Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications

Content: Preface xiii 1 Preparation of Artificial Metalloenzymes 1Jared C. Lewis and Ken Ellis-Guardiola 1.1 Introduction 1 1.2 ArM Formation via Metal Binding 2 1.2.1 Repurposing Natural Metalloenzymes 2 1.2.1.1 Carboxypeptidase A 3 1.2.1.2 Carbonic Anhydrase 3 1.2.1.3 Metallo-  -lactamase 4 1.2.1.4 Ferritin 5 1.2.2 Exploiting SerendipitousMetal Binding by Proteins 6 1.2.3 Designing Metal-Binding Sites in Scaffold Proteins 8 1.2.4 Introducing Metal-Binding Sites Using Unnatural Amino Acids 11 1.3 ArM Formation via Supramolecular Interactions 13 1.3.1 Cofactor Binding 14 1.3.1.1 Heme Proteins 14 1.3.1.2 Xylanases 16 1.3.1.3 Serum Albumins 17 1.3.1.4 Lactococcal Multidrug Resistance Regulator 18 1.3.1.5 NikA 18 1.3.1.6 Antibodies 19 1.3.2 Cofactor Anchoring 20 1.3.2.1 (Strept)avidin 20 1.3.2.2 Other Anchoring Scaffolds 22 1.3.2.3 Carboxyanhydrase 22 1.4 ArM Formation via Covalent Linkage 23 1.4.1 Activated Serine and Cysteine Residues 23 1.4.2 Lysine Residues 27 1.4.3 Cysteine Residues 27 1.4.4 Azido Phenylalanine 30 1.5 Conclusion 31 Acknowledgments 32 References 32 2 Preparation of MetalloDNAzymes 41Claire E. McGhee, Ryan J. Lake, and Yi Lu 2.1 Introduction 41 2.2 In Vitro Selection of MetalloDNAzymes in the Presence of Metal Ions 44 2.2.1 Designing a DNAzyme Pool 45 2.2.1.1 Sequence Space 45 2.2.1.2 Choosing the Length of a Random Region 46 2.2.2 Performing In Vitro Selection 46 2.2.2.1 Isolation of Reactive DNA Sequences 47 2.2.2.2 Negative Selection 49 2.2.2.3 Pool Regeneration 49 2.2.2.4 Monitoring Selection Progress 51 2.2.2.5 Sequencing 51 2.2.2.6 Sequence Analysis 52 2.2.3 Optimization of DNAzymes via Truncation and Cis-to-Trans Transformation 52 2.2.4 Reselection of DNAzymes 53 2.3 From In Vitro Selection to Design of MetalloDNAzymes in the Presence of Metallocofactors 53 2.4 Design and Preparation of DNA-Based Hybrid Catalysts 54 2.4.1 Supramolecularly Anchored DNA-Based Hybrid Catalysts 54 2.4.2 Covalently Anchored DNA-Based Hybrid Catalysts 57 2.5 Summary and Future Directions 58 Acknowledgments 59 References 59 3 Experimental Characterization Techniques of Hybrid Catalysts 69Juan Mangas-Sanchez and Eduardo Busto 3.1 Introduction 69 3.2 Characterization of Modified Naturally Occurring Metalloproteins 69 3.3 Characterization of New Metalloenzymes Created from Metal-Free Proteins 73 3.3.1 Characterization of Metalloenzymes Obtained through Direct Metal Salt Complexation 73 3.3.2 Characterization of Metalloenzymes Obtained via Covalent Anchorage 77 3.3.3 Characterization of ArtificialMetalloenzymes via Non-covalent Supramolecular Anchoring 84 3.3.4 Experimental Characterization of ArtificialMetalloenzymes with Dual Activities 87 3.4 Characterization of DNAzymes 88 3.5 Conclusions 92 Acknowledgments 92 References 92 Contents vii 4 Computational Studies of Artificial Metalloenzymes: From Methods and Models to Design and Optimization 99Jaime Rodriguez-Guerra, Lur Alonso-Cotchico, Giuseppe Sciortino, Agusti Lledos, and Jean-Didier Marechal 4.1 Introduction 99 4.2 From Computational Transition Metal Catalysis to Artificial Metalloenzymes Design 100 4.3 The Toolbox of the Artificial Enzyme Modeler 105 4.3.1 Few Generalities on Molecular Modeling 105 4.3.2 Accurate Physical Models 106 4.3.3 Simplified Physical Models 109 4.3.4 Advantages of MM-Like Methods 109 4.3.5 Hybrid and Multiscale Models 112 4.4 Application of ComputationalMethods to the Optimization and Design of ArtificialMetalloenzymes 113 4.4.1 Modifying Naturally Occurring Metalloenzymes 113 4.4.1.1 Optimizing Biomolecule   Cofactor and Biohybrid   Substrate Binding 113 4.4.1.2 Accounting for Changes in the First Coordination Sphere 115 4.4.1.3 Computational Redesign of Native Metalloenzyme Activity and Selectivity 116 4.4.1.4 Mechanistic Elucidation of Redesigned Metalloenzymes 117 4.4.2 Generation of ArtificialMetalloenzymes from Metal-Free Enzymes 119 4.4.2.1 De Novo ArtificialMetalloenzymes: A General Overview 119 4.4.2.2 The Particularities of De Novo Metalloenzymes 121 4.4.2.3 Protein Interactions with Artificial Cofactors 122 4.4.2.4 Substrate Binding and Complete Mechanism 125 4.5 Outlook 127 4.6 Conclusion 128 Acknowledgments 128 References 129 5 Directed Evolution of Artificial Metalloenzymes: Bridging Synthetic Chemistry and Biology 137Ruijie K. Zhang, David K. Romney, S. B. Jennifer Kan, and Frances H. Arnold 5.1 Evolution Enables Chemical Innovation 137 5.1.1 Strategies for Directed Evolution 138 5.1.2 Directed Evolution as an UphillWalk in the Protein Fitness Landscape 139 5.2 Directed Evolution Applied to Natural Metalloenzymes 140 5.2.1 Enhancing the Stability of a Carbonic Anhydrase 140 5.2.2 Expanding the Scope of P450-Catalyzed Oxidation Reactions 142 5.3 Directed Evolution of Hemoproteins for Abiological Catalysis 144 5.3.1 Nonnatural Carbene Transfer Reactions with Engineered P450BM3 Variants 145 5.3.2 Nonnatural Nitrene Transfer Reactions with Engineered P450BM3 Variants 146 5.3.3 Engineering Cytochrome c for Nonnatural Catalysis 151 5.3.4 Engineering Myoglobin for Nonnatural Catalysis 151 5.3.5 Directed Evolution of Myoglobin-Derived Catalysts Created through Metal-Ion Replacement 154 5.4 Metalloenzymes with Artificial Cofactors or Metal-Binding Sites 155 5.4.1 Artificial Hydrolase with Biotic Metal Ions in De Novo Binding Sites 155 5.4.2 Artificial Hydrogenases Derived from Streptavidin 157 5.4.3 Cross-Coupling with a Pd   Streptavidin Conjugate 160 5.4.4 Alkene Metathesis Catalyzed by an Ru   Streptavidin Conjugate 160 5.4.5 Carbene Transfer with Conjugate of Rhodium and Proline Oligopeptidase 162 5.5 Conclusion 164 Acknowledgments 166 References 166 6 Artificial Metalloenzymes for Hydrogenation and Transfer Hydrogenation Reactions 171Manuel Basauri-Molina and Robertus J. M. Klein Gebbink 6.1 Impact of Metallohydrogenases in the Field of Artificial Metalloenzymes 171 6.2 Biotinylated Metal Complexes in Avidin and Streptavidin 173 6.2.1 Hydrogenation of N-Protected Amino Acids 173 6.2.2 Transfer Hydrogenation of Ketones 178 6.2.3 Transfer Hydrogenation of Imines 180 6.2.4 ATHases in Cascade Reactions 182 6.3 Artificial Enzymes with Covalent Metalloprotein Constitution 184 6.3.1 Papain and Photoactive Yellow Protein 184 6.3.2 Serine Proteases 188 6.3.3 Human Carbonic Anhydrase 191 6.4 Chemocatalysts Embedded in Protein Motifs 191 6.5 Conclusions 193 References 194 7 Hybrid Catalysts for Oxidation Reactions 199Christine Cavazza, CarolineMarchi-Delapierre, and StephaneMenage 7.1 Metal Switch 201 7.2 Structural Modulation of Natural Enzymes 201 7.3 Cofactor Replacement: Reconstitution Strategy 206 7.4 Rational Design of Enzymes 209 7.5 De Novo Synthetic Active Site 211 7.6 De Novo Protein Scaffold 216 7.7 Concluding Remarks 219 References 220 8 Hybrid Catalysts as Lewis Acid 225Gerard Roelfes, Ivana Drienovska, and Lara Villarino 8.1 Introduction 225 8.2 C   C Bond-Forming Reactions 225 8.2.1 Diels   Alder Reactions 225 8.2.1.1 DNA-Based Hybrid Catalysts 226 8.2.1.2 Metallopeptide-Based Hybrid Catalyst 231 8.2.1.3 Protein-Based Hybrid Catalysts 231 8.2.2 Conjugate Addition Reactions 236 8.2.2.1 Michael Addition 236 8.2.2.2 Friedel   Crafts Alkylation 238 8.3 C   X Bond-Forming Reactions 240 8.3.1 Oxa-Michael Additions 240 8.3.1.1 DNA-Based Hybrid Catalyst 242 8.3.1.2 Protein-Based Hybrid Catalysts 242 8.3.2 Fluorinations 243 8.4 Hydrolytic Reactions 244 8.4.1 DNA-Based Hybrid Catalyst 244 8.4.2 Protein-Based Hybrid Catalyst 244 8.5 Conclusions and Outlook 246 References 246 9 Hybrid Catalysts for C   H Activation and Other X   H Insertion Reactions 253Thomas R.Ward andMichelaM. Pellizzoni 9.1 General Introduction 253 9.2 ArtificialMetalloenzymes for C   H Insertion 253 9.2.1 Introduction 253 9.2.2 ArtificialMetalloenzymes Based on the Biotin   Streptavidin Technology 254 9.2.3 ArtificialMetalloenzymes Based on the Myoglobin Scaffold 257 9.2.4 ArtificialMetalloenzymes Based on POP Scaffold 260 9.2.4.1 Si   H insertion 260 9.2.4.2 Cyclopropanation 261 9.3 Repurposing Hemoproteins for C   H Insertion Reactions 262 9.3.1 Introduction 262 9.3.2 Cyclopropanation 262 9.3.3 Aziridination 265 9.3.4 C   H Amination 266 9.3.5 N   H Insertion 269 9.3.6 S   H Insertion 271 9.3.7 Sulfimidation 274 9.3.8 Sigmatropic Rearrangement 275 9.3.9 Halogenation 276 9.4 Conclusion 279 References 279 10 Hybrid Catalysts for Other C   C and C   X Bond Formation Reactions 285Peter J. Deuss,Megan V. Doble, Amanda G. Jarvis, and Paul C.J. Kamer 10.1 Introduction 285 10.2 Allylic Substitution 286 10.2.1 Chiral Phosphane Ligands Based on Chiral Building Blocks from Nature 286 10.2.2 Phosphane-Modified Synthetic Polypeptides 287 10.2.3 Phosphane-Modified Proteins 289 10.2.4 Oligonucleotides-Based Hybrid Catalysts 291 10.3 Palladium-Catalyzed Cross-Coupling Reactions 296 10.4 Hydroformylation 302 10.5 Phenylacetylene Polymerization 304 10.6 Olefin Metathesis 307 10.7 Summary and Future Trends 312 Acknowledgments 314 References 314 11 Metal   Enzyme Hybrid Catalysts in Cascade and Multicomponent Processes 321Boi Hoa San, Jess Gusthart, Seung Seo Lee, and Kyeong Kyu Kim 11.1 Introduction 321 11.2 Metal-Based Catalyst Hybrids with Enzymes for Cascade and Multicomponent Processes 322 11.2.1 Gold Nanoparticle-Based Enzyme Hybrid 324 11.2.2 Palladium and Platinum Nanoparticle-Based Enzyme Hybrids 326 11.2.3 Other Metals Used for Metal   Enzyme Hybrid Catalysts 330 11.2.4 Organometallic Material Hybrid with Protein/Enzyme 333 11.3 Design Strategy for Metal   Enzyme Hybrid Catalysts in Multicomponent Cascade Reactions 334 11.3.1 Design Strategies for DevelopingMultistep Reactions in Metal   Enzyme Hybrid Catalysts 335 11.4 Reaction Mechanisms of Metal   Enzyme Hybrid Catalysts in Multicomponent Cascade Reactions 339 11.4.1 Examples of Cascade Reactions 340 11.4.2 Mechanisms of Commonly Used Enzymes 341 11.5 Conclusion and Future Perspectives 343 Acknowledgments 343 References 343 12 Metalloenzyme-Inspired Systems for Alternative Energy Harvest 353Markus D. Karkas, Oscar Verho, and Bjoern Akermark 12.1 Introduction: Artificial Photosynthesis 353 12.2 Hydrogen Evolution 355 12.2.1 Hydrogenases: Iron-Based Metalloenzymes for Hydrogen Evolution 355 12.2.2 Other Metal-Based Biohybrid Systems for Hydrogen Production 363 12.3 Hybrid Systems for OverallWater Splitting 364 12.4 Bioinspired Systems for O2 Reduction 364 12.4.1 Simple Bioelectrodes for Applications in Biosensing 366 12.4.2 Multicatalytic Hybrid Systems for More Efficient Bioelectrodes 367 12.4.3 Future Directions in Bioelectrocatalysis Research 370 12.5 Conclusions and Outlook 372 Acknowledgments 373 References 373 13 Synthesis and Application of Hybrid Catalysts with Metalloenzyme-Like Properties 383Jose M. Palomo 13.1 Introduction 383 13.2 Synthesis of Pd Nanobiohybrids (Pd(0)NPs-Enzyme Hybrids) 384 13.3 Synthesis of Au Nanobiohybrids 387 13.4 Synthesis of Ag Nanobiohybrids 391 13.5 Synthesis of Cu Nanobiohybrids 392 13.6 Synthesis of Pt Nanobiohybrids 394 13.7 Chemical Applications of Nanobiohybrids 395 13.7.1 Synergistic Effect 396 13.7.2 Dual Activity in Cascade Processes 396 13.8 Conclusions 399 Acknowledgments 400 References 400 Index 405