Molecular dynamics of an α-helical polypeptide: Temperature dependence and deviation from harmonic behavior
- 1 February 1982
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 79 (4), 1346-1350
- https://doi.org/10.1073/pnas.79.4.1346
Abstract
The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) alpha-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 (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
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