Title: Comprehensive analysis of sequences of a protein switch.

Authors: Chen, Szu-Hua; Meller, Jaroslaw; Elber, Ron

Published In Protein Sci, (2016 Jan)

Abstract: Switches form a special class of proteins that dramatically change their three-dimensional structures upon a small perturbation. One possible perturbation that we explore is that of a single point mutation. Building on the pioneering experimental work of Alexander et al. (Alexander et al. PNAS, 2007; 104,11963-11968) that determines switch sequences between α and α+β folds we conduct a comprehensive sequence sampling by a Markov Chain with multiple fitness criteria to identify new switches given the experimental folds. We screen for switch sequences using a combination of contact potential, secondary structure prediction, and finally molecular dynamics simulations. Statistical properties of switch sequences are discussed and illustrated to be most sensitive to mutation at the N- and C- termini of the switch protein. Based on this analysis, a particularly stable putative switch pair is identified and proposed for further experimental analysis.

PubMed ID: 26073558

MeSH Terms: Amino Acid Sequence; Markov Chains; Molecular Dynamics Simulation*; Protein Folding; Protein Structure, Secondary; Proteins/chemistry*