Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories

Subject of this work is the analysis of molecular dynamics (MD) trajectorie s of neurophysins I (NPI) and II (NPII) and their complexes with the neurop hyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respective ly, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII /VP)(2) and (NPI/OT)(2) heterotetramers and two more trajectories for the N PII2 and NPI2 homodimers (six trajectories in total). Using essential dynam ics which, to our judgement, is equivalent to factor analysis, we found tha t only about 10 degrees of freedom per trajectory are necessary and suffici ent to describe in full the motions relevant for the function of the protei n. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow a nharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.