Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins

Calculations of pK values of individual titratable groups in one structure of Bacillus circulans xylanase and two similar structures of Bacillus agara dhaerens xylanase were performed by combination of molecular dynamics simul ation and a continuum electrostatic model. The influence of the starting st ructure 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 tha n calculations based on a single structure. This study emphasizes the featu res of the collected ensemble rather than the precision of the finally obta ined values. The evolution along the trajectory of individual averaged pK, values and their components, such as contribution of desolvation penalty an d interactions with protein permanent charges, were analyzed. For the major ity of titratable sites, it was shown that simulation time shorter than 500 ps is insufficient to represent their ionization behavior. Calculations ba sed on slightly different initial structures of Bacillus agaradhaerens xyla nase demonstrated that the averaged pK, value for some groups is correlated to the initial structure, even for a long molecular dynamic trajectory.