Water-assisted proton transfer in ferredoxin I

Area of Science:

• Biochemistry
• Computational Chemistry
• Protein Science

Background:

• Ferredoxin I (FdI) from Azotobacter vinelandii is a proton-pumping protein.
• Previous studies indicated water molecules stabilize between Asp(15) and the [3Fe-4S](0) cluster, potentially aiding proton transfer.
• Understanding proton transfer mechanisms is crucial for biological energy conversion.

Purpose of the Study:

• To investigate the role of water molecules in assisting proton transfer (PT) in FdI.
• To generalize molecular mechanics with proton transfer (MMPT) for condensed-phase reactions.
• To elucidate the mechanism and energetics of proton transfer between Asp(15) and the [3Fe-4S](0) cluster.

Main Methods:

• Molecular mechanics with proton transfer (MMPT) simulations.
• Umbrella sampling simulations.
• Electronic structure calculations.

Main Results:

• Proton transfer between Asp(15) and the [3Fe-4S](0) cluster is a concerted process facilitated by water molecules.
• No stable hydronium ion intermediate is formed during the forward proton transfer.
• The calculated free energy difference for the forward reaction (11.7 kcal/mol) closely matches experimental values (13.3 kcal/mol).
• Water-unassisted proton transfer exhibits a significantly higher energy barrier (≈35 kcal/mol) compared to water-assisted transfer (≈10 kcal/mol).

Conclusions:

• Water molecules play a critical role as proton relays in FdI, lowering the activation energy for proton transfer.
• The MMPT method provides a reliable framework for studying proton transfer reactions in condensed phases.
• Computational findings align well with experimental data, validating the proposed mechanism.