Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts.

ABSTRACT: Understanding allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of

SUBMITTER: Johnson QR 

PROVIDER: S-EPMC5001807 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature