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Study of protein fluctuation with an effective inter‐Cα atomic potential derived from average distances between amino acids in proteins

The conformational dynamics around the native structure of bovine pancreatic trypsin inhibitor (BPTI) in both the oxidized and reduced forms was analyzed by a Monte Carlo method using an approximate residue–residue potential derived from the statistics of average distances between Cα atoms of residues as proposed by the present author (T. Kikuchi, J Comput Chem 1996, 17, 226–237). The results from using this effective potential are similar to those from molecular dynamics simulations, taking all atoms into account, and are consistent with temperature factors from an X‐ray analysis and disulfide formation from a kinetic experiment. This agreement suggests that the essential nature of the potential energy surface formed by the potential around the native structure closely mimics the actual energy landscape within the resolution of Cα atomic fluctuation. Furthermore, it is expected that the potential we found can describe the basic properties of folding kinetics. Examination of the fluctuation property of the native structure of BPTI threaded by a sequence from cytochrome b562 reveals differences specific to the sequence and this result also shows that the dynamical properties obtained in our calculations are not only ascribed to the geometrical constraints of the initial conformation but also the force field specifically produced by a sequence. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 713–719, 1999