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

The potential energy time series obtained from molecular dynamics simulations of the B1 domain of protein G and plastocyanin both in vacuo and in water were analyzed by means of recurrence quantification analysis. This methodology is robust for nonlinear, nonstationary processes, and demonstrated the existence of a flat recurrence spectrum occurring beyond a previously described scaling region of protein dynamics, as well as the existence of clustered modes of very long period (approximately 500 ps) elicited by the solvent. The number of these modes was approximately related to the number of structural domains of the studied proteins. Thus the methodology may be useful to distinguish processes intrinsic to protein folding dynamics from those which develop from hydration. (C) 2001 Elsevier Science B.V. All rights reserved.