Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication.

Redox reactions play important roles in almost all biological processes, including photosynthesis and respiration, which are two essential energy processes that sustain all life on earth. It is thus not surprising that biology employs redox-active metal ions in these processes. It is largely the redox activity that makes metal ions uniquely qualified as biological cofactors and makes bioinorganic enzymology both fun to explore and challenging to study.

Even though most metal ions are redox active, biology employs a surprisingly limited number of them for electron transfer (ET) processes. Prominent members of redox centers involved in ET processes include cytochromes, iron–sulfur clusters, and cupredoxins. Together these centers cover the whole range of reduction potentials in biology (Figure ​(Figure1).1). Because of their importance, general reviews about redox centers1−77 and specific reviews about cytochromes,8,24,78−90 iron–sulfur proteins,91−93 and cupredoxins94−104 have appeared in the literature. In this review, we provide both classification and description of each member of the above redox centers, including both native and designed proteins, as well as those proteins that contain a combination of these redox centers. Through this review, we examine structural features responsible for their redox properties, including knowledge gained from recent progress in fine-tuning the redox centers. Computational studies such as DFT calculations become more and more important in understanding the structure–function relationship and facilitating the fine-tuning of the ET properties and reduction potentials of metallocofactors in proteins. Since this aspect has been reviewed extensively before,105−110 and by other reviews in this thematic issue,2000,2001,2002 it will not be covered here.






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Figure 1


Reduction potential range of redox centers in electron transfer processes.

Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers.

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 Mossbauer 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.

Cytochromes c: Evolutionary, Structural and Physicochemical Aspects

Glutathione and soluble thiol content were examined in a broad spectrum of bacteria. Significant soluble thiol was present in all cases. The thiol compound was glutathione in most of the gram-negative bacteria but not in most of the gram-positive bacteria studied. Glutathione was absent in four anerobes and one microaerophile but was present in a blue-green bacterium. The glutathione content of Escherichia coli increased significantly during transition from exponential to stationary phase.

Occurrence of glutathione in bacteria.

If one has the amino acid sequences of a set of homologous proteins as well as their phylogenetic relationships, one can easily determine the minimum number of mutations (nucleotide replacements) which must have been fixed in each codon since their common ancestor. It is found that for 29 species of cytochrome c the data fit the assumption that there is a group of approximately 32 invariant codons and that the remainder compose two Poisson-distributed groups of size 65 and 16 codons, the latter smaller group fixing mutations at about 3.2 times the rate of the larger. It is further found that the size of the invariant group increases as the range of species is narrowed. Extrapolation suggests that less than 10% of the codons in a given mammalian cytochrome c gene are capable of accepting a mutation. This is consistent with the view that at any one point in time only a very restricted number of positions can fix mutations but that as mutations are fixed the positions capable of accepting mutations also change so that examination of a wide range of species reveals a wide range of altered positions. We define this restricted group as the concomitantly variable codons. Given this restriction, the fixation rates for mutations in concomitantly variable codons in cytochrome c and fibrinopeptide A are not very different, a result which should be the case if most of these mutations are in fact selectively neutral as Kimura suggests.

An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

Chemical characterization of high potential iron proteins from Chromatium and Rhodopseudomonas gelatinosa.

Cytochrome c2 of Rhodospirillum rubrum I. MOLECULAR PROPERTIES OF THE PROTEIN AND AMINO ACID SEQUENCES OF ITS PEPTIDES DERIVED BY THE ACTION OF TRYPSIN AND THERMOLYSIN

Atypical soluble haem proteins from a strain of rhodopseudomonas palustris sp.

A high-potential non-haem iron protein from the facultative photoheterotrophe Rhodopseudomonas gelatinosa.

Some effects of iron deficiency on Rhodopseudomonas spheroides strain Y.

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