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Hinsen, K ; Kneller, GR

Influence of geometrical constraints on the dynamics of polypeptide-chains

Physical Review E 52 (6) 6868-6874 Part B

par Administrateur - publié le , mis à jour le

Abstract :

Based on the equations of motion for linked rigid bodies that we derived recently [G. Kneller and K. Hinsen, Phys Rev. E 50, 1559 (1994)], we develop a technique for the simulation of molecular systems with constraints. We apply it to analyze the importance of the-various degrees of freedom of a polypeptide chain for its dynamics. We find that keeping the peptide planes rigid does not change the dynamics much, but that the bending degrees of freedom of the alpha-carbon bond geometry are essential for large-amplitude backbone motions. This means that the phi and psi angles commonly used to characterize protein conformations and protein backbone dynamics do not constitute a sufficient set of variables to perform dynamical simulations.