Volume 6, Issue 4 p. 738-746
Full Paper

Calculation of the Redox Potential of the Protein Azurin and Some Mutants

Marieke van den Bosch

Marieke van den Bosch

Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349

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Marcel Swart Dr.

Marcel Swart Dr.

Department of Organic and Inorganic Chemistry, Free University de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands

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Jaap G. Snijders† Prof.

Jaap G. Snijders† Prof.

Department of Theoretical Chemistry, Groningen University, Nijenbogh 4, 9747 AG Groningen, The Netherlands

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Herman J. C. Berendsen Prof.

Herman J. C. Berendsen Prof.

Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands

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Alan E. Mark Prof.

Alan E. Mark Prof.

Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands

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Chris Oostenbrink Dr.

Chris Oostenbrink Dr.

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland

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Wilfred F. van Gunsteren Prof.

Wilfred F. van Gunsteren Prof.

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland

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Gerard W. Canters Prof.

Gerard W. Canters Prof.

Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349

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First published: 06 April 2005
Citations: 49

Graphical Abstract

Thermodynamic integration and MD simulations have been used to calculate the effect of mutations on the redox potential of the copper protein azurin. The thermodynamic cycle depicted here is used as a check for consistency.

Abstract

Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy calculations based on classical molecular-dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials. The precision of the free-energy calculations with the λ coupling-parameter approach is evaluated as function of the number and sequence of λ values, the sampling time and initial conditions. It is found that the precision is critically dependent on the relaxation of hydrogen-bonding networks when changing the atomic-charge distribution due to a change of redox state or pH value. The errors in the free energies range from 1 to 10 kBT, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.