Role of Water in Transient Cytochrome c₂ Docking

Abstract

Cytochrome c (cyt c) is a small water-soluble redox protein that facilitates electron transfer in photosynthesis and respiration by alternately docking to integral membrane proteins such as the photosynthetic reaction center (RC). Recently, a high-resolution X-ray structure was solved for the RC−cyt c 2 complex of Rhodobacter sphaeroides, revealing important contacts between the RC in its ground state and reduced cyt c 2 mediated by bridging water molecules. In this article, we compare the variations in these contacts and in the interface in general for both redox states of cyt c 2 that resulted from full-atom simulations of the complexes embedded in a membrane with explicit water molecules. Molecular dynamics simulations of the two redox states of the RC−cyt c 2 system were performed using the CHARMM27 parameters developed for the oxidized and reduced forms of the heme prosthethic group. In its overall dynamics, the encounter complex was found to be very similar in both redox states, exhibiting at the interface a stable hydrophobic tunneling domain and a broad basin of attraction. The differences between the redox states are subtle and involve the formation of a structured cluster of water molecules in the reduced cyt c 2 system. Fluctuations of water and residues at the interface increase upon oxidation and probably mediate the undocking process. The observed differences between the two redox states of the system can only be attributed to the different electrostatic potentials generated by heme in the interface region, as no other modifications were introduced. As the time scale of the undocking process is beyond the time scales reachable by full atomic molecular dynamics simulation of the system, we employed steered molecular dynamics to investigate and compare the energetics associated with the unbinding of RC−cyt c 2 in the reduced and oxidized forms.

Structure of Complex III with Bound Cytochrome c in Reduced State and Definition of a Minimal Core Interface for Electron Transfer

“…Examples are (homologous yeast residues in parentheses) Arg-19 and Ala-87 in the complex of cyt c peroxidase and cyt c from yeast (6), and Ala-79 (Ala-87) in the complex of cyt c 552 with the Cu A domain of cyt c oxidase (30), Gln-14 (Arg-19) and Thr-36 (Val-34) in the cyt c 2 ⅐reaction center complex (7), as well as Thr-18 in the complex of yeast cyt c with the cyt f domain of the cyt b 6 f complex (40). The analogous cation-interaction of the reaction center⅐cyt c 2 complex has been observed as the most stable contact in molecular dynamic simulations (31,41). The core interface appears to be a central feature of the interaction of cyt c with many, structurally not related, binding partners.…”

“…Molecular dynamics simulations with the photosynthetic reaction center and cyt c 2 also indicated that the differences between the redox states are subtle. A structured cluster of water molecules was observed in the reduced cyt c 2 system, whereas fluctuations of water and residues at the interface increased upon oxidation (31). The authors suggested that the higher mobility may mediate the undocking process.…”

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

“…c 2 - bc 1 complex electrostatic interactions would be replaced by direct salt bridges. Purely for dielectric reasons these salt bridges would be 10-fold stronger than water-mediated interactions 27 making the bc 1 complex residence time of cyt. c 2 at least e 10 -fold longer and, thus, disrupting the overall efficiency of cyt.…”

Differential influence of dynamic processes on forward and reverse electron transfer across a protein-protein interface

“…1 has disclosed a fruitful area for examination, but falls far short of a complete picture of the influence of intracomplex dynamics on interprotein ET reactions. Among the issues to be addressed are the degree to which the addition of glycerol may be (i) changing the energy landscapes themselves, not merely the rates with which the landscapes are traversed (48), and (ii) influencing water activity (49)(50)(51).…”