David M J Lilley & Fritz Eckstein 
Ribozymes and RNA Catalysis [PDF ebook] 

Preface: Foreword: Twenty-five years of ribozymes; Chapter 1: Ribozymes and RNA Catalysis Introduction and Primer; 1.1. What are ribozymes?; 1.2. What is the role of ribozymes in cells?; 1.3. Ribozymes bring about significant rate enhancements; 1.4. Why study ribozymes?; 1.5. Folding RNA into the active conformation; 1.6. The catalytic resources of RNA – making a lot of a little; 1.7. Mechanisms and catalytic strategies of ribozymes; 1.8. The impact of new methodologies to study ribozymes; 1.9. Finally; Chapter 2: Proton Transfer in Ribozyme Catalysis; 2.1 Scope of Chapter and Rationale; 2.2 Overview of Proton Transfer Chemistry; 2.3 General Considerations for Proton Transfer in RNA Enzymes; 2.3.1 Classes of Protonation Sites in RNA; 2.3.2 Driving Forces for p Ka Shifting in RNA; 2.3.3 Quantitative Contributions of Proton Transfer to RNA Catalysis; 2.4 Proton Transfer in Small Ribozymes: 5 case studies; 2.4.1 Why Small Ribozymes?; 2.4.2 Proton Transfer in the Hepatitis Delta Virus Ribozyme; 2.4.3 Proton Transfer in the Hairpin Ribozyme; 2.4.4 Proton Transfer in the Hammerhead Ribozyme; 2.4.5 Proton Transfer in the VS Ribozyme; 2.4.6 Proton Transfer in the glm S Ribozyme; 2.5 Conclusion and Perspectives; 2.6 References and Footnotes; Chapter 3: Finding the hammerhead active site; 3.1. Introduction; 3.2. Background; 3.3. Experimental data; 3.1.1 Mechanistic Hypothesis Leads to Identification and Functional Test of Active Site Components; 3.1.2. Structural Hypothesis-Large-scale Conformational Changes are Required for Catalysis; 3.1.3. Molecular Modeling of a Hammerhead Active Fold that Satisfies Structural and Biochemical Constraints; 3.4. Current Status and Future Prospects; Chapter 4: Hammerhead Ribozyme Crystal Structures and Catalysis; 4.1 Introduction; 4.2 A Catalytic RNA Prototype; 4.3 A Small Ribozyme; 4.4 The Chemistry of Phosphodiester Bond Isomerization; 4.5 The Hammerhead Ribozyme Structure Nailed Down; 4.6 Catalysis in the Crystal; 4.7 Making Movies From Crystallographic Snapshots; 4.8 An Ever-Growing List of Concerns; 4.9 Occam’s Razor Can Slit Your Throat; 4.10 The Structure of a Full-Length Hammerhead Ribozyme; 4.11 Do the Minimal and Full-Length Hammerhead Crystal Structures Have Anything in Common?; 4.12 How the Does the Minimal Hammerhead Work?; 4.13 A Movie Sequel with a Happy Ending; 4.14 Concluding remarks; Chapter 5: The Hairpin and Varkud Satellite Ribozymes; 5.1. The nucleolytic ribozymes; 5.2. The hairpin ribozyme; 5.2.1 The structure of the hairpin ribozyme; 5.2.2 Metal ion-dependent folding of the hairpin ribozyme; 5.2.3 Observing the cleavage and ligation activities of the hairpin ribozyme; 5.2.4 The mechanism of the hairpin ribozyme; 5.3. The VS ribozyme; 5.3.1 The structure of the VS ribozyme; 5.3.2 The structure of the substrate; 5.3.3 The location of the substrate; 5.3.4 The active site of the VS ribozyme; 5.3.5 Candidate catalytic nucleobases; 5.3.6 The mechanism of the VS ribozyme; 5.4. Some striking similarities between the hairpin and VS ribozymes; Chapter 6: Catalytic Mechanism of the HDV Ribozyme; 6.1. Introduction; 6.1.1. Hepatitis Delta Virus Biology; 6.1.2. Cleavage Reactions of Small Ribozymes; 6.2. HDV structure; 6.2.1. Determination of Crystal Structures; 6.2.2. Structure Overview; 6.2.3. Active Site; 6.3. Catalytic Strategies for RNA Cleavage; 6.4. The Active Site Nucleobase: C75; 6.4.1. Exogenous Base Rescue Reactions; 6.4.2. The Role of C75 in HDV Catalysis; 6.4.3. Resolving the Kinetic Ambiguity; 6.5. Metal ions in the HDV Ribozyme; 6.5.1. Structural Metal Ions; 6.5.2. Catalytic Metal Ions; 6.6. Contributions of Non-active-site Structures to Catalysis; 6.7. Dynamics in HDV Function; 6.8. Varieties of Experimental Systems; 6.9. Models for HDV Catalysis; 6.10. Conclusion; Chapter 7: Mammalian self-cleaving ribozymes; 7.1 Introduction; 7.2 General features of small self-cleaving sequences; 7.3 Genome-wide selection of self-cleaving ribozymes; 7.4 The CPEB3 ribozyme; 7.4.1 Expression of the CPEB3 ribozyme; 7.4.2 Structural features of the CPEB3 and HDV ribozymes; 7.4.3 Linkage of HDV to the human transcriptome; 7.5 Possible biological roles of self-cleaving ribozymes; 7.6 Closing remarks; Chapter 8: The Structure and Action of glm S Ribozymes; 8.1 Introduction; 8.2 Biochemical characteristics of glm S ribozymes; 8.2.1 Divalent metal ions support structure and not chemistry; 8.2.2 Ligand specificity of glm S ribozymes; 8.2.3 Evidence for a coenzyme role for Glc N6P; 8.3 Atomic-resolution structure of glm S ribozymes; 8.3.1 Secondary and tertiary structures of glm S ribozymes; 8.3.2 Metabolite recognition by glm S ribozymes; 8.4 Mechanism of glm S ribozyme self-cleavage; 8.5 Can glm S ribozymes be drug targets?; 8.6 Conclusions; Chapter 9: A Structural Analysis of Ribonuclease P. 9.1 Introduction; 9.2 Chemistry of RNase P RNA; 9.2.1 Universal; 9.2.2 SN2-type reaction; 9.2.3 p H-dependence of the reaction: hydroxide ion as the nucleophile; 9.2.4 Metal ions in catalysis ; 9.3 Phylogenetic variation and structure of RNase P RNA; 9.4 Early studies of the RNase P RNA structure; 9.5 Crystallographic studies of bacterial RNase P RNAs; 9.6 Modeling an RNase P RNA:t RNA complex; 9.7 Modeling the bacterial RNase P holoenzyme; 9.8 Substrate recognition; 9.9 Archaeal and Eucaryal holoenzymes – more proteins; 9.10 Concluding remarks; Chapter 10: Group I Introns: Biochemical and Crystallographic Characterization of the Active Site Structure; 10.1. Group I intron origins; 10.2 Group I intron self-splicing; 10.3 What has changed in group I intron knowledge in the last decade; 10.4 The structure of group I introns; 10.5 Crystallography of group I introns; 10.5.1 The Tetrahymena LSU P4-P6 domain; 10.5.2 The Tetrahymena intron catalytic core; 10.5.3 The Twort orf142-I2 ribozyme; 10.5.4 The Azoarcus sp. BBH72 t RNAile intron; 10.6 The structural basis for group I intron self-splicing; 10.6.1 Recognition of the 5′ splice site; 10.6.2 Does the ribozyme undergo conformational changes upon P1 docking?; 10.6.3 A binding pocket for guanosine; 10.6.4 Packed stacks; 10.7 Biochemical characterization of the structure; 10.7.1 Metal ion binding and specificity switches; 10.7.2 Identification of ligands to the catalytic metal ions; 10.7.3 Correlation with metal ion binding sites within the crystal structures; 10.7.4 Nucleotide analog interference techniques; 10.8 What makes a catalytic site?; 10.9 Back to the origins; Chapter 10: Group II introns: catalysts for splicing, genomic change and evolution; 11.1 Introduction: The place of group II introns among the family of ribozymes; 11.2 The basic reactions of group II introns; 11.3 The biological significance of group II introns; 11.3.1 Evolutionary significance; 11.3.2 Significance and prevalence in modern genomes; 11.4 Domains and parts: the anatomy of a group II intron; 11.4.1. Domain 1; 11.4.2. Domain 2; 11.4.3. Domain 3; 11.4.4. Domain 4; 11.4.5. Domain 5; 11.4.6. Domain 6; 11.4.7. Other domains and insertions; 11.4.8. Alternative structural organization and split introns; 11.5. A big, complicated family: the diversity of group II introns; 11.6. Group II intron tertiary structure; 11.7. Group II intron folding mechanisms; 11.7.1. A slow, direct path to the native state:; 11.7.2. A folding control element in the center of D1; 11.7.3. Proteins and group II intron folding; 11.8 Setting the stage for catalysis: proximity of the splice sites and branch-site; 11.8.1. Recognition of exons and ribozyme substrates; 11.8.2. Branch-site recognition and the coordination loop; 11.9. A single active-site for group II intron catalysis; 11.10 The group II intron active-site: what are the players?; 11.10.1. Active-site players in D1 and surrounding linker regions; 11.10.2. Domain 3 and the J2/3 linker; 11.10.3. Domain 5: structural and catalytic regions; 11.11 The chemical mechanism of group II intron catalysis; 11.12 Proteins and group II intron function; 11.12.1. Maturases; 11.12.2. CRM-domain plant proteins; 11.12.3. ATPase proteins; 11.13 Group II introns and their many hypothetical relatives; 11.14 Group II introns: RNA processing enzymes, transposons, or tiny living things?; Chapter 12: The GIR1 branching ribozyme; 12.1 Introduction; 12.2 Distribution and structural organization of twin-ribozyme introns; 12.3 The biological context; 12.3.1 Three processing pathways of a twin-ribozyme intron; 12.3.2 Processing of the I-Dir I m RNA; 12.3.3 Conformational switching in GIR1; 12.4 Biochemical characterization; 12.4.1 GIR1 catalyzes three different reactions; 12.4.2 Characterization of the branching reaction; 12.4.3 The biochemistry of GIR1; 12.5 Modelling the structure of GIR1; 12.5.1 The overall structure; 12.5.2 Coaxially stacked helices; 12.5.3 The junctions and tertiary interactions involving peripheral elements; 12.5.4 The active site; 12.6 Phylogenetic considerations; 12.7 Concluding remarks; Chapter 13: Is the spliceosome a ribozyme?; 13.1 Similarity to group II self-splicing introns; 13.2 Role of sn RNA in the spliceosome active site; 13.3 Conformation of the U2-U6 complex and parallels to group II intron structures; 13.4 RNA-mediated regulation in the spliceosome; Chapter 14: Peptidyl Transferase Mechanism: The Ribosome as a Ribozyme; 14.1 Introduction: Historical background; 14.2 The ribosome; 14.3 The peptidyl transfer reaction; 14.3.1 Characteristics of the reaction off the ribosome; 14.3.2 Enzymology of the peptidyl transfer reaction; 14.3.2.1 Potential mechanisms of rate acceleration by the ribosome; 14.3.2.2 Experimental approaches to reaction on the ribosome; 14.3.2.3 p H-rate profiles; 14.3.2.4 Activation parameters; 14.4 The active site; 14.4.1 Structures of the reaction intermediates; 14.4.2 Conformational rearragements of the active site; 14.4.2.1 Induced fit; 14.4.2.2 Role of the P-site substrate; 14.4.2.3 Conformational flexibility of the active site; 14.4.3 Probing the catalytic mechanism: Effects of base substitutions; 14.4.4. Importance of the 2?-OH of A76 of the P-site t RNA; 14.5 Conclusions and evolutionary considerations; Chapter 15: Folding Mechanisms of Group I Ribozymes; 15.1. The multi-domain architecture of group I ribozymes; 15.2. RNA Folding Problem; 15.2.1 Hierarchical Folding of t RNA; 15.2.2 Coupling of Secondary and Tertiary Structure; 15.3. Late events: Formation of Tertiary Domains in the Tetrahymena Ribozyme; 15.3.1 Time-resolved Footprinting of Intermediates; 15.3.2 Misfolding of the intron core; 15.3.3 Peripheral Stability Elements; 15.4. Kinetic Partitioning among Parallel Folding Pathways; 15.4.1 Theory and Experiment; 15.4.2 Single Molecule Folding Studies; 15.4.3 Estimating the Flux through Footprinting Intermediates; 15.4.4. Kinetic Partitioning in vivo; 15.5. Early Events: Counterion-dependent RNA collapse; 15.5.1 Compact Non-Native Form of b I5 Ribozyme; 15.5.2 Small Angle X-ray Scattering of Tetrahymena Ribozyme; 15.5.3 Native-like Folding Intermediates in the Azoarcus Ribozyme; 15.5.4 Early Folding Intermediates of the P4-P6 RNA; 15.6. Counterions and Folding of Group I Ribozymes; 15.6.1 Metal Ions and RNA Folding; 15.6.2 Valence and Size of Counterions Matter; 15.6.3 Specific Metal Ion Coordination and Folding; 15.7. Protein-dependent folding of group I ribozymes; 15.7.1 Stabilization of RNA Tertiary Structure; 15.7.2 Stimulation of Refolding by RNA Chaperones; 15.8. Conclusion;