Dynamics Simulation Studies of Apoazurin of Alcaligenes denitr 8 canst

Molecular dynamics simulations using the stochastic boundary method were carried out for apoazurin of Alcaligenes denitrifcans. For a region centered on the exposed tryptophyl residue (W118), simulations in vacuo and with inclusion of model water molecules were carried out. The simulations are in accord with the experimental finding that the interior tryptophan (W48) is less mobile than the exterior tryptophan (W118). In simulations with and without solvent the motion of W118 is strongly correlated with residues connected along the backbone and residues close to the face of the indole ring. The 50-ps simulated tryptophan fluorescence anisotropies did not reveal the slowly decaying component (1 60 ps) found experimentally. Estimates of energy transfer between W48 and W118 give rates similar to the experimental value provided that the initial state is lLb. Variations of rate of f20% are found when the relative motions of the two residues are taken into account. x e internal motions of protein molecules have generated much interest in recent years because of their possible significance in protein function (Gurd & Rothgeb, 1979; Williams, 1979; Karplus & McCammon, 1981, 1983). A variety of techniques for the study of protein dynamics have been developed including high-resolution X-ray diffraction (Petsko & Ringe, 1984; Debrunner & Frauenfelder, 1982; Artymiuk et al., 1979), NMR (Richarz et al., 1980; Gall et al., 1981, +This work was supported by a grant from the National Science Foundation (to G.R.F. and M.K.). We also thank the National Science Foundation for the computation time on CRAY-1 and CRAY-2 supercomputers and the service provided by University of Minnesota Supercomputer Center. The Evans & Sutherland graphic system PS300 was provided by NSF Grant PCM-8304504. *The University of Chicago. at Berkeley, Berkeley, CA 94720. tinsreid bei Munchen, West Germany. #John Simon Guggenheim Fellow. Present address: Department of Chemistry, University of California ‘ 1 Present address: Max-Planck-Institut fur Biochemie, D-8033 Mar-