Paper Citing NAMD - Abstract
Varol, Onur; Yuret, Deniz; Erman, Burak; Kabakcioglu, Alkan
Mode coupling points to functionally important residues in myosin II
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1777-1786, SEP 2014
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non-Gaussian vibrational modes on fluctutational dynamics. We show that an information-theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II.
