Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6

• Published in: Proteins, structure, function, and bioinformatics Vol. 54; no. 1; pp. 135 - 152
• Main Authors: Bento, Isabel, Matias, Pedro M., Baptista, António M., da Costa, Patricia N., van Dongen, Walter M.A.M., Saraiva, Lígia M., Schneider, Thomas R., Soares, Cláudio M., Carrondo, Maria A.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.01.2004
• Subjects: Amino Acids - chemistry; angstrom resolution; continuum electrostatic; cooperativity; crystal-structure; Crystallography, X-Ray; Cytochrome c Group - chemistry; Desulfovibrio desulfuricans - chemistry; dielectric-constants; electron-proton coupling; electrostatic calculations; free-energy; Heme - chemistry; Hydrogen-Ion Concentration; ionizable residues; Models, Molecular; molecular modeling; Oxidation-Reduction; photosynthetic reaction centers; Protein Conformation; redox-Bohr; redox-linked changes; rhodopseudomonas-viridis; Static Electricity; tetraheme cytochrome; Thermodynamics; vulgaris miyazaki-f; X-ray crystallography
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10431

The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found in sulfate‐reducing bacteria, which is believed to act as a partner of hydrogenase. The three‐dimensional structure of the oxidized and reduced forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using high‐resolution X‐ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox‐Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox‐linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redox‐cooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox‐Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox‐linked conformational changes in side‐chain residues, results in a significant decrease in the solvent accessibility of hemes I and II. Proteins 2004. © 2003 Wiley‐Liss, Inc.