COMPUTATIONAL SIMULATION AND ANALYSIS OF DYNAMIC ASSOCIATION BETWEEN PLASTOCYANIN AND CYTOCHROME-F - CONSEQUENCES FOR THE ELECTRON-TRANSFERREACTION

This work is a theoretical analysis in four stages of association betw een the blue copper protein plastocyanin and the heme protein cytochro me f, which are physiological partners in the photosynthetic electron- transfer chain. In the first stage, 32 000 trajectories of approach by plastocyanin to cytochrome f were generated with implicit considerati on of hydration and with gradual cooling of the system from 300 to 0 K . Approximately 2000 trajectories resulted in local minima of energy, i.e., in docking. The molecular configurations having relatively low e nergies were grouped, by structural similarity, into six families. In the second stage, six configurations having the lowest energies, one f rom each family, were subjected to thorough molecular dynamics simulat ion, for 260 ps. Extensive hydration of the proteins was treated expli citly. The whole plastocyanin molecule and the relevant parts of the c ytochrome f molecule were given conformational freedom. In the third s tage, the following three contributions to the energy of binding were calculated: polarization of water by the proteins, determined from num erical solutions of the Poisson-Boltzmann equation; nonelectrostatic ( van der Waals and other) interactions involving the proteins and water ; and the Coulombic interactions within and between the protein molecu les. Total energy of association was calculated with a thermodynamic c ycle; several realistic sets of parameters gave consistent results. Th e configuration having the most favorable Coulombic interactions turne d out to have the second highest total energy. This finding exemplifie s the importance of allowing for hydration and for conformational flex ibility in docking calculations and perils of neglecting these factors . In the fourth stage, electronic coupling between the copper and heme sites in the six configurations was analyzed and compared by the Path ways method. The configuration providing the most efficient path for e lectron tunneling turned out to be different from the most stable conf iguration. There are indications that the evident interaction between Lys65 in cytochrome f and Tyr83 in plastocyanin may involve the ammoni um group of the former and the aromatic ring of the latter. These surp risingly strong noncovalent interactions, so-called charge-pi interact ions, have recently been discovered and are important for molecular re cognition. Modeling and structural optimization of these interactions are beyond the state of the art in molecular mechanics, but these stud ies should become possible with improved force fields. The electron-tr ansfer reaction between cupriplastocyanin and ferrocytochrome f is fas t in the noncovalent complex and undetectably slow in the covalent com plex. This contrast is explained in terms of our theoretical analysis.