PICOSECOND TIMESCALE RIGID-HELIX AND SIDE-CHAIN MOTIONS IN DEOXYMYOGLOBIN

The contribution of rigid-body motions to the atomic trajectories in a 100 ps molecular dynamics simulation of deoxymyoglobin is examined. T wo types of rigid-body motions are considered: one in which the helice s are rigid units and one in which the side-chains are rigid units. Us ing a quaternion-based algorithm, fits of the rigid reference structur es are made to each time frame of the simulation to derive trajectorie s of the rigid-body motions. The fitted trajectories are analysed in t erms of atomic position fluctuations, mean-square displacements as a f unction of time, velocity autocorrelation functions and densities of s tates. The results are compared with the corresponding quantities calc ulated from the full trajectory. The relative contribution of the rigi d helix motions to the helix atom dynamics depends on which quantity i s examined and on which subset of atoms is chosen; rigid-helix motions contribute 86% of the rms helix backbone atomic position fluctuations , but 30% of the helix atom (backbone and side-chain) mean square disp lacements and only 1.1% of total kinetic energy. Only very low-frequen cy motions contribute to the rigid-helix dynamics; the rigid-body anal ysis allows characteristic rigid-helix vibrations to be identified and described. Treating the side-chains as rigid bodies is found to be an excellent approximation to both their diffusive and vibrational mean- square displacements: 96% of side-chain atom mean-square displacements originate from rigid side-chain motions. However, the errors in the s ide-chain atomic positional fits are not always small. An analysis is made of factors contributing to the positional error for different typ es of side-chain.