Cytochrome c₂Exit Strategy:  Dissociation Studies and Evolutionary Implications

Abstract

Small, water-soluble, type c cytochromes form a transient network connecting major bioenergetic membrane protein complexes in both photosynthesis and respiration. In the photosynthesis cycle of Rhodobacter sphaeroides, cytochrome c2 (cyt c2) docks to the reaction center (RC), undergoes electron transfer, and exits for the cytochrome bc1 complex. Translations of cyt c2 about the RC-cyt c2 docking interface and surrounding membrane reveal possible exit pathways. A pathway at a minimal elevation allowed by the architecture of the RC is analyzed using both an all-atom steered molecular dynamics simulation of the RC-cyt c2 complex and a bioinformatic analysis of the structures and sequences of cyt c. The structure-based phylogenetic analysis allows for the identification of structural elements that have evolved to satisfy the requirements of having multiple functional partners. The patterns of evolutionary variation obtained from the phylogenetic analysis of both docking partners of cyt c2 reveal conservation of key residues involved in the interaction interfaces that would be candidates for further experimental studies. Additionally, using the molecular mechanics Poisson-Boltzmann surface area method we calculate that the binding free energy of reduced cyt c2 to the RC is nearly 6 kcal/mol more favorable than with oxidized cyt c2. The redox-dependent variations lead to changes in structural flexibility, behavior of the interfacial water molecules, and eventually changes in the binding free energy of the complex.

Nanodomains of Cytochromeb 6 fand Photosystem II Complexes in Spinach Grana Thylakoid Membranes

“…The latter value agreed with theory-based estimates of the cytc 2 -RC interaction, which calculated an unbinding force of 600 to 1000 pN (Pogorelov et al, 2007). By measuring an in situ membrane protein complex stabilized by the membrane bilayer and by interactions with neighbors, repeated measurements are possible that report functional interactions, with no extraction or unfolding of the cytb 6 f complex.…”

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.…”

Dynamics of Recognition between tRNA and Elongation Factor Tu

“…MM-PBSA (Molecular Mechanics-Poisson Bolzmann Surface Area) is a method developed to calculate trends in binding free energies from MD trajectories 34,35,36,37 . It has previously been used to calculate free energies of binding for protein·RNA systems 38 as well as systems containing Mg 2+ 39 .…”

“…Free Energy Calculations-Free energies of binding for the ternary complex were determined using the MM-PBSA method 34,35,38,36,39,37 . The form of the free energy is 〈ΔG binding 〉 = 〈ΔG polar +ΔG nonpolar +ΔE elec +ΔE VdW −TΔS〉.…”