Subject: small peptide models (summary)

From: "Emadeddin Tajkhorshid" <[email-masked]>
Date: Sun, 2 Aug 1998 17:34:30 -0700

Dear all

I got two answers to my question and many requests for the summary. Many thanx
to Wayne Steinmetz and Randall B. Murphy for their replies.
*****************************************************************************
Original Q:
> I am looking for some examples of small polypeptide structures which can be
> used for testing the efficiency of a program doing some semiempirical
> calculations. With this regard, the experimentally resolved structures which
> are not very large are the main intrest. Any other model which may be
> interesting or any reference with this regard is highly appreciated.
****************************************************************************
From:    Wayne Steinmetz <[email-masked]>
Date:    Mon Jul 27,  5:43pm -0700
To:      [email-masked]
Cc:
Subject: Re: CCL:small peptide models
Check the recent work of Barbara Imperiali at Cal Tech.  Her group prepared
a small tetra or hexapeptide which had a well defined beta turn in solution.
The conformation was confirmed by NMR.  I can't give you the reference as
the file was lost by a student.

Another noteworthy paper appeared in the 10 July 1998 issue of Science.
Vol 281, pp. 253-256.  Kortemme et al. designed and prepared a peptide
with 20 amino acids.  The peptide has a well defined three-stranded
beta=sheet.

Steve Mayo designed and prepared a peptide with 28 amino acids that has the
zinc-finger motif without zinc.  Science, vol. 278, pp. 82-87 (3 October 1997).

For a review of small helical peptides, see Bryson et al., volume 270, pp.
935-941, 10 Nov. 1995.

You did not indicate how small is small.  Conotoxins are fairly small peptides
whose well defined conformation and whose stability is due to the presence
of 2 disulfide bridges.  This family of toxins has received a great deal of
attention as small peptides often do not have a well defined structure.

****************************************************************************
From:    Randall B. Murphy Ph.D. <[email-masked]>
Date:    Wed Jul 29, 10:18am -0400
To:      [email-masked]
Cc:
Subject: Re: CCL:small peptide models
Enkephalin may be the best.  We have done it, so have lots of other
people, and there are many experimental, NMR, and X-ray structures to
commpare.  It would be nice if it was a little more rigid, but to us this
is a good choice.

There are several Scheraga papers using calculations to compare to various NMR
structures. We have one in PNAS in I think 1985, so this goes back a ways.

best regards

Randall B. Murphy
Associate Professor of Chemistry
New York University
[email-masked]
********************************************************************************

-- 
Emad
*********************************************************************
E. Tajkhorshid				
German Cancer Research Center; DKFZ             Tel: +49 6221 42 2340
Dept. Molecular Biophysics (H0200)              FAX: +49 6221 42 2333
P.O.Box 101949			   
69009 Heidelberg, Germany     Email: [email-masked] 
*********************************************************************
* "Never express yourself more clearly than you think." -Niels Bohr *
*********************************************************************