Monte Carlo, Molecular Dynamics and Network Analysis of The Gramicidin Water Channel and Proton Transfer Pathways to QB in Photosynthetic Reaction Centers

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields such as used in MCCE (Multi-Conformation Continuum Electrostatics) capture electrostatic interactions in biomolecules with an implicit solvent, to give the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here we present an explicit treatment of water molecules in the Gramicidin A channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the non-polarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question. The bacterial reaction center, bRC carries out a series of electron and proton transfer reactions following absorption of a photon. bRCs catalyze the sequential transfer of two electrons and two protons to reduce the ubiquinone bound in the QB site, to produce the product QH2, which dissociates from the protein. PSII uses plastoquinone as QB, carrying out the same reactions to create a reduced quinone product. However, in PSII the QB site is close to the stromal surface, while in bRCs the H subunit caps the protein, requiring a longer path for protons to enter to bind to the quinone. In bRCs a large number of acidic or basic residues buried in the protein near QB influence the electrochemistry of the quinone and provide a tangled web of possible paths for proton transfer. The system has been very well studied by site-directed mutagenesis. These studies show that Asp-L210 and Asp-L213 may share a proton in the ground state, serving as a proton loading site (PLS) for the first proton delivered to the quinone, Glu-L212 is the PLS for the second proton provided to QB. bRCs also have a well characterized external cluster made up of Asp-H124, His-H126, His-H128 which are proposed to be a proton collection site. In this thesis, MD simulation for wild-type and mutants bRCs with network analysis was used to investigate the role of these residues in proton pathways by tracing the complex H-bond networks in bRCs. The hydrogen bond network for the mutant AspL213Asn shows large change in the connections between polar residues and QB indicating this residue plays a key role in proton transfer. Other mutations changed: His-H126/128, which have the most of connections between surface and inner residues; Asp-L210/M17, which mostly connect with surface residues. H126/128 and Asp L210/M17 have been proposed as entries for protons and either could be an alternative choice if the other is blocked