Coordination chemistry in protein cages principles design and applications

COORDINATION CHEMISTRY IN PROTEIN CAGES COORDINATION CHEMISTRY IN PROTEIN CAGES Principles, Design, and Applications Edited by TAKAFUMI UENO YOSHIHITO WATANABE Copyright C 2013 by John Wiley & Sons, Inc All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River 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Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic formats For more information about Wiley products, visit our web site at www.wiley.com Library of Congress Cataloging-in-Publication Data: Coordination chemistry in protein cages principles, design, and applications / edited by Takafumi Ueno, Yoshihito Watanabe pages cm Includes index ISBN 978-1-118-07857-0 (cloth) Protein drugs Protein drugs–Physiological transport Carrier proteins I Ueno, Takafumi, 1971– editor of compilation II Watanabe, Yoshihito, editor of compilation RS431.P75C66 2013 615.1 9–dc23 2012045122 Printed in the United States of America ISBN: 9781118078570 10 CONTENTS Foreword Preface Contributors xiii xv xvii PART I COORDINATION CHEMISTRY IN NATIVE PROTEIN CAGES The Chemistry of Nature’s Iron Biominerals in Ferritin Protein Nanocages Elizabeth C Theil and Rabindra K Behera 1.1 Introduction 1.2 Ferritin Ion Channels and Ion Entry 1.2.1 Maxi- and Mini-Ferritin 1.2.2 Iron Entry 1.3 Ferritin Catalysis 1.3.1 Spectroscopic Characterization of ␮-1,2 Peroxodiferric Intermediate (DFP) 1.3.2 Kinetics of DFP Formation and Decay 1.4 Protein-Based Ferritin Mineral Nucleation and Mineral Growth 1.5 Iron Exit 1.6 Synthetic Uses of Ferritin Protein Nanocages 1.6.1 Nanomaterials Synthesized in Ferritins 6 8 12 13 16 17 18 v vi CONTENTS 1.6.2 Ferritin Protein Cages in Metalloorganic Catalysis and Nanoelectronics 1.6.3 Imaging and Drug Delivery Agents Produced in Ferritins 1.7 Summary and Perspectives Acknowledgments References Molecular Metal Oxides in Protein Cages/Cavities 19 19 20 20 21 25 Achim Măuller and Dieter Rehder 2.1 Introduction 2.2 Vanadium: Functional Oligovanadates and Storage of VO2+ in Vanabins 2.3 Molybdenum and Tungsten: Nucleation Process in a Protein Cavity 2.4 Manganese in Photosystem II 2.5 Iron: Ferritins, DPS Proteins, Frataxins, and Magnetite 2.6 Some General Remarks: Oxides and Sulfides References 25 26 28 33 35 38 38 PART II DESIGN OF METALLOPROTEIN CAGES De Novo Design of Protein Cages to Accommodate Metal Cofactors 45 Flavia Nastri, Rosa Bruni, Ornella Maglio, and Angela Lombardi 3.1 Introduction 3.2 De Novo-Designed Protein Cages Housing Mononuclear Metal Cofactors 3.3 De Novo-Designed Protein Cages Housing Dinuclear Metal Cofactors 3.4 De Novo-Designed Protein Cages Housing Heme Cofactor 3.5 Summary and Perspectives Acknowledgments References Generation of Functionalized Biomolecules Using Hemoprotein Matrices with Small Protein Cavities for Incorporation of Cofactors 45 47 59 66 79 79 80 87 Takashi Hayashi 4.1 Introduction 4.2 Hemoprotein Reconstitution with an Artificial Metal Complex 4.3 Modulation of the O2 Affinity of Myoglobin 87 89 90 CONTENTS 4.4 Conversion of Myoglobin into Peroxidase 4.4.1 Construction of a Substrate-Binding Site Near the Heme Pocket 4.4.2 Replacement of Native Heme with Iron Porphyrinoid in Myoglobin 4.4.3 Other Systems Used in Enhancement of Peroxidase Activity of Myoglobin 4.5 Modulation of Peroxidase Activity of HRP 4.6 Myoglobin Reconstituted with a Schiff Base Metal Complex 4.7 A Reductase Model Using Reconstituted Myoglobin 4.7.1 Hydrogenation Catalyzed by Cobalt Myoglobin 4.7.2 A Model of Hydrogenase Using the Heme Pocket of Cytochrome c 4.8 Summary and Perspectives Acknowledgments References Rational Design of Protein Cages for Alternative Enzymatic Functions vii 95 95 99 100 102 103 106 106 107 108 108 108 111 Nicholas M Marshall, Kyle D Miner, Tiffany D Wilson, and Yi Lu 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 5.10 Introduction Mononuclear Electron Transfer Cupredoxin Proteins CuA Proteins Catalytic Copper Proteins 5.4.1 Type Red Copper Sites 5.4.2 Other T2 Copper Sites 5.4.3 Cu, Zn Superoxide Dismutase 5.4.4 Multicopper Oxygenases and Oxidases Heme-Based Enzymes 5.5.1 Mb-Based Peroxidase and P450 Mimics 5.5.2 Mimicking Oxidases in Mb 5.5.3 Mimicking NOR Enzymes in Mb 5.5.4 Engineering Peroxidase Proteins 5.5.5 Engineering Cytochrome P450s Non-Heme ET Proteins Fe and Mn Superoxide Dismutase Non-Heme Fe Catalysts Zinc Proteins Other Metalloproteins 5.10.1 Cobalt Proteins 5.10.2 Manganese Proteins 5.10.3 Molybdenum Proteins 5.10.4 Nickel Proteins 111 112 116 118 118 120 121 122 124 124 125 127 128 129 131 132 133 134 135 135 136 137 137 viii CONTENTS 5.10.5 Uranyl Proteins 5.10.6 Vanadium Proteins 5.11 Summary and Perspectives References 138 138 139 142 PART III COORDINATION CHEMISTRY OF PROTEIN ASSEMBLY CAGES Metal-Directed and Templated Assembly of Protein Superstructures and Cages 151 F Akif Tezcan 6.1 Introduction 6.2 Metal-Directed Protein Self-Assembly 6.2.1 Background 6.2.2 Design Considerations for Metal-Directed Protein Self-Assembly 6.2.3 Interfacing Non-Natural Chelates with MDPSA 6.2.4 Crystallographic Applications of Metal-Directed Protein Self-Assembly 6.3 Metal-Templated Interface Redesign 6.3.1 Background 6.3.2 Construction of a Zn-Selective Tetrameric Protein Complex Through MeTIR 6.3.3 Construction of a Zn-Selective Protein Dimerization Motif Through MeTIR 6.4 Summary and Perspectives Acknowledgments References Catalytic Reactions Promoted in Protein Assembly Cages 151 152 152 153 155 159 162 162 163 166 170 171 171 175 Takafumi Ueno and Satoshi Abe 7.1 Introduction 7.1.1 Incorporation of Metal Compounds 7.1.2 Insight into Accumulation Process of Metal Compounds 7.2 Ferritin as a Platform for Coordination Chemistry 7.3 Catalytic Reactions in Ferritin 7.3.1 Olefin Hydrogenation 7.3.2 Suzuki–Miyaura Coupling Reaction in Protein Cages 7.3.3 Polymer Synthesis in Protein Cages 7.4 Coordination Processes in Ferritin 7.4.1 Accumulation of Metal Ions 7.4.2 Accumulation of Metal Complexes 175 176 177 177 179 179 182 185 188 188 192 CONTENTS 7.5 Coordination Arrangements in Designed Ferritin Cages 7.6 Summary and Perspectives Acknowledgments References Metal-Catalyzed Organic Transformations Inside a Protein Scaffold Using Artificial Metalloenzymes ix 194 197 198 198 203 V K K Praneeth and Thomas R Ward 8.1 Introduction 8.2 Enantioselective Reduction Reactions Catalyzed by Artificial Metalloenzymes 8.2.1 Asymmetric Hydrogenation 8.2.2 Asymmetric Transfer Hydrogenation of Ketones 8.2.3 Artificial Transfer Hydrogenation of Cyclic Imines 8.3 Palladium-Catalyzed Allylic Alkylation 8.4 Oxidation Reaction Catalyzed by Artificial Metalloenzymes 8.4.1 Artificial Sulfoxidase 8.4.2 Asymmetric cis-Dihydroxylation 8.5 Summary and Perspectives References PART IV 203 204 204 206 208 211 212 212 215 216 218 APPLICATIONS IN BIOLOGY Selective Labeling and Imaging of Protein Using Metal Complex 223 Yasutaka Kurishita and Itaru Hamachi 9.1 Introduction 9.2 Tag–Probe Pair Method Using Metal-Chelation System 9.2.1 Tetracysteine Motif/Arsenical Compounds Pair 9.2.2 Oligo-Histidine Tag/Ni(ii)-NTA Pair 9.2.3 Oligo-Aspartate Tag/Zn(ii)-DpaTyr Pair 9.2.4 Lanthanide-binding Tag 9.3 Summary and Perspectives References 10 Molecular Bioengineering of Magnetosomes for Biotechnological Applications 223 225 225 227 230 235 237 237 241 Atsushi Arakaki, Michiko Nemoto, and Tadashi Matsunaga 10.1 Introduction 10.2 Magnetite Biomineralization Mechanism in Magnetosome 10.2.1 Diversity of Magnetotactic Bacteria 241 242 242 x CONTENTS 10.2.2 Genome and Proteome Analyses of Magnetotactic Bacteria 10.2.3 Magnetosome Formation Mechanism 10.2.4 Morphological Control of Magnetite Crystal in Magnetosomes 10.3 Functional Design of Magnetosomes 10.3.1 Protein Display on Magnetosome by Gene Fusion Technique 10.3.2 Magnetosome Surface Modification by In Vitro System 10.3.3 Protein-mediated Morphological Control of Magnetite Particles 10.4 Application 10.4.1 Enzymatic Bioassays 10.4.2 Cell Separation 10.4.3 DNA Extraction 10.4.4 Bioremediation 10.5 Summary and Perspectives Acknowledgments References PART V 11 244 246 250 251 252 255 257 258 259 260 262 264 266 266 266 APPLICATIONS IN NANOTECHNOLOGY Protein Cage Nanoparticles for Hybrid Inorganic–Organic Materials 275 Shefah Qazi, Janice Lucon, Masaki Uchida, and Trevor Douglas 11.1 Introduction 11.2 Biomineral Formation in Protein Cage Architectures 11.2.1 Introduction 11.2.2 Mineralization 11.2.3 Model for Synthetic Nucleation-Driven Mineralization 11.2.4 Mineralization in Dps: A 12-Subunit Protein Cage 11.2.5 Icosahedral Protein Cages: Viruses 11.2.6 Nucleation of Inorganic Nanoparticles Within Icosahedral Viruses 11.3 Polymer Formation Inside Protein Cage Nanoparticles 11.3.1 Introduction 11.3.2 Azide–Alkyne Click Chemistry in sHsp and P22 11.3.3 Atom Transfer Radical Polymerization in P22 11.3.4 Application as Magnetic Resonance Imaging Contrast Agents 275 277 277 278 279 279 282 282 283 283 285 287 290 CONTENTS 11.4 Coordination Polymers in Protein Cages 11.4.1 Introduction 11.4.2 Metal–Organic Branched Polymer Synthesis by Preforming Complexes 11.4.3 Coordination Polymer Formation from Ditopic Ligands and Metal Ions 11.4.4 Altering Protein Dynamics by Coordination: Hsp-Phen-Fe 11.5 Summary and Perspectives Acknowledgments References 12 Nanoparticles Synthesized and Delivered by Protein in the Field of Nanotechnology Applications xi 292 292 292 295 296 298 298 298 305 Ichiro Yamashita, Kenji Iwahori, Bin Zheng, and Shinya Kumagai 12.1 Nanoparticle Synthesis in a Bio-Template 12.1.1 NP Synthesis by Cage-Shaped Proteins for Nanoelectronic Devices and Other Applications 12.1.2 Metal Oxide or Hydro-Oxide NP Synthesis in the Apoferritin Cavity 12.1.3 Compound Semiconductor NP Synthesis in the Apoferritin Cavity 12.1.4 NP Synthesis in the Apoferritin with the Metal-Binding Peptides 12.2 Site-Directed Placement of NPs 12.2.1 Nanopositioning of Cage-Shaped Proteins 12.2.2 Nanopositioning of Au NPs by Porter Proteins 12.3 Fabrication of Nanodevices by the NP and Protein Conjugates 12.3.1 Fabrication of Floating Nanodot Gate Memory 12.3.2 Fabrication of Single-Electron Transistor Using Ferritin References 13 Engineered “Cages” for Design of Nanostructured Inorganic Materials 305 305 307 308 311 312 312 313 317 318 321 326 329 Patrick B Dennis, Joseph M Slocik, and Rajesh R Naik 13.1 13.2 13.3 13.4 13.5 13.6 Introduction Metal-Binding Peptides Discrete Protein Cages Heat-Shock Proteins Polymeric Protein and Carbohydrate Quasi-Cages Summary and Perspectives References 329 331 332 334 340 346 347 ... Japan PART I COORDINATION CHEMISTRY IN NATIVE PROTEIN CAGES Coordination Chemistry in Protein Cages: Principles, Design, and Applications, First Edition Edited by Takafumi Ueno and Yoshihito... (2) Design of Metalloprotein Cages, (3) Coordination Chemistry of Protein Assembly Cages, (4) Applications in Biology, (5) Applications in Nanotechnology, and (6) Coordination Chemistry Inspired... I COORDINATION CHEMISTRY IN NATIVE PROTEIN CAGES The Chemistry of Nature’s Iron Biominerals in Ferritin Protein Nanocages Elizabeth C Theil and Rabindra K Behera 1.1 Introduction 1.2 Ferritin