Computational analyses of the surface properties of protein-protein interfaces.
Several potential applications of structural biology depend on discovering how one macromolecule might recognize a partner. Experiment remains the best way to answer this question, but computational tools can contribute where this fails. In such cases, structures may be studied to identify patches of exposed residues that have properties common to interaction surfaces and the locations of these patches can serve as the basis for further modelling or for further experimentation. To date, interaction surfaces have been proposed on the basis of unusual physical properties, unusual propensities for particular amino-acid types or an unusually high level of sequence conservation. Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied. These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.
Gruber
Jan
J
Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU, England.
Zawaira
Alexander
A
Saunders
Rhodri
R
Barrett
C Paul
CP
Noble
Martin E M
ME
D019295:Computational Biology / Q000379:methods*; D003460:Crystallization; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013499:Surface Properties; D018909:src Homology Domains
D046911:Macromolecular Substances; D011506:Proteins