Biophysical and Structural Aspects of Bioenergetics (eBook)

Chapter 1: Principles of Molecular Bioenergetics and the Proton Pump of Cytochrome Oxidase; 1: Introduction: General Principles of Bioenergetic Systems; 2: The Structure of Cytochrome Oxidase; 3: Hysteretic Properties of Cytochrome Oxidase; 4: The Mechanism of oxygen Reduction to Water; 5: Some Considerations Concerning the Mechanism of the Proton Pump; 6: Where Do We Go From Here?; Chapter 2: Proton Entry, Exit and Pathways in Cytochrome Oxidase: Insight from "conserved" Water; 1: Overview; 2: Heme-copper Oxidases, Their Evolution and General Function; 3: Water and Protein Function; 4: Water and the Proton Pumping Function; 5: Gating of the Pump; 6: Summary; 7: Acknowledgements; 8: References; Chapter 3: Structural Chemical Studies on the Reaction Mechanism of Cytochrome c Oxidase; 1: Introduction; 2: The Mechanism of O2 Reduction; 3: The Mechanism of Proton Pumping; 4: Acknowledgements; Chapter 4: Mechanisms of Redox-coupled Proton Pumping by Respiratory Oxidases; 1: Introduction; 2: Redox-driven Proton Pumping - General Principles; 3: Structure; 4: Electron and Proton Transfer During CcO Turnover; 5: Proton pumping; 6: Molecular Mechanisms for Proton Pumping; 7: Final Remarks; 8: Acknowledgement; 9: References; Chapter 5: Quantum Chemical Models of O2 Bond Cleavage and Proton Pumping in Cytochrome Oxidase; 1: Introduction; 2: Models and Methods; 3: The A to PM Step: Mechanism for O-O Bond Cleavage; 4: The Catalytic Cycle: Mechanism for Proton Pumping; 5: Proton Gating or Guiding; 6: Summary; 7: References; Chapter 6: The bc1 Complex: What is There Left to Argue About?; 1: Introduction; 2: Control of Turnover by the Bifurcated Reaction at the Qo-site; 3: The ES-complex; 4: Constraints from the ES-Complex Model; 5: Proton-coupled Electron Transfer; 6: The Second Electron Transfer, from SQ to Heme bL; 7: Kinetic Estimation of SQ Occupancy; 8: Estimation of SQ Occupancy from Bypass Rates; 9: Mobility in the Qo-site; 10: Other Problematic Short Circuits and Their Prevention; 11: Double-gating; 12: Coulombic Gating in a Sequential Mechanism; 13: Double Occupancy; 14: Location of ES-complex or Activated State at some Alternative Position; 15: Studies using Glu-272 Mutants to Explore the Role of Glu-272 in Control of the Qo-site Reaction and Protection Against Excess ROS Production; 16: Conclusions; 17: Acknowledgements; 18: References; Chapter 7: Insights into the Mechanism of Mitochondrial Complex I from its Distant Relatives, the [NiFe] Hydrogenases; 1: Introduction; 2: The Three Modules Of Complex I; 3: [Nife] Hydrogenases, A Model For The Q-Module Of Complex I; 4: Addressing The Function Of Cluster N2 By EPR Spectroscopy And Site Directed Mutagenesis; 5: Implications For The Mechanism Of Proton Pumping By Complex I; Chapter 8: Current Knowledge about the Mechanism of Energy Transduction by Respiratory Complex I; 1: Introduction; 2: Complex I in Energy Transduction; 3: The Location of the Cofactors and Substrate Binding Sites in Complex I; 4: The Redox Reaction: Oxidation of NADH and Reduction of Quinone; 5: Mechanisms of Proton Pumping; Chapter 9: Structure of Photosystem II from Thermosynechococcus elongates; 1: Introduction; 2: Optimised Crystallisation of Photosystem II from Thermosynechococcus elongates; 3: Structure of Photosystem II from Thermosynechococcus elongates; 4: Mechanism of Water Oxidation; 5: Concluding Remarks; 6: Abbreviations; 7: Acknowledgements; 8: References; Chapter 10: A Structural View of Proton Transport by Bacteriorhodopsin; 1: Introduction; 2: Structure of Bacteriorhodopsin; 3: Photochemical Reaction Cycle; 4: Evaluating the Crystallography; 5: Trapping the Right Structure and the Right Intermediate State; 6: Retinal Motions: The Pump; 7: Conformational Cascades in Response to Relaxation of the Retinal; 8: Crystallographic vs. Non-Crystallographic Evidence; 9: Pump Energetics; Chapter 11:The Dynamics of Proton Transfer Across Bacteriorhodopsin Explored by FT-IR Spectroscopy; 1: Introduction; 2: FT-IR Spectroscopy; 3: Bacteriorhodopsin; 4: References; Chapter 12: Intraprotein Proton Transfer - Concepts and Realities from the Bacterial Photosynthetic Reaction Center; 1: Introduction; 2: Proton Transfer vs. Electron Transfer; 3: The Grotthuss Mechanism and Hydrogen Bonded Chains; 4: Free Energy Relationships - Marcus and Br°nsted; 5: Proton Transfer in Biology; 6: "Normal" Acids and Bases; 7: Proton coupled electron transfer in the acceptor quinone function of photosynthetic reaction centers; 8: Concluding Remarks; 9: Acknowledgements; 10: References; Chapter 13:Infrared Protein Spectroscopy as a Tool to Study Protonation Reactions within Proteins; 1: Introduction; 2: Types of Information from Protein (FT)IR Spectroscopy; 3: Principles of (FT)IR Spectroscopy; 4: ATR-FTIR Spectroscopy; 5: Strategies to Assign IR Bands; 6: IR Properties of Amino Acids; 7: Examples of Protein Infrared Spectroscopy Applications; 8: Outlook; 9: References; Chapter 14: Inhibitors of Mitochondrial F1-ATPase; 1: Introduction; 2: High-resolution Structures of F1-ATPase; 3: Characterised Sites of Inhibition; 4: Potential Medical Significance; 5: Concluding Remarks; 6: Abbreviations; 7: Acknowledgements; 8: References; Chapter 15: The Passion of the Permease; 1: Introduction; 2: Background; 3: Overall Structure of LacY; 4: The Substrate-binding Site; 5: Residues Involved in H+ Translocation and Coupling; 6: Proposed Mechanism of Lactose/ H+ Symport; Chapter 16: Hydride Transfer and Proton Translocation by Nicotinamide Nucleotide Transhydrogenase; 1: The Function of Proton-translocating Transhydrogenase; 2: The Global Architecture of Transhydrogenase; 3: The dII Component; 4: dI2dIII1 Complexes: Catalytic Properties and High-resolution Structures; 5: Considerations Relevant to the Mechanism of Proton Translocation by Transhydrogenase; 6: Hypothesis for the Mechanism of Proton Translocation by Transhydrogenase; 7: Future Directions; 8: Acknowledgements;