Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers

Abstract

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the QA site cycles between quinone, QA, and anionic semiquinone, QA •-, being reduced once and never binding protons. In the QB site, ubiquinone is reduced twice by QA •-, binds two protons and is released into the membrane as the quinol, QH2. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. QA is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to QB. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as Asp M17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

Characterizing Protein Protonation Microstates Using Monte Carlo Sampling

“…MCCE can also include explicit waters with multiple positions . However, as is customary, all water molecules in the crystal structure are deleted and replaced by implicit solvent in lysozyme while 28 crystallographic waters are retained in the RCs, as explicit water molecules play an important role in the proton transfer pathway. , All protonatable residues (Glu, Asp, Arg, Lys, His, Tyr, and Cys and N- and C-termini) have both charged and neutral conformers available. At each charge state, side-chain conformers are made that differ in the number and position of polar side-chain protons.…”

Evolution in the Design of Water Oxidation Catalysts with Transition-Metals: A Perspective on Biological, Molecular, Supramolecular, and Hybrid Approaches

“…Notably, molecular dynamics simulations with crystal structures of photosystem II reveal a series of hydrogen-bond wires, starting from the Mn cluster, and extending toward the Cl1 and O4 channels . Such wires are believed to carry out proton transfer in the PSII networks. ,, In fact, it is crucial to take notice of the secondary coordination sphere and the prolonged H-bonding network of the OEC while designing synthetic catalysts. The amino acid residue containing polypeptides can be replaced by judicious choice of organic and inorganic groups providing appropriate biomimetic local coordination.…”

“… 36 Such wires are believed to carry out proton transfer in the PSII networks. 36 , 128 , 129 In fact, it is crucial to take notice of the secondary coordination sphere and the prolonged H-bonding network of the OEC while designing synthetic catalysts. The amino acid residue containing polypeptides can be replaced by judicious choice of organic and inorganic groups providing appropriate biomimetic local coordination.…”

Light-induced reversible reorganizations in closed Type II reaction centre complexes: physiological roles and physical mechanisms

“…sphaeroides [39], which would suggest similar structural changes in bRC and PSII. However, the mechanisms of proton transfer associated with the reduction of Q B appear to be different in PSII and bRC [40,41], and thus, details of the nature and mechanisms of the structural dynamics might also be different.…”