Paper Citing NAMD - Abstract
Liu, Ming S.; Wang, Die; Morimoto, Hiroyuki; Yim, Howard C. H.; Irving, Aaron T.; Williams, Bryan R. G.; Sadler, Anthony J.
Molecular dynamics reveal a novel kinase-substrate interface that regulates protein translation
JOURNAL OF MOLECULAR CELL BIOLOGY, 6:473-485, DEC 2014
A key control point in gene expression is the initiation of protein translation, with a universal stress response being constituted by inhibitory phosphorylation of the eukaryotic initiation factor 2 alpha(eIF2 alpha). In humans, four kinases sense diverse physiological stresses to regulate eIF2 alpha to control cell differentiation, adaptation, and survival. Herewe develop a computational molecular model of eIF2 alpha and one of its kinases, the protein kinase R, to simulate the dynamics of their interaction. Predictions generated by coarse- grained dynamics simulations suggest a novel mode of action. Experimentation substantiates these predictions, identifying a previously unrecognized interface in the protein complex, which is constituted by dynamic residues in both eIF2 alpha and its kinases that are crucial to regulate protein translation. These findings call for a reinterpretation of the current mechanism of action of the eIF2 alpha kinases and demonstrate the value of conducting computational analysis to evaluate protein function.
