Paper Citing NAMD - Abstract
Koumanov, A.; Karshikoff, A.; Friis, E.P.; Borchert, T.V.
Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 105:9339-9344, SEP 27 2001
Calculations of pK values of individual titratable groups in one structure of Bacillus circulans xylanase and two similar structures of Bacillus agaradhaerens xylanase were performed by combination of molecular dynamics simulation and a continuum electrostatic model. The influence of the starting structure and the simulation length was investigated. The results agree well with the observations of other authors that calculations using an ensemble of structures describe titration properties of proteins more accurately than calculations based on a single structure. This study emphasizes the features of the collected ensemble rather than the precision of the finally obtained values. The evolution along the trajectory of individual averaged pK, values and their components, such as contribution of desolvation penalty and interactions with protein permanent charges, were analyzed. For the majority of titratable sites, it was shown that simulation time shorter than 500 ps is insufficient to represent their ionization behavior. Calculations based on slightly different initial structures of Bacillus agaradhaerens xylanase demonstrated that the averaged pK, value for some groups is correlated to the initial structure, even for a long molecular dynamic trajectory.
