Subject: Data of protien-peptide complexes

From: Liu Zhijie <[email-masked]>
Date: Wed, 24 Jul 2002 09:47:51 -0400 (EDT)

Dear CCLers,

     I am developing a potential to evaluate the binding affinity of
protein-peptide complexes only based on structual information, but I
found it is difficult to find enough experimental protein-peptide
dissociation constants data to examine my potential. Could any of you
give me some references on the protein-ligand database (which includes
the dissociation constant data and related complex structure, and has more
protein-peptide data)?

     Thanks in advance

     Zhijie Liu

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From: Sergio <[email-masked]>
Date: Wed, 24 Jul 2002 18:24:26 +0200

Dear Liu, check out these papers and please notify me if you get something out 
of your program, I would like to use it if possible.

Ding L, Coombs GS, Strandberg L, Navre M, Corey DR, Madison EL., 1995. Origins 
of the specificity of tissue-type plasminogen activator. Proc Natl Acad Sci 
15:7627-7631.

Coombs GS, Dang AT, Madison EL, Corey DL, 1996. Distinct mechanisms contribute 
to stringent substrate specificity of tissue-type plasminogen activator. J 
Biol Chem. 23:4461-4467.

Coombs GS, Rao MS, Olson AJ, Dawson PE, Madison EL, 1998. Revisiting catalysis 
by chymotrypsin family serine proteases using peptide substrates and 
inhibitors with unnatural main chains. J Biol Chem. 20:24074-24709.

Corey DR, Willett WS, Coombs GS, Craik CS, 1995. Trypsin specificity increased 
through substrate-assisted catalysis. Biochemistry 34:11521-7.

These have all Km/Kcat constants between trypsin and a series of peptide 
substrates, no synthetic stuff used here, all natural.

Best Regards

Sergio