Premium
Discriminating between homodimeric and monomeric proteins in the crystalline state
Author(s) -
Ponstingl Hannes,
Henrick Kim,
Thornton Janet M.
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20001001)41:1<47::aid-prot80>3.0.co;2-8
Subject(s) - monomer , intermolecular force , chemistry , yield (engineering) , word error rate , atom (system on chip) , crystallography , mathematics , molecule , thermodynamics , physics , computer science , organic chemistry , artificial intelligence , embedded system , polymer
Scores calculated from intermolecular contacts of proteins in the crystalline state are used to differentiate monomeric and homodimeric proteins, by classification into two categories separated by a cut‐off score value. The generalized classification error is estimated by using bootstrap re‐sampling on a nonredundant set of 172 water‐soluble proteins whose prevalent quaternary state in solution is known to be either monomeric or homodimeric. A statistical potential, based on atom‐pair frequencies across interfaces observed with homodimers, is found to yield an error rate of 12.5%. This indicates a small but significant improvement over the measure of solvent accessible surface area buried in the contact interface, which achieves an error rate of 15.4%. A further modification of the latter parameter relating the two most extensive contacts of the crystal results in an even lower error rate of 11.1%. Proteins 2000;41:47–57. © 2000 Wiley‐Liss, Inc.