Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes.

TitleEmpirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes.
Publication TypeJournal Article
Year of Publication2009
AuthorsGuharoy, M., and P. Chakrabarti
JournalJ Comput Aided Mol Des
Volume23
Issue9
Pagination645-54
Date Published2009 Sep
ISSN1573-4951
KeywordsAlanine, Amino Acids, Animals, Computational Biology, Humans, Hydrogen Bonding, Models, Molecular, Mutagenesis, Site-Directed, Protein Binding, Protein Conformation, Protein Interaction Mapping, Solvents, Structure-Activity Relationship, Thermodynamics, Water
Abstract

We report a simple algorithm to scan interfaces in protein-protein complexes for identifying binding 'hot spots'. The change in side-chain solvent accessible area (DeltaASA) of interface residues has been related to change in binding energy due to mutating interface residues to Ala (DeltaDeltaG (X --> ALA)) based on two criteria-hydrogen bonding across the interface and location in the interface core-both of which are major determinants in specific, high-affinity binding. These relationships are used to predict the energetic contribution of individual interface residues. The predictions are tested against 462 experimental X --> ALA mutations from 28 interfaces with an average unsigned error of 1.04 kcal/mol. More than 80% of interface hot spots (with experimental DeltaDeltaG > or = 2 kcal/mol) could be identified as being energetically important. From the experimental values, Asp, Lys, Tyr and Trp are found to contribute most of the binding energy, burying >45 A2 on average. The method described here would be useful to understand and interfere with protein interactions by assessing the energetic importance of individual interface residues.

DOI10.1007/s10822-009-9282-3
Alternate JournalJ. Comput. Aided Mol. Des.
PubMed ID19479323
Research group: