Investigating allosteric communication with local search paths on protein residue networks
Susan Khor · arXiv (Cornell University) · 2015
We compare paths constructed on protein residue networks via a Euclidean Distance Search (EDS) to paths found using the commonly used Breadth First Search (BFS) method in terms of their ability to capture allosteric communication within proteins. We find that EDS paths are more stable and have better communication propensity than BFS paths. Further, EDS paths outperformed BFS paths at capturing key features of allosteric communication in a type III receptor tyrosine kinase (KIT), and at identifying protein sequence segments where known mutational hotspots are found. These findings suggest that EDS paths are more plausible discrete models of intra-protein communication pathways than BFS paths.