Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures.
Redox potentials often differ dramatically for homologous proteins that have identical redox centers. For two types of iron-sulfur proteins, the rubredoxins and the high-potential iron-sulfur proteins (HiPIPs), no structural explanations for these differences have been found. We calculated the classical electrostatic potential at the redox site using static crystal structures of four rubredoxins and four HiPIPs to identify important structural determinants of their redox potentials. The contributions from just the backbone and polar side chains are shown to explain major features of the experimental redox potentials. For instance, in the rubredoxins, the presence of Val 44 versus Ala 44 causes a backbone shift that explains a approximately 50 mV lower redox potential in one of the four rubredoxins. This result is consistent with experimental redox potentials of five additional rubredoxins with known sequence. Also, we attribute the unusually lower redox potentials of two of the HiPIPs studied to a less positive electrostatic environment around their redox sites. Finally, molecular dynamics simulations of solvent around static rubredoxin crystal structures indicate that water alone is a major factor in dampening the contribution of charged side chains, in accord with experiments showing that mutations of surface charges produce relatively little effect on redox potentials.
Swartz
P D
PD
Center for Bioengineering, University of Washington, Seattle 98195-1750, USA.
Beck
B W
BW
Ichiye
T
T
D000409:Alanine; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D002844:Chromatium; D003013:Clostridium; D003198:Computer Simulation; D003901:Desulfovibrio; D016969:Desulfovibrio vulgaris; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D045322:Photosynthetic Reaction Center Complex Proteins; D011487:Protein Conformation; D012416:Rubredoxins / Q000737:chemistry* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D012984:Software; D055672:Static Electricity; D014633:Valine
D001426:Bacterial Proteins; D007506:Iron-Sulfur Proteins; D045322:Photosynthetic Reaction Center Complex Proteins; D012416:Rubredoxins; C007943:high potential iron-sulfur protein; D014633:Valine; D000409:Alanine