دانلود کتاب Handbook of Flavoproteins: Volume 2 Complex Flavoproteins, Dehydrogenases and Physical Methods

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Preface\n1 The reaction mechanisms of Groups A and B flavoprotein monooxygenases\n 1.1 Introduction\n 1.2 Enzymes acting upon aromatic substrates – Group A\n 1.2.1 Reactions catalyzed\n 1.2.2 Protein structures\n 1.2.3 Detailed mechanism of PHBH\n 1.2.3.1 Reductive half-reaction\n 1.2.3.2 Oxidative half-reaction\n 1.2.3.3 Hydroxylation chemistry\n 1.2.3.4 Summary\n 1.3 Enzymes acting upon non-aromatic substrates – Group B\n 1.3.1 Reactions catalyzed and subclasses\n 1.3.1.1 BVMOs\n 1.3.1.2 FMOs\n 1.3.1.3 NMOs\n 1.3.1.4 YUCCAs\n 1.3.2 Structural features\n 1.4 References\n2 Flavin-dependent monooxygenases in siderophore biosynthesis\n 2.1 Iron, an essential but scarce nutrient\n 2.2 Siderophores\n 2.2.1 Siderophores are important virulence factors\n 2.2.2 Structural diversity of siderophores\n 2.3 Flavin-dependent N-hydroxylating monooxygenases\n 2.4 Catalytic cycle of NMOs\n 2.4.1 Flavin reduction in NMOs\n 2.4.2 Flavin oxidation in NMOs\n 2.5 Three-dimensional structure of NMOs\n 2.5.1 FAD-binding domain\n 2.5.2 NADPH-binding domain\n 2.5.3 L-Ornithine-binding domain\n 2.6 The structural basis of substrate specifi city in NMOs\n 2.7 Mechanism of stabilization of the C4a-hydroperoxyfl avin by NADP+\n 2.8 Activation of NMOs by amino acid binding\n 2.9 Unusual NMOs\n 2.10 High-throughput screening assay to identify inhibitors of NMOs\n 2.11 Conclusions\n 2.12 References\n3 The flavin monooxygenases\n 3.1 Introduction\n 3.2 Occurrence and classifi cation\n 3.2.1 Amino acid sequence motifs\n 3.2.2 DNA screening\n 3.3 Single-component fl avin monooxygenases\n 3.3.1 Subclass A\n 3.3.2 Subclass B\n 3.3.3 Subclass C\n 3.3.4 Subclass D\n 3.3.5 Subclass E\n 3.3.6 Subclass F\n 3.4 Conclusions\n 3.5 References\n4 Structure and catalytic mechanism of NADPH-cytochrome P450 oxidoreductase: a prototype of the difl avin oxidoreductase family of enzymes\n 4.1 Introduction\n 4.2 Properties of CYPOR fl avins\n 4.3 Domain structure and function\n 4.4 Membrane binding domain (MBD)\n 4.5 FMN domain\n 4.6 Cytochrome P450 binding: role of the FMN domain and connecting domain\n 4.7 FAD domain\n 4.8 Mechanism of hydride transfer\n 4.9 Interfl avin electron transfer\n 4.10 FMN to heme electron transfer\n 4.11 P450 catalysis\n 4.12 Other CYPOR electron acceptors\n 4.13 CYPOR domain movement and control of electron transfer\n 4.14 Physiological functions of CYPOR and effects of CYPOR defi ciency\n 4.15 Human CYPOR defi ciency (PORD)\n 4.16 Contribution of CYPOR to inter-individual variation in human drug metabolism\n 4.17 Unanswered questions and future directions\n 4.18 References\n5 The xanthine oxidoreductase enzyme family: xanthine dehydrogenase, xanthine oxidase, and aldehyde oxidase\n 5.1 Introduction\n 5.2 Overall structures\n 5.3 Reaction mechanism\n 5.4 Electron transfer from the molybdenum center to other redox-active centers\n 5.5 Reaction of FAD with NAD+ or molecular oxygen\n 5.6 Inhibitors of xanthine oxidoreductase\n 5.7 References\n6 Assimilatory nitrate reductase\n 6.1 Introduction and scope\n 6.2 Enzyme structure\n 6.3 Kinetics and mechanism\n 6.4 Post-translational regulation\n 6.5 Interconversion of sulfi te oxidase and nitrate reductase activities\n 6.6 Conclusions\n 6.7 References\n7 Succinate dehydrogenase (Complex II) and fumarate reductase\n 7.1 History of Complex II\n 7.2 Overview of Complex II\n 7.3 Structure of Complex II\n 7.4 Catalytic assays\n 7.5 Catalytic mechanism and domain movement\n 7.6 Electron transfer\n 7.7 Quinone-binding site of Complex II\n 7.8 Assembly of the covalent FAD cofactor into Complex II\n 7.9 Concluding remarks\n 7.10 References\n8 Flavoprotein disulfi de reductases and structurally related flavoprotein thiol/disulfi de-linked oxidoreductases\n 8.1 Introduction\n 8.2 Group 1 FDR enzymes: classic dithiol/disulfi de oxidoreductases with a single CXXXXC disulfi de redox center\n 8.2.1 Dihydrolipoamide dehydrogenase (LipDH)\n 8.2.2 Glutathione reductase (GR) – two new structural studies on this classic member of the group\n 8.2.3 Trypanothione reductase (TryR)\n 8.2.4 Mycothione reductase (MycR)\n 8.3 Group 2A FDR enzymes – enzymes of the Group 1 structural fold requiring an additional C-terminal Cys-based redox center\n 8.3.1 Mercuric ion reductase (MerA)\n 8.3.2 High Mr thioredoxin reductases (TrxR and TGR)\n 8.4 Group 2B FDR enzymes – low Mr thioredoxin reductase (TrxR) and structurally related enzymes\n 8.5 Group 3 FDR enzymes – enzymes with cysteine sulfenic acid or mixed Cys-S-S-CoA redox center\n 8.6 Group 4 FDR enzymes – Group 1-fold enzymes catalyzing novel reactions\n 8.7 Group 5 FDR enzymes – enzymes with a si side pair of Cys residues widely separated in sequence\n 8.8 References\n9 Flavoenzymes in pyrimidine metabolism\n 9.1 Introduction\n 9.2 Pyrimidine/dihydropyrimidine interconversions\n 9.2.1 Overview\n 9.2.2 Dihydroorotate dehydrogenases\n 9.2.2.1 General\n 9.2.2.2 Mechanisms of the pyrimidine half-reactions\n 9.2.2.3 Mechanisms of the non-pyrimidine half-reactions\n 9.2.3 Dihydrouridine synthases\n 9.2.3.1 General\n 9.2.3.2 Pyrimidine half-reactions\n 9.2.3.3 Non-pyrimidine half-reaction\n 9.2.4 Dihydropyrimidine dehydrogenases\n 9.2.4.1 General\n 9.2.4.2 Pyrimidine half-reaction\n 9.3 Methylations\n 9.3.1 Overview\n 9.3.2 Flavin-dependent thymidylate synthase\n 9.3.3 Folate/FAD-dependent methyl transferase (TrmFO )\n 9.4 References\n10 Excited state electronic structure of flavins and flavoproteins from theory and experiment\n 10.1 Introduction\n 10.2 Flavin photophysics and the electronic structure of its excited states\n 10.2.1 Moments of the charge distribution\n 10.2.2 Experimental techniques for the determination of excited state electronic structure\n 10.3 Linear dichroism measurements of reduced anionic flavin transition dipole moments and complimentary calculations\n 10.4 Experimental studies of excited state electronic structure of flavins and complementary calculations\n 10.4.1 Oxidized fl avin\n 10.4.2 Excited state structure of OYE and OYE charge transfer complex\n 10.4.3 DNA photolyase and Δ μ⃗k0\n 10.4.4 Experimental results for the fl avin neutral radical\n 10.5 Computational studies on fl avins\n 10.5.1 Calculations for oxidized fl avins\n 10.5.2 Computational results for semiquinone fl avin\n 10.5.3 Computational studies on reduced fl avins\n 10.6 Spectroscopic studies bearing on excited electronic states of flavins\n 10.6.1 Time-resolved studies of oxidized fl avin\n 10.6.2 The triplet state of fl avins\n 10.7 Photoinduced electron transfer in flavins\n 10.8 Applications of flavin photochemistry\n 10.9 Conclusions\n 10.10 References\n11 Structural properties of the alkanesulfonate monooxygenase system that dictate function\n 11.1 Introduction\n 11.2 Sulfur limitation in bacterial systems\n 11.3 FMN reductase of the alkanesulfonate monooxygenase system\n 11.4 Monooxygenase enzymes of the bacterial luciferase family\n 11.4.1 Structural properties of the bacterial luciferase family\n 11.4.2 Structural dynamics of alkanesulfonate monooxygenase\n 11.4.3 Active site structure in the bacterial luciferase family\n 11.4.4 Catalytic mechanisms of the bacterial luciferase family\n 11.4.5 Mechanistic properties of alkanesulfonate monooxygenase\n 11.5 Mechanism of fl avin transfer\n 11.6 Conclusions\n 11.7 References\n12 Single molecule methods to study flavoproteins\n 12.1 Flavoproteins and electron-transfer reactions\n 12.2 Bulk vs. single-molecule methods\n 12.3 Single-molecule techniques for the study of biological systems\n 12.3.1 Atomic force microscopy\n 12.3.2 Optical tweezers\n 12.3.3 AFM based force spectroscopy\n 12.3.3.1 The avidin-biotin complex\n 12.3.3.2 Antigen-antibody interaction\n 12.3.3.3 Molecular interactions in transient complexes\n 12.4 Single-molecule experiments with fl avoenzymes\n 12.4.1 Fluorescence measurements\n 12.4.2 Force measurements in fl avoproteins\n 12.5 References\n13 Applications of Saccharomyces pastorianus Old Yellow Enzyme to asymmetric alkene reductions\n 13.1 Identifi cation and initial characterization\n 13.1.1 History of OYE1\n 13.1.2 OYE 1 structure and roles of key residues\n 13.1.2.1 Histidine 191 and Asparagine 194\n 13.1.2.2 Tyrosine 196\n 13.1.2.3 Threonine 37\n 13.1.2.4 Tryptophan 116\n 13.2 Substrate specifi city of OYE 1\n 13.2.1 Ketones and aldehydes\n 13.2.2 Esters\n 13.2.3 Nitro alkenes\n 13.3 Conclusions\n 13.4 References\n14 Contributions of protein environment to the reduction potentials of fl avin-containing proteins\n 14.1 Introduction\n 14.2 Computation of Esq/hq on the basis of the crystal structures\n 14.3 Calculation of Esq/hq and determination of redox-linked amino acid residues\n 14.4 Influence of the protein backbone conformation on Esq/hq\n 14.5 Influence of the loop region near the fl avin binding site on Esq/hq\n 14.6 Influence of the FMN phosphate group on Esq/hq\n 14.7 Conclusions\n 14.8 References\n15 Methods based on continuum electrostatics and their application to fl avoproteins – a review\n 15.1 Introduction\n 15.2 The continuum electrostatic model based on the Poisson-Boltzmann equation\n 15.2.1 The physical basis of the Poisson-Boltzmann equation\n 15.2.2 Electrostatic potentials and electrostatic energies\n 15.3 Association of fl avoproteins\n 15.3.1 Electrostatic docking of fl avoproteins\n 15.3.2 Similarity of electrostatic potentials of proteins\n 15.4 Titration behavior of proteins\n 15.4.1 Microstate model\n 15.4.2 DTPA – An illustrative example\n 15.4.3 Theoretical analysis of the protonation of fl avoproteins\n 15.5 Recent and upcoming developments\n 15.6 References\n16 Flavoproteins and blue light reception in plants\n 16.1 Introduction (light reception in plants)\n 16.2 Plant phototropins\n 16.2.1 LOV domain structure\n 16.2.2 LOV photochemistry\n 16.2.3 LOV signal propagation\n 16.3 Cryptochromes\n 16.3.1 Cryptochrome structure\n 16.3.2 Cryptochrome photochemistry\n 16.3.3 Cryptochrome signal transduction\n 16.4 Outlook\n 16.5 References\n17 Ultrafast dynamics of flavins and flavoproteins\n 17.1 Introduction\n 17.2 Ultrafast dynamics of flavins\n 17.2.1 Steady-state spectroscopic properties\n 17.2.2 Oxidized flavins\n 17.2.3 Anionic and neutral radical flavins\n 17.2.4 Anionic and neutral fully-reduced flavins\n 17.3 Electron transfer in model flavodoxin\n 17.3.1 Experiment design, reaction scheme and probing strategy\n 17.3.2 Femtosecond charge separation, frozen active-site configuration and critical free energies\n 17.3.3 Ultrafast charge recombination, vibrational quantum effect and hot ground-state cooling\n 17.3.4 Photoinduced redox cycle, reaction time scales, and vibrational coupling generality\n 17.4 Enzymatic reactions and repair photocycles in DNA photolyases\n 17.4.1 Dynamics and mechanism of cyclobutane pyrimidine dimer repair by CPD photolyase\n 17.4.1.1 Sequential splitting dynamics of the cyclobutane ring\n 17.4.1.2 Electron tunneling pathways and functional role of adenine moiety\n 17.4.2 Dynamics and mechanism of repair of UV-induced (6-4) photoproduct by (6-4) photolyase\n 17.4.2.1 Ultrafast electron and proton transfer dynamics\n 17.4.2.2 Catalytic repair photocycle\n 17.5 Signal transduction in blue-light photoreceptors\n 17.5.1 Photoaddition of cysteine to fl avin in phototropin\n 17.5.2 Switching of fl avin hydrogen bond in BLUF protein\n 17.5.3 Ultrafast flavin dynamics in cryptochrome\n 17.6 Conclusions\n 17.7 References\nIndex