It should be possible to quantitatively understand functional properties of a protein given its 3-dimensional structure. The proposed work will analyze how the energy released from reduction of 02 to water in the binuclear center (BNC) of Heme-Cu oxidases drives vectorial proton transfer, generating a transmembrane electrochemical gradient. The hypothesis is that on reaction changes in BNC bonding, geometry and/or charge distribution are transmitted to the rest of the protein. This then changes the distribution of ionized groups and hydrogen bond connectivity in proton input and exit regions. MCCE (Multi-Conformation Continuum Electrostatics) will be used to follow these changes throughout the protein, providing: (1) net protein uptake at each stage in the reaction cycle (which can be compared with measured values) and specific sites where protons are bound (which is difficult to determine experimentally). (2) modifications of reaction free energies by the protein environment and identification of residues that influence chemistry; (3) transmembrane AW generated on each step and a breakdown of how much is contributed by electron transfer, proton transfer or dipolar rearrangements; (4) identification of conformational changes that could serve as gates in proton pumping - these would permit access of protons to different sides of the membrane in different stages of the reaction. Information about explicit changes in the BNC will be obtained from collaboration with others carrying out high level DFT analysis of the reaction chemistry. These changes will be used to drive targeted molecular dynamics. The resultant structures will be evaluated with MCCE to see how the reaction at the BNC modifies the protein. The calculations will determine interspecies variation comparing the bovine cytocbrome c oxidase to that found in P. dinitificans and Rb. sphaero ides and to the homologous E. coli quinol oxidase. The effects of mutation will be predicted. Protein structural motifs that stabilize charge transfers deep inside membrane proteins and couple these electron transfers to transmembrane proton transfer will be identified.
| Gunner, M R; Mao, Junjun; Song, Yifan et al. (2006) Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations. Biochim Biophys Acta 1757:942-68 |
| Song, Yifan; Mao, Junjun; Gunner, M R (2006) Electrostatic environment of hemes in proteins: pK(a)s of hydroxyl ligands. Biochemistry 45:7949-58 |
| Song, Yifan; Michonova-Alexova, Ekaterina; Gunner, M R (2006) Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral? Biochemistry 45:7959-75 |
| Song, Yifan; Mao, Junjun; Gunner, M R (2003) Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates. Biochemistry 42:9875-88 |
