Temperature Dependence of the Redox Potential of Rubredoxin from Pyrococcus furiosus:  A Molecular Dynamics Study

• Published in: Biochemistry (Easton) Vol. 35; no. 43; pp. 13772 - 13779
• Main Authors: Swartz, Paul D, Ichiye, Toshiko
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 29-10-1996
• Subjects: Archaea - chemistry; Computer Simulation; Electrochemistry; Iron - metabolism; Iron-Sulfur Proteins - chemistry; Iron-Sulfur Proteins - metabolism; Oxidation-Reduction; Pyrococcus furiosus; Rubredoxins - chemistry; Rubredoxins - metabolism; Software; Temperature; Water - metabolism
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi960611x

Molecular dynamics simulations are used to evaluate the temperature dependent differences in structure, solvation, and energies for the iron−sulfur protein rubredoxin from the hyperthermophilic archebacterium Pyrococcus furiosus to understand the unusual temperature dependence of its redox potential [Adams, M. W. W. (1992) Adv. Inorg. Chem. 38, 341−396]. Simulations of both redox states performed at 295 and 363 K reveal that almost no backbone structure alteration occurs at the higher temperature and that the radius of gyration of the protein is temperature and redox state independent. The most striking change is that the penetration of the redox site by solvent molecules in the reduced form at 295 K, which was also seen in simulations of the reduced form of the mesophilic Clostridium pasteurianum rubredoxin at 295 K (Yelle, R. B., et al. (1995) Proteins 22, 154−167], is no longer seen to a significant extent in either redox state at 363 K. Comparing 295 to 363 K, the calculated change in the electrostatic potential of about −300 mV and in the negative of the potential energy of about −550 meV is consistent with the observed change in redox potential of −160 mV. Moreover, the calculated change is in the wrong direction if the penetrating water is excluded. These results show that changing solvent accessibility may be responsible for the temperature dependence of the redox potential of P. furiosus rubredoxin.