Water-assisted Proton Transfer in Ferredoxin I

Stephan Lutz,Ivan Tubert-Brohman,Yonggang Yang,Markus Meuwly

doi:10.1074/jbc.m111.230003

Abstract

The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. It was shown previously that individual water molecules can stabilize between Asp(15) and the buried [3Fe-4S](0) cluster and thus can potentially act as a proton relay in transferring H(+) from the protein to the μ(2) sulfur atom. Here, we generalize molecular mechanics with proton transfer to studying proton transfer reactions in the condensed phase. Both umbrella sampling simulations and electronic structure calculations suggest that the PT Asp(15)-COOH + H(2)O + [3Fe-4S](0) → Asp(15)-COO(-) + H(2)O + [3Fe-4S](0) H(+) is concerted, and no stable intermediate hydronium ion (H(3)O(+)) is expected. The free energy difference of 11.7 kcal/mol for the forward reaction is in good agreement with the experimental value (13.3 kcal/mol). For the reverse reaction (Asp(15)-COO(-) + H(2)O + [3Fe-4S](0)H(+) → Asp(15)-COOH + H(2)O + [3Fe-4S](0)), a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (ΔE ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ΔE ≈ 35 kcal/mol.

Highlights

There are three profoundly different ways to characterize the role of water in a specific context
Individual water molecules have been implicated in mediating proton transfer, and their role has been characterized by spectroscopic means [5]
Two prominent examples are electron transfer processes [13] and ATP hydrolysis [14, 15]. Proteins performing such proton transfer (PT)3 reactions are referred to as “proton pumps,” among which cytochrome c oxidase found in the mitochondrial electron-transfer chain (16 –19) and bacteriorhodopsin found in photochemical reaction centers (20 –23) are prime examples

Summary

Introduction

There are three profoundly different ways to characterize the role of water in a specific context. We introduced a new method for studying PT in protein-sized systems using molecular dynamics (MD) simulations [44, 45] This approach, named molecular mechanics with proton transfer (MMPT), is inspired by QM/MM simulations but combines a potential energy surface (PES; the “QM” part), suitable for describing the proton transfer between an acceptor and a donor atom, with a force field (the MM part) for the remaining degrees of freedom. No crystallographic water molecules near the iron-sulfur cluster were reported, detailed atomistic simulations showed that the active site of FdI is water-accessible and that the active site water is stabilized over extended periods of time and could potentially act as a proton relay [47, 54]. The water-uncatalyzed reaction, which is characterized by density functional theory methods, yields much higher barriers and is unlikely to occur

Methods

Results

Conclusion