Normal modes and phase transition of the protein chain based on the Hamiltonian formalism

被引：3

作者：

Leong, Hon-Wai ^{[1
]}

Chew, Lock Yue ^{[1
]}

Huang, Kerson ^{[2
,3
]}

机构：

[1] Nanyang Technol Univ, Sch Phys & Math Sci, Div Phys & Appl Phys, Singapore 637371, Singapore

[2] Nanyang Technol Univ, Inst Adv Studies, Nanyang Execut Ctr 02 18, Singapore 639673, Singapore

[3] MIT, Dept Phys, Cambridge, MA 02139 USA

来源：

PHYSICAL REVIEW E | 2010年 / 82卷 / 01期

关键词：

VIBRATIONAL ANALYSIS; SINGLE-PARAMETER; COIL TRANSITION; ALPHA-HELIX; DYNAMICS; POLYPEPTIDES; FLUCTUATIONS; PEPTIDES; BETA-POLY(L-ALANINE); REFINEMENT;

D O I：

10.1103/PhysRevE.82.011915

中图分类号：

O35 [流体力学]; O53 [等离子体物理学];

学科分类号：

070204 ; 080103 ; 080704 ;

摘要：

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 alpha helix and the beta sheet, under the assumption that they are stabilized purely through hydrogen bonding. In addition, we obtain the free-energy relations of the alpha helix, the beta sheet, and the random coil of a 15-residue polyalanine. Interestingly, our results predict a phase transition from an alpha helix to a beta sheet at a critical temperature.

引用

页数：9

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