Calculation of the redox potential of the protein azurin and some mutants.

Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy calculations based on classical molecular-dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials.

Electronic structures and nonlinear optical properties of trinuclear transition metal clusters M-(mu-S)-M' (M = Mo, W; M' = Cu, Ag, Au).

A series of trinuclear metal clusters MS4(M'PPh3)2(M'PPh3) (M = Mo, W; M' = Cu, Ag, Au) have been studied using the density functional theory (DFT) method. The static polarizabilities and hyperpolarizabilities of the model clusters have been calculated using the finite-field (F-F) method. The model clusters, divided into two groups, are alike in the structure of two fragments of rhombic units M-(mu-S)2-M' (M = Mo, W; M' = Cu, Ag, Au), perpendicular to each other, which are joined by sharing the bridge metal M.

Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore.

Molecular dynamics simulation techniques together with time-dependent density functional theory calculations have been used to investigate the effect of photon absorption by a 4-hydroxy-cinnamic acid chromophore on the structural properties of the photoactive yellow protein (PYP) from Ectothiorodospira halophila. The calculations suggest that the protein not only modifies the absorption spectrum of the chromophore but also regulates the subsequent isomerization of the chromophore by stabilizing the isomerization transition state. Although signaling from PYP is thought to involve partial unfolding of the protein, the mechanical effects accompanying isomerization do not appear to directly destabilize the protein.