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

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