title: Normal modes and phase transition of the protein chain based on the Hamiltonian formalism.
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.
authors.affiliation: Division of Physics & Applied Physics, School of Physical & Mathematical Sciences, Nanyang Technological University, SPMS-04-01, 21 Nanyang Link, Singapore.
authors.forename: Hon-Wai
authors.initials: HW
authors.lastname: Leong
authors.forename: Lock Yue
authors.initials: LY
authors.lastname: Chew
authors.forename: Kerson
authors.initials: K
authors.lastname: Huang
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D044367:Phase Transition; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D011506:Proteins