Subject: CCL: protein-protein dissociation constant

From: [email-masked]
Date: Fri, 17 Jan 2003 14:43:19 -0600

Javier,

        I am not aware of any databases of protein-protein dissociation 
constants either.

        First, take a look at the article, Horton, N. and Lewis, M. 
Protein Sci (1992) 1, 169, which describes the development of a 
semi-empirical, fast method to calculate Kd's for protein - protein 
complexes based on atomic solvation parameters, accessible surface areas, 
etc.  I think there were a decent number of experimentally determined Kd's 
listed somewhere in the paper.

        Second, not to self-promote, but you might also want to get a copy 
of my Ph.D. thesis (Purdue Univ., Chem. Dept, 1991).  In collaboration 
with Eli Lillly and Company, I used AMBER FEP methodology to calculate the 
relative self-association free energies of several insulin analogues using 
various thermodynamic cycles involving insulin monomers and dimers.  I 
never published this work, because I couldn't get the relative numbers to 
tightly agree with experiment, but I did correctly predict the trends in 
self-association for 5 different insulin complexes.  The Ph.D. thesis does 
contain a table or two with experimentally determined Kd data from 
analytical ultracentrifugation measurements.

        Third,  you might want to consider the program PLOGP from the 
Institute of Physical Chemistry, Peking (contact Gao Ying at
[email-masked]).  Primary literature reference is : Tao, P et al. 
J. Mol. Model. (1999) 5, 189.  This very interesting program calculates
logP values for peptides and even entire proteins, and you can visualize 
the molecular lipophilicity as a contour map, etc.

        Regards,
        Jim Metz

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
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Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
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