Biophysical and Structural Aspects of Bioenergetics

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 degreesnsted;

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;