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We have carried out a very long (300 ps) molecular dynamics simulation of the protein myoglobin. This trajectory is approximately three times longer than the longest previous molecular dynamics simulation of a protein, and ten times longer than protein simulations of comparable size (1,423 atoms in our model). Here we report results from this long simulation concerning the average structure, the mean...
A simple model is presented for the motion of phenylalanine and tyrosine rings in proteins. The model consists of restricted rotational diffusion of the rings about the side chain C alpha--C beta (chi 1) and C beta--C gamma (chi 2) axes combined with 180 degree ring flips. The model is used to evaluate order parameters for nuclear magnetic resonance relaxation and fluorescence depolarization probes...
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