PROTEIN DYNAMICS DETERMINED BY BACKBONE CONFORMATION AND ATOM PACKING

To study the factors determining the collective motions in thermal, co nformational fluctuations of a globular protein, molecular dynamics si mulations were performed with a backbone model and an atomic-level mod el, In the backbone model, only the C-alpha atoms were explicitly trea ted with two types of pairwise interactions assigned between the C-alp ha atoms: atom-packing interactions to take into account the effect of tight atom packing in the protein interior and chain-restoring intera ctions to maintain the backbone around the native conformation, A quas i-harmonic method was used to decompose the overall fluctuations into independent, collective modes, The modes assigned to large conformatio nal fluctuations showed a good correlation between the backbone and at omic-level models, From this study, it was suggested that the collecti ve modes were motions in which a protein fluctuates, keeping the terti ary structure around the native one and avoiding backbone overlap and, hence, rough aspects of the collective modes can be derived without d etails of the atomic interactions, The backbone model is useful in obt aining the overall backbone motions of a protein without heavy simulat ions, even though the simulation starts from a poorly determined confo rmation of experiments and in sampling main chain conformations, from which the side chain conformations may be predicted.