Paper Citing NAMD - Abstract
Sharp, Kim A.; Kasinath, Vignesh; Wand, A. Joshua
Banding of NMR-derived methyl order parameters: Implications for protein dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2106-2117, SEP 2014
Our understanding of protein folding, and function has began to more explicity incorporate dynamical aspects. Nuclear magnetic resonance has energed as a powerful experimental metho for obtainging comprehensive site-resolved insight into protein motion. It has been observed that methyl-group motion tends to chuster into three "classes" when expresed in terms of the popular Lipari-Szabo model-free squared generalized order parameter. Here the origins of the three classes or bands in the distribution of order parameters are examined. As a first step, a Bayesian based approach which makes no priori assumption about the existence or number of bands, is developed to detect the banding of O-axis(2) values derived either from NMR experiments or molecular dynamics simulation. The analysis is applied to seven protein with extensive molecular dynamics simulation of these proteiin in explicit water to examine the relationship between O-2 and fine details of the motion of methly bearing side chains. All of the proteins studied display banding with some subtle difference. We propse a very simple yet palusible physical mechanismfor banding. Finally our Bayesian method is used to analyze the measure distribtions of methyl group motions in the catabolite activating protein and serveral its mutants in various liganded states and distions of methyl group motions in the catabolite activating protein and several of its mutants in various lighoded states and discuss the functional implications of the observed banding to protein dynamics and function.
