Calculation of the redox potential of the protein azurin and some mutants

van den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H. J. C., Mark, A. E., Oostenbrink, C., van Gunsteren, W. F. and Canters, G. W. (2005) Calculation of the redox potential of the protein azurin and some mutants. Chembiochem, 6 4: 738-746. doi:10.1002/cbic.200400244


Author van den Bosch, M.
Swart, M.
Snijders, J. G.
Berendsen, H. J. C.
Mark, A. E.
Oostenbrink, C.
van Gunsteren, W. F.
Canters, G. W.
Title Calculation of the redox potential of the protein azurin and some mutants
Journal name Chembiochem   Check publisher's open access policy
ISSN 1439-4227
Publication date 2005-04-08
Sub-type Article (original research)
DOI 10.1002/cbic.200400244
Volume 6
Issue 4
Start page 738
End page 746
Total pages 9
Place of publication Weinheim
Publisher Wiley-v C H Verlag Gmbh
Language eng
Subject 0601 Biochemistry and Cell Biology
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 coupling-parameter approach is evaluated as function of the number and sequence of lambda 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 k(B)T, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.
Keyword Biochemistry & Molecular Biology
Chemistry, Medicinal
free-energy calculation
GROMOS force field
molecular dynamics
simulations
thermodynamics
Free-energy Perturbation
Blue Copper Proteins
Molecular-dynamics Simulations
Pseudomonas-aeruginosa
Reduction Potentials
Resolution
Site
Ph
Plastocyanin
Computation
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Thu, 20 Sep 2007, 03:56:49 EST