Calculation of the redox potential of the protein azurin and some mutants.
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 lambda 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.
van den Bosch
Marieke
M
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Swart
Marcel
M
Snijders
Jaap G
JG
Berendsen
Herman J C
HJ
Mark
Alan E
AE
Oostenbrink
Chris
C
van Gunsteren
Wilfred F
WF
Canters
Gerard W
GW
D019943:Amino Acid Substitution; D001400:Azurin / Q000737:chemistry* / Q000235:genetics; D003198:Computer Simulation; D003300:Copper / Q000737:chemistry; D004563:Electrochemistry; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D011550:Pseudomonas aeruginosa / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
D001400:Azurin; D003300:Copper