Premium
Evaluation of the protein solvent‐accessible surface using reduced representations in terms of critical points of the electron density
Author(s) -
Becue A.,
Meurice N.,
Leherte L.,
Vercauteren D.P.
Publication year - 2004
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20033
Subject(s) - sasa , accessible surface area , surface (topology) , resolution (logic) , electron density , solvent , radius , chemistry , atomic radius , side chain , macromolecule , chain (unit) , computation , set (abstract data type) , molecule , computational chemistry , crystallography , chemical physics , electron , materials science , computer science , mathematics , physics , algorithm , geometry , organic chemistry , quantum mechanics , paleontology , biochemistry , computer security , polymer , artificial intelligence , biology , programming language
Abstract The aim of our study is the development of a method for calculating the interface of dimerization of protein–protein complexes based on simplified medium‐resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent‐Accessible Surface Area (SASA) of macromolecules could be applied to medium‐resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 Å crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side‐chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side‐chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1117–1126, 2004