Subject: protein-protein Dissociation Constant SUMARY

From: Javier Cuervo <[email-masked]>
Date: Tue, 28 Jan 2003 17:30:03 -0800 (PST)

Thank you for the information given, has being really helpful,
here is the sumary

from:[email-masked]

No databases that I am aware of, but PubMed is a good resource for journal
articles that may be of help.

http://www.ncbi.nlm.nih.gov/PubMed/

from:[email-masked]

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

Javier Cuervo
Graduate Student 
Computational Science Research Center SDSU