Computational alanine scanning mutagenesis - An improved methodological approach

• Tipo: Artigo em Revista Científica Internacional
• Data: 2007

Autores

Irina S Moreira (Autor) Outra; Pedro A Fernandes (Autor) FCUP; Maria J Ramos (Autor) FCUP

Revista

Título: Journal of Computational Chemistry

Vol. 28

Páginas: 644-654

ISSN: 0192-8651

Editora: Wiley-Blackwell

Indexação

ISI Web of Knowledge - 191 Citações

Scopus - 200 Citações

Classificação Científica

FOS: Ciências exactas e naturais > Química

Outras Informações

ID Authenticus: P-004-C1D

DOI: 10.1002/jcc.20566

Abstract (EN): Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (Delta Delta G(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations. (C) 2006 Wiley Periodicals, Inc.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 11