Computational Alanine Scanning Mutagenesis: Characterizing the hotspots of ILK-Ankyrin Repeat and PINCH1 Complex

Abstract

From the last two decades, computational alanine scanning mutagenesis (cASM) have been successively applied to a variety of protein complexes to study the energetics and structural characteristics of hot spot residues at protein interface. The cASM combines a continuum approach to model solvent interactions with a MM-based approach to atomistically model protein-protein interactions. In the present study, this methodology was used to study the hotspot residues involved in the binding complex of Integrin linked kinase containing Ankyrin repeats with PINCH1 which have profound effect in cell migration, spreading and signalling. Molecular dynamic simulations using a continuum solvent approach (MM-PB/GBSA) were used in one of our previous study and later alanine scanning with post processing protocol was done as a downstream analysis to predict accurately the differences in binding free energies in solution between wild-type and alanine mutated complexes (Delta Delta G(bind)).