Procrustean rotation in concert with principal component analysis of molecular dynamics trajectories: Quantifying global and local differences between conformational samples

2009 ◽  
Vol 131 (22) ◽  
pp. 225102 ◽  
Author(s):  
Daniel G. Oblinsky ◽  
Bryan M. B. VanSchouwen ◽  
Heather L. Gordon ◽  
Stuart M. Rothstein
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Principal Component ◽  
Component Analysis ◽  
Global And Local

A theoretical model for the collective motion of proteins by means of principal component analysis

Open Physics ◽  
2011 ◽  
Vol 9 (1) ◽  
Author(s):  
Hiqmet Kamberaj
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Relaxation Time ◽  
Friction Coefficient ◽  
Principal Component ◽  
Component Analysis ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dynamical Friction ◽  
Collective Coordinates

AbstractA coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the Ca atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2–0.4 ps and slow relaxation time of long diffusion about 1–2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from −0.746 to −0.938 for the real part and from −0.528 to −0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

Sign in / Sign up

Export Citation Format

Share Document