Bioinorganic Chemistry: A Survey

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1 Bioinorganic Chemistry: A Survey

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3 Bioinorganic Chemistry: A Survey Eiichiro Ochiai AMSTERDAM BOSTON HEIDELBERG LONDON OXFORD NEW YORK PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO Academic Press is an imprint of Elsevier

4 Cover Design: Joanne Blank Cover Image Ei-Ichiro Ochiai Academic Press is an imprint of Elsevier 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, California , USA 84 Theobald s Road, London WC1X 8RR, UK Copyright 2008, Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permissions may be sought directly from Elsevier s Science & Technology Rights Department in Oxford, UK: phone: ( 44) , fax: ( 44) , permissions@elsevier.com. You may also complete your request online via the Elsevier homepage ( ), by selecting Support & Contact then Copyright and Permission and then Obtaining Permissions. Library of Congress Cataloging-in-Publication Data Application Submitted British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. ISBN: For information on all Academic Press publications visit our Web site at Typeset by Charon Tec Ltd., A Macmillan Company ( Printed in China

5 Contents Preface xiii Introduction: Basics of Bio/Ecosystems and Biochemistry, and Other Basic Concepts 1 Biosphere (Ecosystem) 1 Components of the Biosphere Living Organisms 1 Bodily Structures of Living Organisms 3 Cells, the Basic Functional Units of Living Organisms 3 Biochemical Compounds Essential to Life 4 Carbohydrates 5 Monosaccharides 5 Polysaccharides and Derivatives 7 Lipids 8 Fats and Phospholipids 9 Steroids 10 Proteins and Amino Acids 10 Structures 10 Reactions Formation and Hydrolysis of Protein 16 Vitamins (Coenzymes), Nucleotides, and Others 17 Coenzymes 17 Nucleotides 18 Other Vitamins 19 DNA/RNA (Polynucleotide) 19 Structures 19 Reactions 23 Types of Biochemical Reactions 24 Reactions of Acid-Base Type 24 Reactions of Oxidation-Reduction Type 25 The Idea of Oxidation State 26 The Oxidation State of C in Organic Compounds and Recognition of Oxidation-Reduction Reactions 26 Other Kinds of Oxidation-Reduction Reactions 29 Free Radical Reactions 30 Transition State Theory of Reaction, and Enzyme Kinetics 30 Energy Profile and Transition State Theory of Reaction 31 Enzyme Kinetics 32 Enzyme Reaction Mechanism 33 CHAPTER 1 The Distribution of Elements The Distribution of Elements in the Earth s Crust, Seawater, and Organisms The Engines That Drive the Biochemical Cycling of the Elements 41 v

6 vi Contents 1.3. Flow of the Elements Biogeochemical Cycling Historical Change in the Biogeochemical Cycling of Elements 45 CHAPTER 2 Biological Needs for and the Behaviors of Inorganic Elements Introduction Inorganic Elements in the Biological Systems Inorganic Elements Involved at the Molecular Level Inorganic Elements Involved at the Cellular Level Inorganic Elements Involved at the Physiological Level Biological Systems Involved in the Metabolism of Inorganic Elements Why Has a Specific Organism Chosen Specific Elements for Its Specific Needs? Behaviors of Inorganic Elements-I: Fundamentals of Coordination Chemistry Coordination Compounds or Metal Complexes Ligand Field Theory How the Predominant Structure Is Determined Thermodynamic Tendency to Form Coordination Compounds Chelate Effect Ligand Substitution Reactions Kinetic Factors Oxidation Reduction and Reduction Potential Behaviors of Inorganic Elements-II: Basics of Organometallic Chemistry Metal Carbonyls and the 18-Electron (18 e ) Rule Other Organometallic Compounds Some Special Types of Reactions Involving Organometallic Compounds 76 CHAPTER 3 How Do Enzymes Work? Enzymatic Enhancement of Reaction Rate: General Considerations Transition State Theory The Dynamic Effects A Composite Theory Metalloenzymes/Proteins and Metal-Activated Enzymes 89 CHAPTER 4 Reactions of Acid-Base Type and the Functions of Metal Cations General Considerations Different Types (Definitions) of Acid-Base Reactions of Acid-Base Type Catalyzed by Enzymes Acidity Scale and Acid Character of Metal Cations: Prominence of Zn(II) and Mg(II) Kinetic Factors Enhancement of Reaction by Protein Residues Mg(II)-Dependent Enzymes Rubisco (Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase) Pyruvate Kinase Zn(II)-Dependent Enzymes Carbonic Anhydrase 103

7 Contents vii Thermolysin, Carboxypeptidase A, and Others Leucine Aminopeptidase Alkaline Phosphatase and Purple Acid Phosphatase Alcohol Dehydrogenase Other Metal Cation-Dependent Acid-Base Enzymes Aconitase, an Iron-Sulfur Enzyme, and Others Arginase: Mn Enzyme Urease and Other Ni Enzymes Structural Effects of Metal Ions Metal Ions and Polynucleic Acids (DNA and RNA) General Characteristics of Interactions of Metal Ions with Polynucleotides Effects on Structures Catalytic Metal Ions in DNA Polymerases and Nucleases Gene Regulation and Metal Ions Ribozymes 117 CHAPTER 5 Reactions of Oxidation Reduction Type Including Electron Transfer Processes General Consideration Reduction Potential Heme Proteins and Enzymes Iron-Sulfur Proteins Copper Proteins Molybdenum and Tungsten Proteins Kinetic Factors Electron Transfer between and in Protein(s) Iron Enzymes and Proteins Cytochromes and Iron-Sulfur Electron Transfer Proteins Nitrite Reductase and Nitric Oxide Reductase Horseradish Peroxidase (HRP), Catalase, and Cytochrome C Peroxidase Hydrogenase Copper Enzymes and Proteins Blue Copper Proteins Blue Copper Oxidases Cytochrome C Oxidase Nitrite Reductase and Nitrous Oxide Reductase Amine Oxidases Superoxide Dismutase (SOD) Molybdenum Enzymes and Tungsten Enzymes Xanthine Oxidase and Aldehyde Oxidase Sulfite Oxidase and Nitrate Reductase (Assimilatory) DMSO Reductase and Nitrate Reductase (Respiratory or Dissimilatory) Tungsten Enzymes Manganese Oxidoreductases 150

8 viii Contents Manganese Catalase Water Oxidase Ni-Containing Redox Enzymes Ni-Fe (Se) Hydrogenase Carbon Monoxide Dehydrogenase (CODH) Acetyl CoA Synthase (ACS) Methyl-Coenzyme M Reductase 156 CHAPTER 6 Oxygen Carrying Processes and Oxygenation Reactions The Chemistry of Oxygen, Dioxygen, and Related Entities Electronic Structures Basic Reactions of O and O Reactions of Ground State O and O Interactions of Ground State O 2 with Compounds of Transition Metals Reactions of Oxygen Derivatives Reversible O 2 Binding: Oxygen Carriers Monooxygenases Monooxygenases Dependent on Cytochrome P Nonheme Mononuclear Iron Monooxygenases Nonheme Dinuclear Iron Monooxygenases Copper Monooxygenases Dioxygenases Prostaglandin Endoperoxide Synthase 181 CHAPTER 7 Metal-Involving Free Radical Reactions A Survey of Biologically Relevant Free Radicals Why Radicals? Reactivities of Free Radicals B 12 -Coenzyme (Adenosylcobalamin)-Dependent Enzymes Mutases, Diol Dehydratase, and Ethanolamine Ammonia Lyase Homolytic Cleavage of the Cobalt-to-Carbon Bond upon Binding a Substrate Hydrogen Abstraction from Substrates ,2-Shift or Other Reactions of Substrate Free Radicals Ribonucleotide Reductases (Cobalamin-Dependent) S-Adenosyl Methionine (SAM)-Dependent Enzymes Iron-Dependent Ribonucleotide Reductases Galactose Oxidase Other Examples 203 CHAPTER 8 Nitrogen Fixation Nitrogen Metabolism Chemistry of N 2 Reduction 206

9 Contents ix 8.3. Mo-Dependent Nitrogenase Other Nitrogenases 214 CHAPTER 9 Other Essential Elements Introduction Biochemistry of Nitrogen Compounds Biochemistry of Phosphorus Biochemistry of Sulfur Compounds Cellular Processes Marine Biogeochemical Cycling Selenium Chemistry of Selenium as Compared to That of Sulfur Glutathione and Selenium: Glutathione Peroxidase Thioredoxin Reductase Other Selenium-Containing Proteins and Enzymes Boron Silicon Chemistry of Silicon Frustules of Diatoms Spicules in Sponge Other Biological Functions of Silicon Vanadium Vanabins Amavadin Haloperoxidases Chromium Halogens and the Like Formation of Volatile Halocarbons in Macroalgae HOX Formation in Mammals and Others Formation of HOX by a Fungal Chloroperoxidase Formation of HOX by Mammalian Peroxidases 237 CHAPTER 10 Metal-Related Physiology Metabolism of Metallic Elements Iron Metabolism (in Mammals) Ferric Reductase Divalent Metal Transporter (DMT1) Ferroxidase Transferrin (Tf) and Transferrin Receptor (TfR) Ferritin Ferroportin (Fpn)/Hepcidin Regulation of Ferritin and Transferrin 249

10 x Contents Iron Metabolism in Bacteria, Fungi, and Plants Copper Metabolism Outline of Copper Metabolism in Mammals Copper Metabolism in Bacteria and Plants Zinc Metabolism In Mammals In E. coli A Mg(II) Transporter Physiological Roles Played by Metallic Elements Na/K-ATPase and Ca-ATPase Mechanism Ion Selectivity in Metal Ion Transporters and Channels A General Discussion Ca(II) Second Messenger and Other Functions Control of Cytoplasmic Ca(II) Concentration Basic Mechanisms of Ca(II) Physiology Synaptotagmin, an Example of Physiology Mediated by Ca(II) Why Calcium(II)? Zinc-Enriched Neuron (ZEN) Sensors for Small Molecules Oxygen Sensors CO-Sensors NO-Sensors H 2 -Sensors Redox Sensors Plant Hormone Ethylene and Copper Magnetic Navigation Radiation Shields Biological Skeletons (Biominerals) Calcium Carbonate Calcium Oxalate Calcium Phosphate 275 CHAPTER 11 Environmental Bioinorganic Chemistry General Considerations Toxicity of Inorganic Compounds Abundance and Toxicity Toxicity of Reactive Oxygen Species, and Defense Mechanisms Against Them Molecular Mechanisms of Toxicity of Inorganic Compounds Discrimination of Elements by Organisms General Considerations Oxidative Stress and Metals and As General Effects Individual Element s (Acute) Toxicity Cd(II) and Hg(II) 290

11 Contents xi Pb(II) Organometallic Compounds Organotin Compounds Be(II), Al(III) Tl(I) Cr Ni(II) Anions Alzheimer s Disease and Metals Biological Defenses against Toxicity Biological Defense against Mercury Metallothioneins and Phytochelatins Metallothioneins Copper-Thionein (Cu-MT) Phytochelatins Use of Sulfide Defense against Lead Biotransformation of Arsenic Bioremediaion of Metals Biosorption by Brown Algae and by Microbial Surfactants Phytoremediation (Phytoextraction of Metals from Soil) Phytoextraction by Microalgae (Remediation of Polluted Water) Other Types of Bioremediation 308 CHAPTER 12 Medical Applications of Inorganic Compounds: Medicinal Inorganic Chemistry Introduction Cancer Therapy Platinum Compounds Bleomycin Radioactive Pharmaceuticals Gold Compounds for Rheumatoid Arthritis Vanadium Compounds for Diabetes Lithium Compounds for Psychiatric Disorders Other Potential Drugs Containing Inorganic Compounds Diagnostic (Imaging) Agents Gd(III)-Contrasting Agents for MRI m Tc-Radioactive Diagnostic Pharmaceuticals 324 Appendix 327 References 329 Index 351

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13 Preface Bioinorganic chemistry as a discipline is now two and a half decades old, if we consider its birth to be the first International Conference on Bioinorganic Chemistry (ICBIC) held in Florence, Italy in I wrote one of the earliest books on the subject, Bioinorganic Chemistry, an Introduction (Allyn and Bacon) in The emphasis there was on physicochemical data and their interpretations. Since then the scope of research on bioinorganic chemistry has greatly expanded, diversified, and deepened, and the quantity of the literature has exploded. This book does not attempt to summarize the current status of research in all the various areas of the field. It also omits discussion of the methods of research, and hardly deals with biophysical data. For experimental methods, readers are referred to works such as L. Que s Physical Methods in Bioinorganic Chemistry (2000) and an ACS publication, Spectroscopic Methods in Bioinorganic Chemistry (2003); and some textbooks including the ones by J. Cowan, Inorganic Biochemistry, 3 rd ed., Wiley-VCH (2007) and R. M. Roat- Malone, Bioinorganic Chemistry, Wiley-Interscience (2002). Instead of research details, this book aims to provide general readers as well as specialists with an understanding of the basic chemistry of interactions of inorganic substances with biological systems at the molecular level (as much as possible), and also a perspective on the subject, as the subtitle A Survey implies. Since living organisms and the biosphere they constitute are both open systems, they are in contact with and constantly exchanging energy and material with their environments. The environments experienced by a single organism include all the other organisms and the physical environment, which is composed of inorganic substances. This fundamental situation inevitably entails the inclusion of almost all inorganic elements in living organisms. Hence bioinorganic chemistry, or rather what it implies, is not a novelty but a necessity, and should be universal. Indeed we are increasingly being made aware of the fact that inorganic compounds are intimately associated with all biological phenomena. My second book ( The General Principles of Biochemistry of the Elements, Plenum Press, 1987) attempted to lay down several basic principles in order to answer some fundamental questions such as why iron is used for this purpose, and not copper. The present work is to try to extend these ideas while incorporating some of the more recent discoveries. xiii

14 xiv Preface This book looks at the entire picture of the existence of organisms on Earth in terms of chemistry molecules/compounds, their interactions and reactions, and the roles that inorganic elements play and why. The Introduction and the first two chapters give fundamentals of interactions between the biosphere and inorganic compounds from the molecular level to the geochemical level. The Introduction is a brief review of basic concepts of biochemistry, and can be skipped or can be used as a Glossary. Chapter 1 is an overview of biogeochemical aspects of bioinorganic chemistry, and Chapter 2 gives a brief introduction to relevant inorganic chemistry. Chapter 3 is a discussion of the basic issue of why enzymes are so efficient. The information discussed here is not indispensable for understanding the rest of the book, so it can be skipped if circumstances require. Chapters 4 through 9 are concerned mainly with the chemical bases of functions of inorganic elements associated with enzymes and proteins. Chapter 10 deals with workings of inorganic compounds at physiological levels, and Chapter 11 treats the environmental issues including toxicity associated with inorganic elements. The last chapter deals with the medicinal applications of inorganic elements. Two different kinds of exercises are provided at the end of each chapter review questions and problems to explore. Both types of exercises are in line with the spirit of this book; they concern chemical principles of the interactions of inorganic chemicals with the biological systems at a molecular level, without discussing experimental data. Therefore, no question is provided regarding experimental data such as kinetic and spectroscopic data. Such questions, if necessary and appropriate, need to be provided by the instructors. As the volume of relevant literature has become enormous and more details have become available, a single author surely has the difficulty of being sufficiently versed in each and every area of current research. No single book would be able to cover every aspect of the bioinorganic chemistry of even a single element such as calcium in full detail, let alone that of all the significant elements. However, that is in essence what I have tried to do, but not in full detail. In writing this book, I have relied heavily on some excellent summaries in the form of review articles written by experts in each field. I am much indebted to them, and would like to express my gratitude to all those researchers who have contributed to a better understanding of these fascinating aspects of chemical biology.

15 Preface xv One of the results of technical advances made in recent decades is an increase in the structural data on proteins (and nucleic acids), and their accessibility through the PDB (Protein Data Bank). Individual researchers and students alike can now explore protein structures in detail. The availability of the PDB has been of enormous help in writing this book. In addition, several other Internet sites have proven very useful; in particular, the general literature search engines called Scopus and ScienceDirect have been indispensable in writing a book of this nature. I would like to express my gratitude to those individuals and organizations that are responsible for providing such readily accessible databases. This book concludes my efforts over the last three decades to survey the fascinating subject of bioinorganic chemistry. I gratefully acknowledge the comments and suggestions by reviewers: R. J. P. Williams of Oxford University, C. Frank Shaw, III. of Illinois State University, and Murray S. Davies of James Cook Univeristy, Australia. Their comments have improved the manuscript. I also acknowledge gratefully the assistance of J. Woodling of Juniata College Library in finding literature.