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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1982 Feb;79(4):1346–1350. doi: 10.1073/pnas.79.4.1346

Molecular dynamics of an α-helical polypeptide: Temperature dependence and deviation from harmonic behavior

Ronald M Levy *,, David Perahia *,, Martin Karplus *,
PMCID: PMC345966  PMID: 16593164

Abstract

The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) α-helix evaluated from molecular dynamics simulations at seven temperatures between 5 and 300 K are compared with analytic harmonic results and with experimental values. Above 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements. Analysis of the time dependence of the fluctuations shows that low-frequency modes (<75 cm-1) dominate the atomic fluctuations and that there is a contribution with a very long relaxation time (>10 ps). Quantum corrections to the amplitude of the fluctuations are found to be small above 50 K. The mean square amplitudes obtained from the molecular dynamics simulations are compared with the values derived from x-ray temperature (Debye-Waller) factors for metmyoglobin (80, 250, and 300 K) and ferrocytochrome c (300 K).

Keywords: protein dynamics, temperature factor, quantum corrections, fluctuations, normal modes

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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