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Searching... | 30000010253932 | QP623.5.C36 M48 2011 | Open Access Book | Book | Searching... |
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Summary
Summary
This series is no longer available from the Royal Society of Chemistry. Information on the series can now be found at www.bioinorganic-chemistry.org/mils.
Author Notes
Astrid Sigel has studied languages and was an editor of the Metal Ions in Biological Systems series (until Volume 44) and also of the Handbooks on Toxicity of Inorganic Compounds (1988), on Metals in Clinical and Analytical Chemistry (1994; both with H. G. Seiler) and on Metalloproteins (2001; with Ivano Bertini).
Helmut Sigel is Emeritus Professor (2003) of Inorganic Chemistry at the University of Basel, Switzerland, and a previous editor of the MIBS series until Volume 44. He serves on various editorial and advisory boards, published over 300 articles on metal ion complexes of nucleotides, coenzymes, and other ligands of biological relevance, and lectured worldwide. He was named Protagonist in Chemistry (2002) by ICA (issue 339); among further honors are the P. Ray Award (Indian Chemical Society, of which he is also an Honorary Fellow), the Alfred Werner Prize (Swiss Chemical Society), a Doctor of Science honoris causa degree (Kalyani University, India), appointments as Visiting Professor (e.g., Austria, China, Japan, Kuwait, UK) and Endowed Lectureships.
Roland K. O. Sigel is Associate Professor (2009) of Inorganic Chemistry at the University of Zrich, Switzerland. From 2003 to 2008 he was endowed with a Frderungsprofessur of the Swiss National Science Foundation and he is a recipent of an ERC Starting Grant 2010. He received his doctoral degree summa cum laude (1999) from the University of Dortmund, Germany, working with Bernhard Lippert. Thereafter he spent nearly three years at Columbia University, New York, USA, with Anna Marie Pyle (now Yale University). During the six years abroad he received several prestigious fellowships from various sources, and he was awarded the EuroBIC Medal in 2008 and the Alfred Werner Prize (SCS) in 2009. His research focuses on the structural and catalytic role of metal ions in ribozymes, especially group II introns, and on related topics. He was also an editor of Volumes 43 and 44 of the MIBS series.
Table of Contents
Historical Development and Perspectives of the Series | p. v |
Preface to Volume 9 | p. vii |
Contributors to Volume 9 | p. xvii |
Titles of Volumes 1-44 in the Metal Ions in Biological Systems Series | p. xxi |
Contents of Volumes in the Metal Ions in Life Sciences Series | p. xxiii |
1 Metal Ion Binding to RNA | p. 1 |
Abstract | p. 2 |
1 Introduction | p. 3 |
2 Details of Ion Coordination | p. 3 |
3 Physiological Relevance of Metal Ions | p. 5 |
4 Monovalent Cations | p. 6 |
5 Divalent Cations | p. 10 |
6 Trivalent Cations | p. 20 |
7 Other Trivalent and Tetravalent Cations | p. 24 |
8 Anions | p. 25 |
9 Subjectivity in the Structure Determination Process | p. 26 |
10 Summary | p. 26 |
Acknowledgments | p. 28 |
Abbreviations and Definitions | p. 28 |
References | p. 29 |
2 Methods to Detect and Characterize Metal Ion Binding Sites in RNA | p. 37 |
Abstract | p. 39 |
1 Introduction | p. 39 |
2 General Considerations | p. 40 |
3 Spectroscopic Methods | p. 46 |
4 Chemical and Biochemical Methods | p. 67 |
5 Computational Methods | p. 80 |
6 Calculation of Binding Constants | p. 85 |
7 Concluding Remarks and Future Directions | p. 89 |
Acknowledgments | p. 90 |
Abbreviations | p. 90 |
References | p. 91 |
3 Importance of Diffuse Metal Ion Binding to RNA | p. 101 |
Abstract | p. 102 |
1 Introduction | p. 102 |
2 Diffuse Ions Provide a Significant Stabilizing Force for RNA Structure | p. 103 |
3 Diffuse Ion is Critical to RNA Folding Kinetics | p. 110 |
4 Theoretical Predictions for the Diffuse Ion Binding to RNAs | p. 113 |
5 Correlated Distribution of Multivalent Diffuse Ions: Theory Versus Experiment | p. 115 |
6 General Conclusions | p. 119 |
Acknowledgments | p. 120 |
Abbreviations | p. 120 |
References | p. 121 |
4 RNA Quadruplexes | p. 125 |
Abstract | p. 125 |
1 Introduction To RNA Quadruplexes | p. 126 |
2 Thermodynamic Stability | p. 127 |
3 Conformational Variations | p. 130 |
4 Biological Function | p. 130 |
5 Conclusions | p. 135 |
Acknowledgment | p. 136 |
Abbreviations | p. 136 |
References | p. 137 |
5 The Roles of Metal Ions in Regulation by Riboswitches | p. 141 |
Abstract | p. 142 |
1 Introduction | p. 142 |
2 Metal Ions that Assist Recognition of Riboswitch Ligands | p. 145 |
3 Metal Ions and Riboswitch Folding | p. 151 |
4 Magnesium-Sensing Riboswitches: Salmonella mgiA | p. 154 |
5 Magnesium-Sensing Riboswitches: The M-Box RNA | p. 161 |
6 Are There Additional Classes of Metal-Sensing Riboswitches? | p. 168 |
Acknowledgments | p. 169 |
Abbreviations | p. 169 |
References | p. 170 |
6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymes | p. 175 |
Abstract | p. 176 |
1 Introduction | p. 176 |
2 Interactions Between Metal Ions and Small Ribozymes | p. 178 |
3 Roles of Metal Ions in Small Ribozymes | p. 183 |
4 Concluding Remarks and Future Directions | p. 189 |
Acknowledgment | p. 190 |
Abbreviations and Definitions | p. 190 |
References | p. 191 |
7 Multiple Roles of Metal Ions in Large Ribozymes | p. 197 |
Abstract | p. 198 |
1 Introduction | p. 198 |
2 Metal Ions in Folding and Catalysis: A Brief Overview | p. 200 |
3 Group I Intron Ribozymes | p. 205 |
4 Group II Intron Ribozymes | p. 212 |
5 RNase P | p. 221 |
6 Concluding Remarks | p. 226 |
Acknowledgments | p. 227 |
Abbreviations | p. 227 |
References | p. 228 |
8 The Spliceosome and Its Metal Ions | p. 235 |
Abstract | p. 235 |
1 Introduction | p. 236 |
2 The Pre-mRNA Splicing Mechanism | p. 238 |
3 Is the Spliceosome a Ribozyme? | p. 241 |
4 Structural Biology of the Spliceosome | p. 243 |
5 Concluding Remarks and Future Directions | p. 247 |
Acknowledgments | p. 248 |
Abbreviations | p. 248 |
References | p. 249 |
9 The Ribosome: A Molecular Machine Powered by RNA | p. 253 |
Abstract | p. 254 |
1 The Ribosome - The Largest Natural Ribozyme | p. 254 |
2 Ribosomal Biogenesis | p. 258 |
3 The Molecular Anatomy of Functional Centers | p. 262 |
4 Metal Ions and the Evolution of the Ribosome | p. 269 |
5 Concluding Remarks | p. 271 |
Acknowledgments | p. 272 |
Abbreviations | p. 272 |
References | p. 273 |
10 Metal Ion Requirements in Artificial Ribozymes That Catalyze Aminoacylation and Redox Reactions | p. 277 |
Abstract | p. 278 |
1 Introduction | p. 278 |
2 Flexizymes | p. 279 |
3 Redox Ribozymes | p. 288 |
4 Conclusions | p. 294 |
Acknowledgments | p. 294 |
Abbreviations | p. 294 |
References | p. 295 |
11 Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspective | p. 299 |
Abstract | p. 300 |
1 Introduction | p. 301 |
2 Expectations of Metal Binding and Crystallographic Observations | p. 304 |
3 Metal Ion Binding and Function in the Structures of Natural and Artificial Ribozymes | p. 309 |
4 Conclusions and Future Prospects | p. 334 |
Acknowledgments | p. 337 |
Abbreviations | p. 337 |
References | p. 333 |
12 Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II) | p. 347 |
Abstract | p. 348 |
1 Introduction | p. 348 |
2 Pt(II) Compounds: Properties and Biological Distribution | p. 350 |
3 Pt(II) Compounds and RNA Processes | p. 358 |
4 In Vitro Studies of RNA-Pt(II) Adducts | p. 361 |
5 Structural Features of Pt(II)-Nucleic Acid Adducts | p. 368 |
6 Concluding Remarks | p. 371 |
Acknowledgments | p. 372 |
Abbreviations | p. 373 |
References | p. 373 |
Subject Index | p. 379 |