Abstract
The successful deciphering of the human genome has highlighted an old challenge in protein science: for most of the resolved protein sequences, we do not know the corresponding structures and functions. Neither do we understand in detail the mechanism by which a protein folds into its biologically active form. Computer experiments offer one way to evaluate the sequence-structure relationship and the folding process but are extremely difficult for detailed protein models. This is because the energy landscape of all-atom protein models is characterized by a multitude of local minima separated by high-energy barriers. Here, we describe an algorithm that allows one to partially overcome this multiple-minima problem. For this purpose a formulation of Lagrange’s equation of motion for proteins described by internal coordinates is presented. Unlike in previous work, not only velocities and accelerations are described by bond length, bond angles, and dihedral angles, but a complete formalism is presented that includes also the positions of atoms and rotation vectors.
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References
A. K. Mazur, V. E. Dorofeev, and R. A. Abagyan, “Derivation and Testing of Explicit Equations of Motion for Polymers Described by Internal Coordinates,” J. Comp. Phys. 92, 261–272 (1991).
E. Hairer, S. P. Nørsett, and G. Wanner, Solving Ordinary Differential Equations I: Nonstiff Problems (Springer, 2002).
A. K. Mazur, “Quasi-Hamiltonian Equations of Motion for Internal Coordinate Molecular Dynamics of Polymers,” J. Comp. Chem. 18, 1354–1364 (1997).
A. V. Finkelstein and O. B. Ptitsyn, Protein Physics: A Course of Lectures (Academic, 2002).
F. Eisenmenger, U. H. E. Hansmann, and Sh. Hayryan, and C.-K. Hu, “[SMMP] a Modern Package for Simulation of Proteins,” Comp. Phys. Comm. 138, 192–212 (2001).
M. J. Sippl, G. Némethy, and H. A. Sheraga, “Intermolecular Potentials from Crystal Data. 6. Determination of Empirical Potentials for O-H...O=C Hydrogen Bonds from Packing Configurations,” J. Phys. Chem. 88, 6231–6233 (1984).
http://mathworld.wolfram.com (Feb. 20, 2006).
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The text was submitted by the authors in English.