Cross-correlation analysis to salt-bridge dynamics in force-induced unfolding of titin kinase

Abstract

In this paper, a theoretical study on the saltbridge dynamics of titin kinase is presented. We focus on the analysis of the spatial-temporal properties of the salt-bridge time series of titin kinase in force-induced unfolding simulated by steered molecular dynamics (SMD). Salt-bridge time series are defined from the SMD trajectories. Scaling analysis reveals two characteristics of the time series in short and long time scales, suggesting there is anti-persistent behavior in short-time scale less than 50 ps, while persistent behavior dominates in long-time scale larger than 100 ps. Using cross-correlation analysis, we study the dynamics of the salt-bridges. From analyzing the eigenvectors of the cross-correlation matrix constructed by the salt-bridge data, we classify salt-bridges into distinct groups. The knowledge of the grouping is useful in identifying force-relevant structural transitions.