title: Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.
abstract: A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism.
authors.affiliation: Physics Department City College of New York, New York, NY 10031, USA. gunner@sci.ccny.cuny.edu
authors.forename: M R
authors.initials: MR
authors.lastname: Gunner
authors.forename: Junjun
authors.initials: J
authors.lastname: Mao
authors.forename: Yifan
authors.initials: Y
authors.lastname: Song
authors.forename: Jinrang
authors.initials: J
authors.lastname: Kim
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry*; D004583:Electrons; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D012996:Solutions; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D011522:Protons; D012996:Solutions; D014867:Water; D001436:Bacteriorhodopsins