Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces

Surendra S. Negi, Werner Braun

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

We have developed a fully automated method, InterProSurf, to predict interacting amino acid residues on protein surfaces of monomeric 3D structures. Potential interacting residues are predicted based on solvent accessible surface areas, a new scale for interface propensities, and a cluster algorithm to locate surface exposed areas with high interface propensities. Previous studies have shown the importance of hydrophobic residues and specific charge distribution as characteristics for interfaces. Here we show differences in interface and surface regions of all physical chemical properties of residues as represented by five quantitative descriptors. In the current study a set of 72 protein complexes with known 3D structures were analyzed to obtain interface propensities of residues, and to find differences in the distribution of five quantitative descriptors for amino acid residues. We also investigated spatial pair correlations of solvent accessible residues in interface and surface areas, and compared log-odds ratios for interface and surface areas. A new scoring method to predict potential functional sites on the protein surface was developed and tested for a new dataset of 21 protein complexes, which were not included in the original training dataset. Empirically we found that the algorithm achieves a good balance in the accuracy of precision and sensitivity by selecting the top eight highest scoring clusters as interface regions. The performance of the method is illustrated for a dimeric ATPase of the hyperthermophile, Methanococcus jannaschii, and the capsid protein of Human Hepatitis B virus. An automated version of the method can be accessed from our web server at http://curie.utmb.edu/ prosurf.html.

Original languageEnglish (US)
Pages (from-to)1157-1167
Number of pages11
JournalJournal of Molecular Modeling
Volume13
Issue number11
DOIs
StatePublished - 2007

Fingerprint

chemical properties
statistical analysis
Chemical properties
Statistical methods
proteins
Proteins
Membrane Proteins
predictions
Methanocaldococcus
Amino Acids
Capsid Proteins
Hepatitis B virus
Adenosine Triphosphatases
scoring
Research Design
Odds Ratio
Amino acids
amino acids
Charge distribution
hepatitis

Keywords

  • Hot spots
  • Molecular recognition
  • Physical chemical properties of interface residues
  • Protein-protein interface

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Catalysis
  • Organic Chemistry
  • Inorganic Chemistry
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. / Negi, Surendra S.; Braun, Werner.

In: Journal of Molecular Modeling, Vol. 13, No. 11, 2007, p. 1157-1167.

Research output: Contribution to journalArticle

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