Calculation of the Redox Potential of the Protein Azurin and Some Mutants
Marieke van den Bosch
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349
Search for more papers by this authorMarcel Swart Dr.
Department of Organic and Inorganic Chemistry, Free University de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
Search for more papers by this authorJaap G. Snijders† Prof.
Department of Theoretical Chemistry, Groningen University, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorHerman J. C. Berendsen Prof.
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorAlan E. Mark Prof.
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorChris Oostenbrink Dr.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland
Search for more papers by this authorWilfred F. van Gunsteren Prof.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland
Search for more papers by this authorGerard W. Canters Prof.
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349
Search for more papers by this authorMarieke van den Bosch
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349
Search for more papers by this authorMarcel Swart Dr.
Department of Organic and Inorganic Chemistry, Free University de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
Search for more papers by this authorJaap G. Snijders† Prof.
Department of Theoretical Chemistry, Groningen University, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorHerman J. C. Berendsen Prof.
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorAlan E. Mark Prof.
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biopysical Chemistry, University of Groningen, Nijenbogh 4, 9747 AG Groningen, The Netherlands
Search for more papers by this authorChris Oostenbrink Dr.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland
Search for more papers by this authorWilfred F. van Gunsteren Prof.
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Hönggerberg, 8093 Zürich, Switzerland
Search for more papers by this authorGerard W. Canters Prof.
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands, Fax: (+31) 71-527-4349
Search for more papers by this authorGraphical Abstract
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.
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