referring to the orientation of the side chains or loops, or
perhaps a very high precision statement about exact location of the
alpha-carbons.  Alternatively, they may be talking about a very short
piece of sequence (4 - 5 residues) in a larger, unrelated protein.
In the case of short sequences in unrelated proteins, it is not
unusual to find  the same sequence in different secondary structures.

	For "proteins,"  however, those that are similar enough to be
considered homologous ALWAYS have the same 3D structure.

Bill Pearson