Table Of ContentSpringer Series in Biophysics 13
Nils G. Walter (cid:129) Sarah A. Woodson (cid:129) Robert T. Batey
Editors
Non-Protein Coding RNAs
123
Editors
Dr. Nils G. Walter Dr. Sarah A. Woodson
Associate Professor of Chemistry Professor of Biophysics
Department of Chemistry Department of Biophysics
University of Michigan Johns Hopkins University
930 N. University 3400 North Charles Street
Ann Arbor, MI 48109-1055 Baltimore, MD 21218
USA USA
Dr. Robert T. Batey
Associate Professor of Chemistry and
Biochemistry
Department of Chemistry and Biochemistry
University of Colorado at Boulder
Box 215, Boulder, CO 80309-0215
USA
ISSN 0932-2353
ISBN 978-3-540-70833-9 e-ISBN 978-3-540-70840-7
Library of Congress Control Number: 2008931054
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Preface
The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers
of RNA interference, Andrew Fire and Craig Mello. This prize, which follows
“RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently
discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought
to outnumber protein coding genes in mammals by perhaps as much as four-fold.
In fact, it appears that the complexity of an organism correlates with the fraction of
its genome devoted to non-protein coding RNAs. Essential biological processes as
diverse as cell differentiation, suppression of infecting viruses and parasitic trans-
posons, higher-level organization of eukaryotic chromosomes, and gene expression
are found to be largely directed by non-protein coding RNAs.
Currently, bioinformatic, high-throughput sequencing, and biochemical
approaches are identifying an increasing number of these RNAs. Unfortunately, our
ability to characterize the molecular details of these RNAs is significantly lacking.
The biophysical study of these RNAs is an emergent field that is unraveling the
molecular underpinnings of how RNA fulfills its multitude of roles in sustaining
cellular life. The resulting understanding of the physical and chemical processes at
the molecular level is critical to our ability to harness RNA for use in biotechnology
and human therapy, a prospect that has recently spawned a multi-billion dollar
industry.
This book assembles chapters from some of the experts in Biophysics of RNA
to provide a snapshot of the current status of this dynamic field. While by necessity
incomplete, this book aims to survey a number of the better characterized non-pro-
tein coding RNAs and the biophysical techniques used to study them. It is written
for students and researchers at all levels of accomplishment interested in under-
standing how non-protein coding RNAs work and how biophysical and computa-
tional approaches can be used to delineate the molecular underpinnings of RNA
function. Many topics are approached with the goal of describing how biophysical
tools and techniques have been used to address fundamental questions in the biol-
ogy of non-protein coding RNAs, rather than a description of RNAs themselves. In
this light, we hope that the book will be of particular use to junior scientists seeking
to tackle new problems in RNA biology from the vantage of biophysics.
v
vi Preface
Following a foreword featuring a general overview of the lessons from the bio-
physical study of RNA, the first three chapters aim to describe how theory, simula-
tion, and experimental probing can be used to unveil the thermodynamics and
kinetics governing RNA folding and dynamics. Chapters 4–6 are devoted to small
self-cleaving ribozymes, as understood through the lens of X-ray crystallography,
ensemble and single molecule fluorescence, and chemical probing. Subsequent
chapters tackle increasingly complex RNAs and their protein complexes. In partic-
ular, Chaps. 7–9 focus upon large ribozymes that use more sophisticated mecha-
nisms of catalysis and even recruit proteins to facilitate function in the cellular
environment. As genetic regulation appears to be an increasingly important role for
non-coding RNAs, Chaps. 10 and 11 concentrate on how X-ray crystallography,
NMR spectroscopy, and fluorescence techniques have revealed how riboswitches
specifically recognize small molecule metabolites to affect gene expression. Many
modern non-protein coding RNAs are assembled into large ribonucleoprotein com-
plexes (RNPs) and Chaps. 12–14 yield insights into how these particles are assem-
bled to form a functional complex. These large RNP machines are by necessity
highly dynamic entities that must adopt a number of conformations, as revealed in
studies of the ribosome by cryo-electron microscopy in Chap. 15. Finally, non-cod-
ing RNAs often interact with other cellular machineries to enable their function, as
discussed in Chaps. 16 and 17. We hope that our selection of topics is both timely
and stimulating for the rapidly growing RNA community and beyond.
USA Nils G. Walter
September 2008 Sarah A. Woodson
Robert T. Batey
Contents
1 RNA 3D Structural Motifs: Definition, Identification,
Annotation, and Database Searching ....................................................... 1
Lorena Nasalean, Jesse Stombaugh, Craig L. Zirbel,
and Neocles B. Leontis
2 Theory of RNA Folding: From Hairpins to Ribozymes ......................... 27
D. Thirumalai and Changbong Hyeon
3 Thermodynamics and Kinetics of RNA Unfolding and Refolding ........ 49
Pan T.X. Li and Ignacio Tinoco
4 Ribozyme Catalysis of Phosphodiester Bond Isomerization:
The Hammerhead RNA and Its Relatives ............................................... 73
William G. Scott
5 The Small Ribozymes: Common and Diverse Features Observed
Through the FRET Lens ........................................................................... 103
Nils G. Walter and Shiamalee Perumal
6 Structure and Mechanism of the glmS Ribozyme ................................... 129
Juliane K. Soukup and Garrett A. Soukup
7 Group I Ribozymes as a Paradigm for RNA Folding and Evolution .... 145
Sarah A. Woodson and Seema Chauhan
8 Group II Introns and Their Protein Collaborators ................................ 167
Amanda Solem, Nora Zingler, Anna Marie Pyle,
and Jennifer Li-Pook-Than
9 Understanding the Role of Metal Ions in RNA Folding and Function:
Lessons from RNase P, a Ribonucleoprotein Enzyme ............................ 183
Michael E. Harris and Eric L. Christian
vii
viii Contents
10 Beyond Crystallography: Investigating the Conformational
Dynamics of the Purine Riboswitch ....................................................... 215
Colby D. Stoddard and Robert T. Batey
11 Ligand Binding and Conformational Changes in the
Purine-Binding Riboswitch Aptamer Domains ..................................... 229
Jonas Noeske, Janina Buck, Jens Wöhnert, and Harald Schwalbe
12 The RNA–Protein Complexes of E. coli Hfq:
Form and Function .................................................................................. 249
Taewoo Lee and Andrew L. Feig
13 Assembly of the Human Signal Recognition Particle ........................... 273
Elena Menichelli and Kiyoshi Nagai
14 Forms and Functions of Telomerase RNA ............................................. 285
Kathleen Collins
15 Ribosomal Dynamics: Intrinsic Instability
of a Molecular Machine ........................................................................... 303
Haixiao Gao, Jamie LeBarron, and Joachim Frank
16 Biophysical Analyses of IRES RNAs from the Dicistroviridae:
Linking Architecture to Function ........................................................... 317
Jeffrey S. Kieft
17 Structure and Gene-Silencing Mechanisms of Small
Noncoding RNAs ...................................................................................... 335
Chia-Ying Chu and Tariq M. Rana
Index .................................................................................................................. 357
Color Plates ....................................................................................................... 365
Contributors
Robert Batey
Department of Chemistry and Biochemistry, Campus Box 215, University
of Colorado-Boulder, Boulder, CO 80309, USA, [email protected]
Janina Buck
Institut für Organische Chemie und Chemische Biologie, Zentrum für
Biomolekulare Magnetische Resonanz, Johann Wolfgang Goethe-Universität,
Max-von-Laue-Strasse 7, N160-314, 60438 Frankfurt am Main, Germany,
[email protected]
Kathleen Collins
Department of Molecular and Cell Biology, University of California at Berkeley,
Berkeley, CA 94720-3200, USA, [email protected]
Andrew Feig
Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI
48202, USA, [email protected]
Joachim Frank
Howard Hughes Medical Institute, Department of Biochemistry and Molecular
Biophysics and Department of Biological Sciences, Columbia University, 650
West 168th Street, NY 10032, USA, [email protected]
Haixiao Gao
Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA,
[email protected]
Michael Harris
Center for RNA Molecular Biology, Department of Biochemistry, CWRU -
School of Medicine, Cleveland, OH 44106, USA, [email protected]
ix
x Contributors
Jeffrey Kief
Department of Biochemistry and Molecular Genetics, Denver School of
Medicine, University of Colorado, 12801 East 17th Ave, Rm L18-9110, Aurora,
CO 80045, USA, [email protected]
Jamie LeBarron
Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA,
[email protected]
Neocles Leontis
Department of Chemistry, Bowling Green State University, 141 Overman Hall,
Bowling Green, OH 43403, USA, [email protected]
Kyoshi Nagai
Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road,
Cambridge CB2 2QH, UK, [email protected]
Jonas Noeske
Institut für Organische Chemie und Chemische Biologie, Zentrum für
Biomolekulare Magnetische Resonanz, Johann Wolfgang Goethe-Universität,
Max-von-Laue-Strasse 7, N160-314, 60438 Frankfurt am Main, Germany,
[email protected]
Anna Marie Pyle
266 Whitney Avenue, Room 334A Bass Building, Yale University, New Haven,
CT 06511, USA, [email protected]
Tariq Rana
Department of Biochemistry and Molecular Pharmacology, University of
Massachusetts Medical School, Worcester, MA 01605, USA,
[email protected]
Harald Schwalbe
Institut für Organische Chemie und Chemische Biologie, Zentrum für
Biomolekulare Magnetische Resonanz, Johann Wolfgang Goethe-Universität,
Max-von-Laue-Strasse 7, N160-314, 60438 Frankfurt am Main, Germany,
[email protected]
William Scott
Department of Chemistry, University of California, 1156 High Street, Santa Cruz,
CA 95064, USA, [email protected]
Garrett Soukup
Department of Biomedical Sciences, Creighton University School of Medicine,
2500 California Plaza, Omaha, NE 68178, USA, [email protected]
Contributors xi
Devarajan (Dave) Thirumalai
Department of Chemistry and Biochemistry, University of Maryland, College
Park, MD 20742, USA, [email protected]
Ignacio Tinoco
Department of Chemistry, University of California, Berkeley, CA 94720-1460,
USA, [email protected]
Olke Uhlenbeck
Department of Biochemistry, Molecular Biology and Cell Biology, Hogan 2-100,
2205 Tech Drive, Evanston, IL 60208, USA,
[email protected]
Nils Walter
Department of Chemistry, University of Michigan, Ann Arbor, 930 N. University,
MI 48109-1055, USA, [email protected]
Jens Wöhnert
Institut für Molekulare Biowissenschaften, Zentrum für Biomolekulare
Magnetische Resonanz, Johann Wolfgang Goethe-Universität,
Max-von-Laue-Strasse 9, N200-2.04, 60438 Frankfurt am Main, Germany,
[email protected]
Sarah Woodson
T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N.
Charles St., Baltimore, MD 21218, USA, [email protected]
