Literature DB >> 17179046

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

Michele Cascella1, Alessandra Magistrato, Ivano Tavernelli, Paolo Carloni, Ursula Rothlisberger.   

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 Cu(2+) + 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 lambda = 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.

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Year:  2006        PMID: 17179046      PMCID: PMC1705813          DOI: 10.1073/pnas.0607890103

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  32 in total

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Journal:  Science       Date:  1993-03-12       Impact factor: 47.728

10.  Electronic structure and solvation of copper and silver ions: a theoretical picture of a model aqueous redox reaction.

Authors:  Jochen Blumberger; Leonardo Bernasconi; Ivano Tavernelli; Rodolphe Vuilleumier; Michiel Sprik
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  30 in total

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Journal:  J Phys Chem B       Date:  2015-12-17       Impact factor: 2.991

2.  Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.

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3.  Fundamental signatures of short- and long-range electron transfer for the blue copper protein azurin at Au/SAM junctions.

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Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-01       Impact factor: 11.205

4.  Polarizable embedding for simulating redox potentials of biomolecules.

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Review 5.  Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.

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Journal:  J Chem Phys       Date:  2016-05-14       Impact factor: 3.488

6.  On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions.

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Journal:  J Chem Theory Comput       Date:  2012-03-29       Impact factor: 6.006

7.  On unjustifiably misrepresenting the EVB approach while simultaneously adopting it.

Authors:  Shina C L Kamerlin; Jie Cao; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-08-06       Impact factor: 2.991

Review 8.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

9.  Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

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Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

Review 10.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

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Journal:  Proteins       Date:  2010-05-01
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