Cover image for Structural and catalytic roles of metal ions in RNA
Title:
Structural and catalytic roles of metal ions in RNA
Series:
Metal ions in life sciences ; 9
Publication Information:
London : Royal Society of Chemistry, 2011
Physical Description:
xxxi, 391 p. : ill. ; 24 cm.
ISBN:
9781849730945

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30000010253932 QP623.5.C36 M48 2011 Open Access Book Book
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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

Pascal Auffinger and Neena Grover and Eric WesthofMichèle C. Erat and Roland K. O. SigelZhi-Jie Tan and Shi-Jie ChenKangkan Halder and Jörg S. HartigAdrian R. Ferré-D' Amaré and Wade C. WinklerAlexander E. Johnson-Buck and Sarah E. McDowell and Nils G. WalterDaniela Donghi and Joachim SchnablSamuel E. ButcherKrista Trappl and Norbert PolacekHiroaki Suga and Kazuki Futai and Koichiro JinJoseph E. WedekindErich G. Chapman and Alethia A. Hostetter and Maire F. Osborn and Amanda L. Miller and Victoria J. DeRose
Historical Development and Perspectives of the Seriesp. v
Preface to Volume 9p. vii
Contributors to Volume 9p. xvii
Titles of Volumes 1-44 in the Metal Ions in Biological Systems Seriesp. xxi
Contents of Volumes in the Metal Ions in Life Sciences Seriesp. xxiii
1 Metal Ion Binding to RNAp. 1
Abstractp. 2
1 Introductionp. 3
2 Details of Ion Coordinationp. 3
3 Physiological Relevance of Metal Ionsp. 5
4 Monovalent Cationsp. 6
5 Divalent Cationsp. 10
6 Trivalent Cationsp. 20
7 Other Trivalent and Tetravalent Cationsp. 24
8 Anionsp. 25
9 Subjectivity in the Structure Determination Processp. 26
10 Summaryp. 26
Acknowledgmentsp. 28
Abbreviations and Definitionsp. 28
Referencesp. 29
2 Methods to Detect and Characterize Metal Ion Binding Sites in RNAp. 37
Abstractp. 39
1 Introductionp. 39
2 General Considerationsp. 40
3 Spectroscopic Methodsp. 46
4 Chemical and Biochemical Methodsp. 67
5 Computational Methodsp. 80
6 Calculation of Binding Constantsp. 85
7 Concluding Remarks and Future Directionsp. 89
Acknowledgmentsp. 90
Abbreviationsp. 90
Referencesp. 91
3 Importance of Diffuse Metal Ion Binding to RNAp. 101
Abstractp. 102
1 Introductionp. 102
2 Diffuse Ions Provide a Significant Stabilizing Force for RNA Structurep. 103
3 Diffuse Ion is Critical to RNA Folding Kineticsp. 110
4 Theoretical Predictions for the Diffuse Ion Binding to RNAsp. 113
5 Correlated Distribution of Multivalent Diffuse Ions: Theory Versus Experimentp. 115
6 General Conclusionsp. 119
Acknowledgmentsp. 120
Abbreviationsp. 120
Referencesp. 121
4 RNA Quadruplexesp. 125
Abstractp. 125
1 Introduction To RNA Quadruplexesp. 126
2 Thermodynamic Stabilityp. 127
3 Conformational Variationsp. 130
4 Biological Functionp. 130
5 Conclusionsp. 135
Acknowledgmentp. 136
Abbreviationsp. 136
Referencesp. 137
5 The Roles of Metal Ions in Regulation by Riboswitchesp. 141
Abstractp. 142
1 Introductionp. 142
2 Metal Ions that Assist Recognition of Riboswitch Ligandsp. 145
3 Metal Ions and Riboswitch Foldingp. 151
4 Magnesium-Sensing Riboswitches: Salmonella mgiAp. 154
5 Magnesium-Sensing Riboswitches: The M-Box RNAp. 161
6 Are There Additional Classes of Metal-Sensing Riboswitches?p. 168
Acknowledgmentsp. 169
Abbreviationsp. 169
Referencesp. 170
6 Metal Ions: Supporting Actors in the Playbook of Small Ribozymesp. 175
Abstractp. 176
1 Introductionp. 176
2 Interactions Between Metal Ions and Small Ribozymesp. 178
3 Roles of Metal Ions in Small Ribozymesp. 183
4 Concluding Remarks and Future Directionsp. 189
Acknowledgmentp. 190
Abbreviations and Definitionsp. 190
Referencesp. 191
7 Multiple Roles of Metal Ions in Large Ribozymesp. 197
Abstractp. 198
1 Introductionp. 198
2 Metal Ions in Folding and Catalysis: A Brief Overviewp. 200
3 Group I Intron Ribozymesp. 205
4 Group II Intron Ribozymesp. 212
5 RNase Pp. 221
6 Concluding Remarksp. 226
Acknowledgmentsp. 227
Abbreviationsp. 227
Referencesp. 228
8 The Spliceosome and Its Metal Ionsp. 235
Abstractp. 235
1 Introductionp. 236
2 The Pre-mRNA Splicing Mechanismp. 238
3 Is the Spliceosome a Ribozyme?p. 241
4 Structural Biology of the Spliceosomep. 243
5 Concluding Remarks and Future Directionsp. 247
Acknowledgmentsp. 248
Abbreviationsp. 248
Referencesp. 249
9 The Ribosome: A Molecular Machine Powered by RNAp. 253
Abstractp. 254
1 The Ribosome - The Largest Natural Ribozymep. 254
2 Ribosomal Biogenesisp. 258
3 The Molecular Anatomy of Functional Centersp. 262
4 Metal Ions and the Evolution of the Ribosomep. 269
5 Concluding Remarksp. 271
Acknowledgmentsp. 272
Abbreviationsp. 272
Referencesp. 273
10 Metal Ion Requirements in Artificial Ribozymes That Catalyze Aminoacylation and Redox Reactionsp. 277
Abstractp. 278
1 Introductionp. 278
2 Flexizymesp. 279
3 Redox Ribozymesp. 288
4 Conclusionsp. 294
Acknowledgmentsp. 294
Abbreviationsp. 294
Referencesp. 295
11 Metal Ion Binding and Function in Natural and Artificial Small RNA Enzymes from a Structural Perspectivep. 299
Abstractp. 300
1 Introductionp. 301
2 Expectations of Metal Binding and Crystallographic Observationsp. 304
3 Metal Ion Binding and Function in the Structures of Natural and Artificial Ribozymesp. 309
4 Conclusions and Future Prospectsp. 334
Acknowledgmentsp. 337
Abbreviationsp. 337
Referencesp. 333
12 Binding of Kinetically Inert Metal Ions to RNA: The Case of Platinum(II)p. 347
Abstractp. 348
1 Introductionp. 348
2 Pt(II) Compounds: Properties and Biological Distributionp. 350
3 Pt(II) Compounds and RNA Processesp. 358
4 In Vitro Studies of RNA-Pt(II) Adductsp. 361
5 Structural Features of Pt(II)-Nucleic Acid Adductsp. 368
6 Concluding Remarksp. 371
Acknowledgmentsp. 372
Abbreviationsp. 373
Referencesp. 373
Subject Indexp. 379