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We use the torsional angles of the protein chain as generalized coordinatesin the canonical formalism, derive canonical equations of motion, andinvestigate the coordinate dependence of the kinetic energy expressed in termsof the canonical momenta. We use the formalism to compute the normal-frequencydistributions of the alpha-helix and the beta-sheet, under the assumption thatthey are stabilized purely through hydrogen bonding. Comparison of their freeenergies show the existence of a phase transition between the alpha-helix andthe beta-sheet at a critical temperature.

Hamiltonian Dynamics of the Protein Chain and Normal Modes of Alpha-Helix and Beta-Sheet