INFLUENCE OF CONSTRAINTS ON THE DYNAMICS OF POLYPEPTIDE-CHAINS

Based on the equations of motion for linked rigid bodies that we deriv ed recently [G. Kneller and K. Hinsen, Phys Rev. E 50, 1559 (1994)], w e develop a technique for the simulation of molecular systems with con straints. We apply it to analyze the importance of the-various degrees of freedom of a polypeptide chain for its dynamics. We find that keep ing the peptide planes rigid does not change the dynamics much, but th at the bending degrees of freedom of the alpha-carbon bond geometry ar e 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 v ariables to perform dynamical simulations.