Dynamics Simulation Studies of Apoazurin of Alcaligenes denitnficans

L. X Q Chen, R. A. Engh, A. T. Brunger, D. T. Nguyen, M. Karplus, G. R. Fleming

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Molecular dynamics simulations using the stochastic boundary method were carried out for apoazurin of Alcaligenes denitrificans. 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 (160 ps) found experimentally. Estimates of energy transfer between W48 and W118 give rates similar to the experimental value provided that the initial state islLb. Variations of rate of ±20% are found when the relative motions of the two residues are taken into account.

Original languageEnglish (US)
Pages (from-to)6908-6921
Number of pages14
Issue number18
StatePublished - Sep 1 1988

ASJC Scopus subject areas

  • Biochemistry

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