Solvent accessibility in native and isolated domain environments: General features and implications to interface predictability

Mohd Firdaus Mohd Raih, Shandar Ahmad, Rong Zheng, Rahmah Mohamed

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

A non-redundant database of 4536 structural domains, comprising more than 790,000 residues, has been used for the calculation of their solvent accessibility in the native protein environment and then in the isolated domain environment. Nearly 140,000 (18%) residues showed a change in accessible surface area in the above two conditions. General features of this change under these two circumstances have been pointed out. Propensities of these interfacing amino acid residues have been calculated and their variation for different secondary structure types has been analyzed. Actual amount of surface area lost by different secondary structures is higher in the case of helix and strands compared to coil and other conformations. Overall change in surface area in hydrophobic and uncharged residues is higher than that in charged residues. An attempt has been made to know the predictability of interface residues from sequence environments. This analysis and prediction results have significant implications towards determining interacting residues in proteins and for the prediction of protein-protein, protein-ligand, protein-DNA and similar interactions.

Original languageEnglish
Pages (from-to)63-69
Number of pages7
JournalBiophysical Chemistry
Volume114
Issue number1
DOIs
Publication statusPublished - 1 Apr 2005

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proteins
Proteins
Conformations
predictions
strands
helices
amino acids
Databases
Ligands
coils
deoxyribonucleic acid
Amino Acids
DNA
ligands
interactions

Keywords

  • Domain-domain interactions
  • Interface area
  • Neural network
  • Solvent accessibility
  • Structure classification

ASJC Scopus subject areas

  • Biochemistry
  • Physical and Theoretical Chemistry
  • Biophysics

Cite this

Solvent accessibility in native and isolated domain environments : General features and implications to interface predictability. / Mohd Raih, Mohd Firdaus; Ahmad, Shandar; Zheng, Rong; Mohamed, Rahmah.

In: Biophysical Chemistry, Vol. 114, No. 1, 01.04.2005, p. 63-69.

Research output: Contribution to journalArticle

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