Normal modes and phase transition of the protein chain based on the Hamiltonian formalism
Name
Leong-2010-Normal modes and pha.pdf
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581.19 KB
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Author(s)
Leong, Hon-Wai
Chew, Lock Yue
Huang, Kerson
Date Issued
July 2010
Journal
Physical Review Letters
Publisher
American Physical Society
Citation
Leong, Hon-Wai, Lock Yue Chew and Kerson Huang. "Normal modes and phase transition of the protein chain based on the Hamiltonian formalism." Physical Review Letters 82.1(2010): 011915. © 2010 by American Physical Society
Version
Final published version
Abstract
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the canonical momenta. We use the formalism to compute the normal-frequency distributions of the α helix and the β sheet, under the assumption that they are stabilized purely through hydrogen bonding. In addition, we obtain the free-energy relations of the α helix, the β sheet, and the random coil of a 15-residue polyalanine. Interestingly, our results predict a phase transition from an α helix to a β sheet at a critical temperature.
MIT Department
Massachusetts Institute of Technology. Department of Physics
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1103/PhysRevE.82.011915
