Cytochromes c

1 Stereochemical and Physicochemical Properties of Hernes.- 1.1 Introduction.- 1.2 Electronic Structure of Iron.- 1.3 Stereochemistry of Metalloporphyrins.- 1.4 Properties of Ligands.- 1.5 Metal-free and Metal-substituted Cytochrome c.- 2 Spectroscopic Studies of Cytochromes.- 2.1 Introduction.- 2.2 Spectroscopic Methods.- 2.2.1 General Aspects of Spectroscopy.- 2.2.2 Spectroscopic Parameters.- 2.2.3 Magnetic Resonance Spectroscopies.- 2.2.3.1NMR Spectroscopy.- 2.2.3.2EPR Spectroscopy.- 2.2.4 Vibrational Spectroscopies.- 2.2.5 Electronic Spectroscopies.- 2.2.5.1 CD Spectroscopy.- 2.2.5.2MCD Spectroscopy.- 2.2.5.3Fluorescence and Phosphorescence Spectroscopies.- 2.2.6 Mössbauer Spectroscopy.- 2.2.7 X-Ray Absorption Spectroscopy.- 2.2.8 The Problems of Assignment and Interpretation.- 2.2.9 Spectroscopic Studies and the Variation of Temperature.- 2.3 Selected Applications of Spectroscopy to Cytochromes c.- 2.3.1 The Type of Heme, its Oxidation State and its Spin-State.- 2.3.1.1 Optical Spectra of Cytochromes.- 2.3.1.2The Spin-State of Iron.- 2.3.1.3The Oxidation State of Iron.- 2.3.2 The Identity and Stereochemistry of Axial Ligands.- 2.3.2.1Histidine-Methionine Axial Ligation.- 2.3.2.2 The EPR-MCD Approach to Identifying Axial Ligands.- 2.3.2.3Axial Ligation of Cytochrome f and Cytochrome c1.- 2.3.2.4The Alkaline Isomer of Mitochondrial Cytochrome c.- 2.3.2.5 Axial Ligation of Cytochromes c?.- 2.3.3 The Protein Structure.- 2.3.3.1Determination of Protein Tertiary Structure.- 2.3.3.2Dynamic Aspects of Protein Structure.- 2.3.3.3Interprotein Complexes.- 2.3.3.4Group Ionisation Constants.- 3 Amino Acid Sequences of Cytochromes c.- 3.1 Introduction.- 3.2 Amino Acid Sequences of Mitochondrial Cytochromes c.- 3.3 Amino Acid Sequences of Cytochromes c1 and Cytochromes f.- 3.4 Amino Acid Sequences of Cytochromes c2.- 3.5 Amino Acid Sequences of Cytochromes c3.- 3.6 Amino Acid Sequences of Cytochromes c4.- 3.7 Amino Acid Sequences of Cytochromes c5.- 3.8 Amino Acid Sequences of Cytochromes c-555.- 3.9 Amino Acid Sequences of Cytochromes c6 (algal cytochrome 'c-553').- 3.10 Amino Acid Sequences of Cytochromes c-551 (Cytochromes c7).- 3.11 Amino Acid Sequences of Class II Cytochromes c (Cytochromes c8).- 3.12 Cytochrome c Peroxidase.- 3.13 The Reaction Centre Cytochrome from Rhodopseudomonas viridis.- 3.14 Amino Acid Sequences of Cytochromes c Which Do Not Fall Into the Established Sequence Classes.- 4 The Structures of Class I Cytochromes c.- 4.1 Introduction.- 4.2 General Features of the Structure of Mitochondrial Cytochrome c.- 4.2.1 A General Mitochondrial Cytochrome c Structure.- 4.2.2 The Polypeptide Fold and Internal Structure.- 4.2.3 The Protein Surface.- 4.3 The Cytochrome Fold and Bacterial Class I Cytochromes.- 4.3.1 A General Class I Cytochrome c Structure.- 4.3.2 The Polypeptide Fold and Internal Structure.- 4.3.3 Protein Surfaces.- 4.3.4 Two Domain Cytochrome c4.- 4.3.5 Dimeric Cytochrome c5.- 4.3.6 Class I Cytochrome c as Part of Larger Proteins.- 4.4 pH Dependent Transitions of Cytochromes c.- 4.4.1 pH Dependent States of Cytochrome c.- 4.4.2 Ionisation of Herne Propionates.- 4.4.3 Side Chain Ionisation Constants.- 4.4.4 The Alkaline Transition of Ferricytochrome c.- 4.5 Differences in Conformation and Dynamics between Reduced and Oxidised Cytochrome c.- 4.5.1 Differences in Properties of the Two Redox States.- 4.5.2 Conformational Differences between the Two Redox States.- 4.5.3 Conformational Differences between Site-Directed Mutants of 5. cerevisiae iso-1 Cytochrome c.- 4.5.4 Dynamic Fluctuations in the Cytochrome c Structure.- 4.5.5 The Physiological Relevance of Conformational Transitions in Cytochrome c.- 4.6 Structural and Functional Effects of Chemical Modifications on Mitochondrial Cytochrome c.- 4.6.1 General Aspects of Chemical Modifications.- 4.6.2 Modification of the Herne.- 4.6.3 Modifications of the Main Chain.- 4.6.4 Modifications of Aromatic Amino Acids.- 4.6.5 Modifications of Aliphatic Amino Acids.- 5 The Structures of Class II, Class III and Class IV Cytochromes c.- 5.1 Introduction.- 5.2 Class II Cytochromes c.- 5.2.1 Introduction.- 5.2.2 Cytochromes c?.- 5.2.3 Structure of Cytochrome c?.- 5.2.4 Class IIb Cytochromes c.- 5.3 Class III Cytochromes c.- 5.3.1 Introduction.- 5.3.2 Cytochromes c3(4 heme).- 5.3.3 Cytochrome c3(3 heme).- 5.4 Class IV Cytochromes c.- 5.4.1 Introduction.- 5.4.2 Rps. viridis PRC Cytochrome c.- 5.4.3 Chr. vinosum PRC Cytochrome c.- 6 Evolution.- 6.1 Introduction.- 6.2 Aspects of Taxonomy.- 6.3 The Construction of Phylogenetic Trees.- 6.4 The Problems and Successes of Molecular Phylogeny.- 6.5 Neutral Mutation and Natural Selection in the Evolution of Cytochrome c.- 6.5.1 The Molecular Clock and the Theory of Random Genetic Drift.- 6.5.2 Covarions.- 6.5.3 The Dimension of Time in Neutral Mutation Theory.- 6.5.4 Changes in the Rate of Evolution - Are They Due to Natural Selection or Neutral Mutation?.- 6.6 Gene Duplication, Gene Fusion and Pseudogenes.- 6.6.1 Gene Duplication in Mitochondrial Cytochromes c.- 6.6.2 Gene Duplication and Gene Fusion in Bacterial Cytochrome c.- 6.7 Lateral Gene Transfer.- 6.8 The Concepts of Genus and Species in Bacteria.- 6.9 Endosymbiotic Origin for Eukaryotic Organelles.- 6.9.1 The Endosymbiotic and Autogenic Theories.- 6.9.2 Cytochrome c-553 (c6) and the Origins of the Chloroplast.- 6.9.3 Cytochrome c and the Origins of the Mitochondrion.- 6.9.4 The Present Status of the Endosymbiotic Theory.- 6.10 Remote Relationships.- 6.10.1 The Evolution of Energy Metabolism.- 6.10.2 The Relationships between Cytochrome c Subclasses and the Problem of Convergence.- 7 Redox Potentials.- 7.1 Introduction.- 7.2 Ligand Binding.- 7.3 The Coordination Structure of the Metal Ion.- 7.3.1 Porphyrin as an Fe Ligand.- 7.3.2 Effects of Porphyrin Substituents.- 7.3.3 Effects of Axial Ligands.- 7.3.4 Geometry of Coordination.- 7.4 Electrostatic Influences on Redox Potential.- 7.4.1 The Influence of Ions in Solution.- 7.4.2 The Influence of Surface Charge.- 7.4.3 The Influence of Redox Centre Burial within the Protein.- 7.4.4 The Influence of Buried Charge.- 7.4.5 Electrostatic Models for Redox Proteins - Recent Developments.- 7.5 Multiple Redox Centres.- 7.6 Proton Binding.- 7.6.1 Theoretical Considerations.- 7.6.2 Structural Basis for the pH Dependence of Redox Potential.- 7.6.3 pH Dependence of Redox Potential and Proton Translocation.- 7.7 Conformational Stabilisation.- 8 Electron-Transfer Mechanisms.- 8.1 Introduction.- 8.2 General Aspects of Electron Transfer.- 8.2.1 Classification of Electron-Transfer Reactions in Metal Complexes.- 8.2.2 What is an Electron?.- 8.2.3 Electron-Transfer Reactions of Inorganic Compounds.- 8.2.4 General Features of Electron-Transfer Proteins.- 8.2.4.1Spin-State and Conformational Changes in Electron-Transfer Proteins.- 8.2.4.2Electron Transmission in Proteins.- 8.2.5 Summary of Reactivity Determinants.- 8.3 Theoretical Considerations of Electron Transfer.- 8.3.1 Classical Description of Electron Transfer.- 8.3.2 Tunnelling in Electron Transfer.- 8.3.3 The Photoinduced Mechanism.- 8.3.4 Summary and Comparison of Theory with Experimental Data.- 8.4 Self-Exchange Reactions of Cytochromes c.- 8.5 Cross-Reactions of Cytochromes c.- 8.5.1 Bimolecular Reactions with Non-Physiological Small Molecules.- 8.5.2 Reactions of Cytochromes c Covalently Labelled with Non-Physiological Redox Reactions.- 8.5.3 Protein:Protein Reactions in Aqueous Solution.- 8.5.4 Bacterial Photosynthetic Reactions.- References.