Recurrence analysis of hydration effects on nonlinear protein dynamics: multiplicative scaling and additive processes

The potential energy time series obtained from molecular dynamics simulatio ns of the B1 domain of protein G and plastocyanin both in vacuo and in wate r were analyzed by means of recurrence quantification analysis. This method ology is robust for nonlinear, nonstationary processes, and demonstrated th e existence of a flat recurrence spectrum occurring beyond a previously des cribed scaling region of protein dynamics, as well as the existence of clus tered modes of very long period (approximately 500 ps) elicited by the solv ent. The number of these modes was approximately related to the number of s tructural domains of the studied proteins. Thus the methodology may be usef ul to distinguish processes intrinsic to protein folding dynamics from thos e which develop from hydration. (C) 2001 Elsevier Science B.V. All rights r eserved.