1. Introduction 22. Structure of the bacterial PSU 52.1 Organization of the bacterial PSU 52.2 The crystal structure of the RC 92.3 The crystal structures of LH-II 112.4 Bacteriochlorophyll pairs in LH-II and the RC 132.5 Models of LH-I and the LH-I-RC complex 152.6 Model for the PSU 173. Excitation transfer in the PSU 183.1 Electronic excitations of BChls 22 3.1.1 Individual BChls 22 3.1.2 Rings of BChls 22 3.1.2.1 Exciton states 22 3.1.3 Effective Hamiltonian 24 3.1.4 Optical properties 25 3.1.5 The effect of disorder 263.2 Theory of excitation transfer 29 3.2.1 General theory 29 3.2.2 Mechanisms of excitation transfer 32 3.2.3 Approximation for long-range transfer 34 3.2.4 Transfer to exciton states 353.3 Rates for transfer processes in the PSU 37 3.3.1 Car→BChl transfer 37 3.3.1.1 Mechanism of Car→BChl transfer 39 3.3.1.2 Pathways of Car→BChl transfer 40 3.3.2 Efficiency of Car→BChl transfer 40 3.3.3 B800-B850 transfer 44 3.3.4 LH-II→LH-II transfer 44 3.3.5 LH-II→LH-I transfer 45 3.3.6 LH-I→RC transfer 45 3.3.7 Excitation migration in the PSU 46 3.3.8 Genetic basis of PSU assembly 494. Concluding remarks 535. Acknowledgments 556. References 55Life as we know it today exists largely because of photosynthesis, the process through which light energy is converted into chemical energy by plants, algae, and photosynthetic bacteria (Priestley, 1772; Barnes, 1893; Wurmser, 1925; Van Niel, 1941; Clayton & Sistrom, 1978; Blankenship et al. 1995; Ort & Yocum, 1996). Historically, photosynthetic organisms are grouped into two classes. When photosynthesis is carried out in the presence of air it is called oxygenic photosynthesis (Ort & Yocum, 1996). Otherwise, it is anoxygenic (Blankenship et al. 1995). Higher plants, algae and cyanobacteria perform oxygenic photosynthesis, which involves reduction of carbon dioxide to carbohydrate and oxidation of water to produce molecular oxygen. Some photosynthetic bacteria, such as purple bacteria, carry out anoxygenic photosynthesis that involves oxidation of molecules other than water. In spite of these differences, the general principles of energy transduction are the same in anoxygenic and oxygenic photosynthesis (Van Niel, 1931, 1941; Stanier, 1961; Wraight, 1982; Gest, 1993). The primary processes of photosynthesis involve absorption of photons by light-harvesting complexes (LHs), transfer of excitation energy from LHs to the photosynthetic reaction centers (RCs), and the primary charge separation across the photosynthetic membrane (Sauer, 1975; Knox, 1977; Fleming & van Grondelle, 1994; van Grondelle et al. 1994). In this article, we will focus on the anoxygenic photosynthetic process in purple bacteria, since its photosynthetic system is the most studied and best characterized during the past 50 years.

Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c. The parameters are based on both protein X-ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6-31G* level. The simulations with the new parameter set reproduce the geometries of the X-ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6-31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins.

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.

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.