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

• Authors: Hiqmet Kamberaj
• Languages of publication: EN

Abstracts

EN

A 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.

Keywords

EN

principal component analysis; collective coordinates; Langevin equation; harmonic bath

• Publisher: De Gruyter Open
• Journal: Open Physics
• Year: 2011
• Volume: 9
• Issue: 1
• Pages: 96-109

Dates

published

1 - 2 - 2011

online

24 - 9 - 2010

Contributors

author

Hiqmet Kamberaj

• Faculty of Technical Sciences, International Balkan University, Avtokomanda Tashko Karaxha BB, Skopje, R. of Macedonia

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Identifiers

DOI

10.2478/s11534-010-0048-2