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Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

✍ Scribed by Steven Hayward; Akio Kitao; Nobuhiro Gō

Publisher
Cold Spring Harbor Laboratory Press
Year
2008
Tongue
English
Weight
771 KB
Volume
3
Category
Article
ISSN
0961-8368

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✦ Synopsis

Abstract

A comparison is made between a 200‐ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distributions of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.

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