Paper Citing NAMD - Abstract
Johnson, Quentin R.; Lindsay, Richard J.; Nellas, Ricky B.; Fernandez, Elias J.; Shen, Tongye
Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue-Residue Contacts
BIOCHEMISTRY, 54:1534-1541, FEB 24 2015
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 residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.
