Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

doi:10.1073/pnas.0607890103

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

*Ecole Polytechnique Fédérale de Lausanne, Laboratory of Computational Chemistry and Biochemistry, 1015 Lausanne, Switzerland; and
^†Consiglio Nazionale delle Ricerche–National Institute for the Physics of Matter–Democritos National Simulation Center and International School for Advanced Studies, Via Beirut 2–4, 34014 Trieste, Italy

Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved October 30, 2006 (received for review September 8, 2006)

Abstract

We have coupled hybrid quantum mechanics (density functional theory; Car–Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu²⁺ + e ⁻ → Cu⁺ half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite-temperature fluctuations of the protein structure are both essential for a correct quantitative description of the electronic properties of this system. We report a redox potential shift with respect to copper in water of 0.2 eV (experimental 0.16 eV) and a reorganization free energy λ = 0.76 eV (experimental 0.6–0.8 eV). The electrostatic field of the protein plays a crucial role in fine tuning the redox potential and determining the structure of the solvent. The inner-sphere contribution to the reorganization energy is negligible. The overall small value is mainly due to solvent rearrangement at the protein surface.

Footnotes

^§To whom correspondence should be addressed. E-mail: ursula.roethlisberger{at}epfl.ch
Author contributions: I.T., P.C., and U.R. designed research; M.C. and A.M. performed research; M.C., A.M., and I.T. analyzed data; and M.C. and U.R. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS direct submission.
↵ ¶ These values are typically within one σ of the average of the equilibrium distribution position in our 300-K QM/MM simulations.
Abbreviations:

ET,

electron transfer;

MD,

molecular dynamics;

QM/MM,

quantum mechanics/molecular mechanics.
Freely available online through the PNAS open access option.