Proton translocation pathways of selected variants of the Green Fluorescent Protein (GFP) and Pseudomonas Fluorescens Mannitol 2-Dehydrogenase (PfM2DH) were investigated via a new Molecular Dynamics-based analysis protocol that allows for direct quantitative comparison between a crystal structure and its time-averaged solute-solvent structure obtained from simulation.Our study of GFP suggests that the proton released from the chromophore upon photoexcitation is likely to remain within the protein, where it diffuses through an extensive internal H-bonding network and is amenable to being recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, such that the solute-(high-density) solvent crystal structures of binary and ternary complexes are properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-depended structural shifts observed by virtue of our analysis.Interestingly, aside from facilitating rigorous validation of an MD simulation, our time-averaged structures also provide a comprehensive portrait of the fully dynamic (i.e., flexible solute) all-occupancy solvation network of a system, from which remarkably enriched proton transfer pathways can be obtained. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.

Time-averaged distributions of solute and solvent motions: Exploring proton wires of biomolecules

248th National Meeting (2014)

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