Chapter 3. Computational Alanine Scanning Mutagenesis for Probing Protein Stability and Protein-Protein Interactions: A Literature Review


Kyung-Hoon Lee
Department of Biology, Chowan University, One University Dr., Murfreesboro, North Carolina, USA

Part of the book: Advances in Chemistry Research. Volume 77


Site-directed mutagenesis is essential for elucidating protein structure-function relationships and understanding protein-protein interactions. Alanine scanning mutagenesis is a versatile strategy for evaluating the rôle and relevance of specific residue side chains on proteins. Computational alanine scanning mutagenesis provides a molecular view of the structural and energetic consequences of mutations and can address the origin of binding affinity and stability of proteins. Computational alanine scannings with MM-PBSA (Molecular mechanics-Poisson Boltzmann Surface Area), MM-GBSA (Molecular Mechanics-Generalized Born Surface Area), FEP (Free Energy Perturbation), and TI (Thermodynamic Integration) methods have been developed to investigate the binding modes in detail at the atomic level and to estimate protein stabilities. The computational alanine scanning methods provide good ways to determine the effect of single residues on the binding affinity and protein stability and to identify hot spot residues on proteins and protein-protein interfaces. Computation of the free energy changes to investigate protein stability and binding affinity has gained tremendous importance due to the considerable potential in drug discovery and structure-based ligand design. In this review article, we introduce recent advances and development in computational alanine scanning methods to understand the stability of proteins and to investigate hot spot residues in the interfaces of protein complexes. We also address the methodologies of the computational techniques used in developing drug design and in protein engineering.

Keywords: alanine scanning mutagenesis, binding affinity, free energy perturbation, free energy simulation, hot spot residue, molecular mechanics/generalized Born surface area, molecular mechanics/Poisson-Boltzmann surface area, molecular dynamics simulation, protein stability, thermodynamic integration


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