J Chem Inf Model - Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH.

Tópicos

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Resumo

Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be 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, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. 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.

Resumo Limpo

proton transloc pathway select variant green fluoresc protein gfp pseudomona fluorescen mannitol dehydrogenas pfmdh investig via explicit solvent molecular dynamicsbas analysi protocol allow direct quantit relationship crystal structur timeaverag solutesolv structur obtain simul studi gfp good agreement previous research suggest proton releas chromophor upon photoexcit can diffus extend intern hydrogen bond network allow proton exit bulk recaptur anion chromophor convers pfmdh identifi probabl ioniz state key residu along proton escap channel catalyt site bulk solvent wherein solut highdens solvent crystal structur binari ternari complex proper reproduc furthermor propos plausibl mechan proton transloc process consist statedepend structur shift observ analysi timeaverag structur generat analys facilit valid md simul result provid comprehens profil dynam alloccup solvat network within around flexibl solut detail hydrogenbond network can infer way potenti drawback aris elucid network examin static crystal structur via altern rigidprotein solvat analysi procedur can overcom complementari studi aim effect use methodolog altern implement eg ligand design current underway

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