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Computational Scanning Mutagenesis of Proteins and Protein Complexes

Understanding the effect of mutation to protein stability and on protein binding affinity is key to designing protein therapeutics and also to explaining the effect of naturally occurring mutations to biological events. We present two novel CHARMm-based computational protocols to calculate the free energy changes of protein stability and binding affinity resulting from amino acid substitutions1. In contrast to existing published methods, the temperature dependence of energy contributions is included in the physical model. This is known to be important in understanding and improving the thermal stability of proteins. Furthermore, the use of Generalized Born solvation model with implicit membrane2 makes the methods applicable to transmembrane proteins. The calculations are fast and automated so that not only alanine scanning, but complete amino acid scanning can be performed on large set of residues easily. Validation results and possible application of the method for the purposes of protein design and bioinformatics are discussed.

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