Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density

A. Becue, N. Meurice, L. Leherte, D. P. Vercauteren

Research output: Contribution to journalArticle

10 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1117-1126
Number of pages10
JournalJournal of Computational Chemistry
Volume25
Issue number9
DOIs
StatePublished - Jul 15 2004
Externally publishedYes

Fingerprint

Carrier concentration
Critical point
Surface area
Electron
Proteins
Protein
Dimerization
Evaluation
Backbone
Radius
Evaluate
Relative Error
Macromolecules
Tables
Amino Acids
Amino acids
Choose
Molecules
Calculate
Model

Keywords

  • Critical points
  • Electron density
  • Medium resolution
  • Reduced representations
  • Solvent accessible surface area
  • Topological analysis

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density. / Becue, A.; Meurice, N.; Leherte, L.; Vercauteren, D. P.

In: Journal of Computational Chemistry, Vol. 25, No. 9, 15.07.2004, p. 1117-1126.

Research output: Contribution to journalArticle

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