cis-trans Isomerization in Biochemistry

Collating the knowledge from over 20,000 publications in chemistry, biology and nanotechnology, this handbook is the first to comprehensively present the state of the art in one ready reference. A team of international authors connects the various disciplines involved, covering cis-trans isomerization of double bonds and pseudo-double bonds, as well as other cis-trans isomerizations. For biochemists, organic chemists, physicochemists, photochemists, polymer and medicinal chemists.

Table of Contents:
Preface xi List of Contributors xiii 1 Nomenclature 1 Christophe Dugave 2 General Mechanisms of Cis-Trans Isomerization: A Rapid Survey 7 Christophe Dugave 2.1 Introduction 7 2.2 Homolytic Cis-Trans Isomerization 7 2.3 Heterolytic Cis-Trans Isomerization 10 3 Mechanisms of Cis-Trans Isomerization aroundt he Carbon–Carbon Double Bonds via the Triplet State 15 Yasushi Koyama, Yoshinori Kakitani, and Hiroyoshi Nagae 3.1 A Concept of a Triplet-Excited Region 15 3.2 Triplet-State Isomerization in Retinal 17 3.2.1 Cis-Trans Isomerization Examined by Electronic Absorption and Raman Spectroscopies and by High-Performance Liquid Chromatography Analysis 17 3.2.2 Triplet-Excited Region in All-trans-Retinal Shown in Terms of Stretching Force Constants Determined by Raman Spectroscopy and Normal Coordinate Analysis 22 3.2.3 Dynamic Triplet-Excited Region in Retinal As Revealed by Deuteration Effects on the Quantum Yields of Isomerization via the T1 State 24 3.2.4 Summary and Future Trends 26 3.3 Triplet-State Isomerization in β-Carotene and Spheroidene 27 3.3.1 Cis-Trans Isomerization in β-Carotene Studied by Electronic Absorption and Raman Spectroscopies and by HPLC Analysis 27 3.3.2 Cis-Trans Isomerization in Spheroidene Studied by Time-Resolved Absorption Spectroscopy and by HPLC Analysis 32 3.3.3 The Triplet-Excited Region of All-trans-Spheroidene in Solution and the Triplet-State Structure of 15-cis-Spheroidene Bound to the Bacterial Reaction Center Determined by Raman Spectroscopy and Normal Coordinate Analysis 35 3.3.3.1 All-trans-Spheroidene in Solution 35 3.3.3.2 15-cis-Spheroidene Bound to the Reaction Center 37 3.3.4 Conformational Changes and the Inversion of Spin-Polarization Identified by Low-Temperature Electron Paramagnetic Resonance Spectroscopy of the Reaction Center-Bound 15-cis-Spheroidene: A Hypothetical Mechanism of Triplet-Energy Dissipation 39 3.3.5 Summary and Future Trends 46 3.4 Spectroscopic and Analytical Techniques for Studying Cis-Trans Isomerization in the T1 State 47 3.4.1 Spectroscopic Techniques: Electronic Absorption, Raman, and Magnetic Resonance Spectroscopies 47 3.4.2 A Useful Analytical Technique: Singular-Value Decomposition Followed by Global Fitting 48 4 Retinal Binding Proteins 53 Hideki Kandori 4.1 Retinal Chromophore in Rhodopsins 53 4.1.1 Specific Color Regulation of the Retinal Chromophore in Protein 53 4.1.2 Unique Photochemistry of the Retinal Chromophore in Protein 56 4.2 Photoisomerization in Visual Rhodopsins 57 4.2.1 Structure and Function of Visual Rhodopsins 57 4.2.2 Primary Process in Vision Studied by Ultrafast Spectroscopy 59 4.2.3 Structural Changes of the Chromophore and Protein upon Retinal Photoisomerization 64 4.3 Photoisomerization in Archaeal Rhodopsins 66 4.3.1 Structure and Function of Archaeal Rhodopsin 66 4.3.2 Primary Process in Bacterial Photosynthesis and Light Sensor Studied by Ultrafast Spectroscopy 68 4.3.3 Structural Changes of the Chromophore and Protein upon Retinal Photoisomerization 69 4.4 Summary and Prospects 72 5 Non-Retinal Chromophoric Proteins 77 Marc Zimmer 5.1 Introduction 77 5.2 Photoactive Yellow Protein 77 5.3 Green Fluorescent Protein and Other GFP-like Proteins 79 5.4 Phytochromes 89 6 Fatty Acids and Phospholipids 95 Chryssostomos Chatgilialoglu and Carla Ferreri 6.1 Introduction 95 6.2 Enzyme-Catalyzed Cis-Trans Isomerization of Unsaturated Fatty Acid Residues in Bacteria 97 6.3 Radical-Catalyzed Cis-Trans Isomerization of Unsaturated Lipids and its Effect on Biological Membranes 101 6.3.1 Geometric Isomerization of Unsaturated Fatty Acids in Solution 101 6.3.2 Isomerization of Phosphatidylcholine in Large Unilamellar Vesicles 103 6.3.3 Biological Consequences 106 6.4 Perspectives and Future Research 110 7 In Silico Dynamic Studies of Cis-Trans Isomerization in Organic and Biological Systems 113 Ute F. Röhrig, Ivano Tavernelli, and Ursula Rothlisberger 7.1 Introduction 113 7.2 Computational Methods 116 7.2.1 Time-Dependent Density Functional Theory (TDDFT) 116 7.2.2 Restricted Open-Shell Kohn–Sham Theory (ROKS) 120 7.3 Theoretical Aspects of CTI 122 7.3.1 Protonated Schiff Bases 123 7.3.2 Formaldimine 124 7.4 CTI in PSB5 and Formaldimine 124 7.4.1 Protonated Schiff Base (PSB5) 124 7.4.2 Formaldimine 129 7.5 CTI in Rhodopsin 132 7.5.1 Introduction 132 7.5.2 Classical and QM/MM Studies of the CTI in Rhodopsin 133 7.6 Summary and Conclusions 137 8 Chemical Aspects of the Restricted Rotation of Esters, Amides, and Related Compounds 143 Christophe Dugave 8.1 Thermodynamic and Kinetic Aspects of Cis-Trans Isomerization 143 8.1.1 Esters and Thioesters 144 8.1.2 Amides and Thioxoamides 145 8.1.3 Oxalamides and Hydrazides 147 8.1.4 Carbamates and Ureas 148 8.2 Influence of the Environment on CTI 150 8.2.1 Solvent and Concentration 150 8.2.2 pH and Salts 152 8.2.3 Temperature 153 8.3 The Study of CTI of Amides and other Conjugated π-Systems 154 8.3.1 Spectroscopic Techniques 154 8.3.1.1 NMR Spectroscopy 154 8.3.1.2 Spectrometric and Fluorimetric Assays 155 8.3.1.3 Other Spectroscopic Techniques 157 8.3.2 Separation of Z and E Isomers 158 8.3.3 Models and Mimics for the Study of Amide CTI: Towards Multiple CTI Pathways 159 8.3.3.1 Acid/H-Bond-Catalyzed CTI 160 8.3.3.2 Nucleophilic/Basic Catalysis of CTI 161 8.3.3.3 Cation-Catalyzed CTI 161 8.3.3.4 Light-Induced CTI 161 9 Amide Cis-Trans Isomerization in Peptides and Proteins 167 Stephan Wawra and Gunter Fischer 9.1 Imidic and Secondary Amide Peptide Bond Conformation 167 9.1.1 Simple Amides 167 9.1.2 Secondary Amide Peptide Bonds 169 9.1.3 Imidic Peptide Bonds 171 9.1.4 Solvent and pH Effects 173 9.1.5 Sequence-Specific Effects 174 9.1.6 Secondary Structure Formation and CTI 178 9.2 Amide Relevant Conformations in Proteins 181 9.3 Native State Peptide Bond Isomerization 183 9.4 Biological Consequences 187 10 Enzymes Catalyzing Peptide Bond Cis-Trans Isomerizations 195 Gunter Fischer 10.1 Introduction 195 10.2 Cyclophilins 199 10.3 FK506 Binding Proteins (FKBPs) 204 10.4 Trigger Factor 209 10.5 Parvulins 210 10.6 Secondary Amide Peptide Bond Cis-Trans Isomerases 213 10.7 Catalytic Mechanism of Peptide Bond Cis-Trans Isomerases 215 11 Tailoring the Cis-Trans Isomerization of Amides 225 Luis Moroder and Christian Renner John J. Lopez, Gabriele Tuchscherer and Manfred Mutter 11.1 Introduction 225 11.2 Substituted Prolines 225 11.2.1 Hydroxyprolines 226 11.2.2 Mercaptoproline 229 11.2.3 Halogenated Prolines 230 11.2.4 Other Proline Analogs 232 11.2.5 Alkylated Proline Analogs 233 11.2.6 Bridged Bicyclic Proline Analogs 235 11.2.7 Locked Proline Mimetics 237 11.3 Pseudoprolines in Chemical Synthesis and Biology 240 11.3.1 From Proline to Pseudoproline 240 11.3.2 Synthesis of Pseudoprolines 242 11.3.3 Pseudoprolines for the Synthesis of Difficult Sequences 244 11.3.4 Pseudoprolines in Bioactive Peptides 245 11.3.5 Pseudoprolines for Enhancing Peptide Cyclization and Turn Induction 246 11.3.6 Pseudoprolines for Modulating Polyproline Helices 247 11.3.7 Pseudoprolines for Modulating Structure and Function of Cyclosporins 249 11.3.8 Pseudoprolines for Targeting Cis Bonds in Peptides and Proteins 251 11.4 Conclusions and Perspectives 252 12 Peptidyl Prolyl Isomerases: New Targets for Novel Therapeutics? 261 Christophe Dugave 12.1 Introduction 261 12.2 Implication of PPIases in Biological Processes and Diseases 262 12.2.1 PPIases and Protein Folding and Trafficking 262 12.2.2 Immunosuppressive Pathways Through Formation of PPIase:Ligand Complexes 263 12.2.3 Modulation of Ion Channels by PPIases 265 12.2.4 Chaperone Activity of Immunophilins in Steroid Receptor Signaling 265 12.2.5 Immunophilins and Neurodegenerative Disorders 266 12.2.6 PPIases and Cell Multiplication 267 12.2.7 Implication of PPIases in Apoptosis 270 12.2.8 PPIases and Infectious Diseases 270 12.3 Structure and SAR studies of PPIases: Structural Evidence and Putative Catalytic Mechanism 272 12.3.1 Generalities 272 12.3.2 Cyclophilins and FKBPs: Similar Molecular Basis for Distinct Catalytic Mechanisms 273 12.3.3 Parvulins 276 12.4 PPIase Inhibitors: From In Vitro Inhibitors to Novel Therapeutics 277 12.4.1 Natural PPIase Inhibitors and Their Analogs 277 12.4.2 Mechanism-Based Inhibitors 282 12.4.3 Library Screening Versus in Silico Design: Current Status and Future Prospects 284 12.5 Conclusion and Perspectives 288 13 Other Cis-Trans Isomerizations in Organic Molecules and Biomolecules 295 Muriel Gondry and Christophe Dugave 13.1 Introduction 295 13.2 Cis-Trans Isomerization around Single Bonds 295 13.2.1 Cis-Trans Isomerism of Aryl Compounds 295 13.2.2 Disulfide Bonds 297 13.2.3 Amide Surrogates with Restricted Rotation of a σ-Bond 298 13.3 C=N-containing Compounds 300 13.3.1 Oximes and Nitroso Compounds 300 13.3.2 Imines and Schiff Bases 300 13.4 Dehydroamino Acids and Dehydropeptides 303 13.4.1 Acryloyl Peptides, Acrylates and Related Molecules 303 13.4.2 Naturally Occurring Dehydroamino Acids and Dehydropeptides 305 13.4.3 Synthetic Dehydroamino Acids and Dehydropeptides 308 13.5 Phototunable Biomolecules Containing an Azobenzene Moiety 310 13.5.1 Phototunable Ligands 310 13.5.2 Phototunable Conformation of Peptides 312 13.5.3 Modifications of Proteins with Photoisomerizable Motifs 313 13.5.4 Other Phototunable Biomolecules 315 14 Cis-Trans Isomerism in Metal Complexes 321 Alzir Azevedo Batista and Salete Linhares Queiroz 14.1 Introduction 321 14.1.1 Trans Effect 324 14.1.2 Protonation of the Leaving Group 326 14.1.3 Separation or Purification of Cis-Trans Isomers 327 14.1.4 Identification of Cis-Trans Isomers 327 14.2 The Cis-Trans Isomerization of Metal Complexes: Mechanisms and Effects 330 14.2.1 Cis or Trans Isomer? 330 14.2.2 Isomerization Processes 331 14.3 Cis-Trans Isomers of Metal Complexes as Potential Therapeutics 334 14.4 Applications of Cis-Trans Isomerization of Metal Complexes in Supramolecular Chemistry 337 14.5 Final Remarks 341 Index 345

About the Author :
Christophe Dugave prepared his PhD in molecular pharmacology under the guidance of Professor Marquet and Professor Gaudry. Then he moved to the University of Sherbrooke (Canada) where he worked as a post-doctoral fellow under the supervision of Professor Deslongchamps. He is currently working at the Department of Protein Engineering and Research of the French Atomic Energy Commission at CEA/Saclay near Paris. His research interests include the synthesis of nonnatural amino acids, pseudopeptides, peptidomimetics, and radiolabeling of peptides and proteins with tritium technetium and other radioisotopes.