Actions for RNA-ligand interactions. Part A, Structural biology methods [electronic resource]

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RNA-ligand interactions. Part A, Structural biology methods [electronic resource] / edited by Daniel W. Celander, John N. Abelson

Published
San Diego, CA ; London : Academic Press, [2000]
Copyright Date
©2000
Physical Description
1 online resource (xxxiii, 549 pages 8 unnumbered pages of color plates) : illustrations
Additional Creators
Celander, Daniel W. (Daniel Walter) and Abelson, John
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Contents
Machine generated contents note: 1.Measurement and Analysis of Equilibrium Binding Titrations: A Beginner's Guide / Dorothy Beckett -- 1.Material Requirements for Binding Measurements -- 2.Monitoring a Binding Reaction -- 3.The Binding Equation and Its Relationship to Binding Measurements -- 4.Plotting and Analysis of Binding Data -- 5.Protein Concentration Is Important: Equilibrium Versus Stoichiometric Conditions -- 6.When Are Total and Free Ligand Concentrations Equal? -- 7.Deviations from Simple Binding -- References -- 2.Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule-Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Maria J. Jezewska -- 1.Introduction -- 2.A Single Titration Curve: Some Simple Considerations of Possible Pitfalls -- 3.Quantitative Equilibrium Spectroscopic Titrations: Thermodynamic Bases -- 4.Nucleotide Binding to the RepA Protein of Plasmid RSF1010 -- 5.Applying the Statistical Thermodynamic Model for the Nucleotide Binding to the RSF1010 RepA Protein Hexamer -- 6.Empirical Function Approach -- 7.MCT Method: General Considerations -- 8.Application of the MCT Method to the Base Specificity Problem in ASFV Pol X-ssDNA System -- 9.Application of MCT Method to Protein-ssDNA Lattice Binding Systems -- 10.Quantitative Analysis of the Binding of the E. coli DnaB Helicase to Unmodified Nucleic Acids Using the MCT Method -- 11.Direct Analysis of the Experimental Isotherm of Protein Ligand Binding to Two Competing Nucleic Acid Lattices -- 12.Using a Single Concentration of a Nonfluorescent Unmodified Nucleic Acid -- 13.Using Short Fluorescent Oligonucleotides in Competition with the Polymer Nucleic Acid -- 14.Conclusions -- Acknowledgments -- References -- 3.Analysis of PKR-RNA Interactions by Sedimentation Velocity / James L. Cole -- 1.Introduction -- 2.Reagents and Cells -- 3.Experimental Design -- 4.Examples -- 5.Conclusions -- Acknowledgments -- References -- 4.Structural and Thermodynamic Analysis of PDZ-Ligand Interactions / Ernesto J. Fuentes -- 1.Introduction -- 2.Structural Studies of the Tiam I PDZ Domain -- 3.Fluorescence Anisotropy Methods for Measuring the Energetics of PDZ-Ligand Interactions -- 4.Double-Mutant Cycle Analysis of PDZ-Binding Pockets -- 5.Peptide Evolution as a Tool for Probing PDZ Specificity -- 6.Conclusions -- Acknowledgments -- References -- 5.Thermodynamic Analysis of Metal Ion-Induced Protein Assembly / Deborah G. Conrady -- 1.Introduction -- 2.Linked Equilibria---General Concepts -- 3.Experimental Approaches---Analytical Ultracentrifugation -- 4.Summary -- Acknowledgments -- References -- 6.Thermodynamic Dissection of Colicin Interactions / Colin Kleanthous -- 1.Introduction -- 2.DNase Domain-Immunity Protein Interactions -- 3.Receptor Binding -- 4.Mapping Binding Epitopes and Signaling Networks -- 5.Discussion -- References -- 7.Energetics of Src Homology Domain Interactions in Receptor Tyrosine Kinase-Mediated Signaling / Stefan T. Arold -- 1.Introduction -- 2.Interactions of Src Homology 2 Domains -- 3.Recognition by the "Two-Pinned Plug" -- 4.Recognition by the β-Turn Motif -- 5.Selectivity Versus Specificity for SH2 Domain Interactions -- 6.Proline Sequence-Recognition Domains -- 7.Interactions of SH3 Domains -- 8.What Constitutes Specificity in SH3 Domain Interactions? -- 9.Selectivity in SH3 Domain Interactions -- 10.Interactions Through Multiple Domains -- 11.Conclusions -- References -- 8.Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase / Petr Herman -- 1.Introduction -- 2.General Principles of Linked Multiequilibria Reactions -- 3.Functional Energetic Linkages in Allosteric Regulation of Rabbit Muscle Pyruvate Kinase -- 4.Functional Linkage Through Steady-State Kinetics -- 5.Structural Perturbations by Ligands -- 6.Functional Linkage Scheme of Allostery for RMPK -- 7.Functional Linkage Through Ligand Binding Measurements -- 8.Protein Structural Dynamics---Amid Hydrogen Exchange Monitored by FT-IR (HX-FT-IR) -- 9.Probing Interfacial Interactions -- 10.Summary Statement -- Acknowledgments -- References -- 9.Analysis of Free Energy Versus Temperature Curves in Protein Folding and Macromolecular Interactions / Chin-Chi Liu -- 1.Stability Curves = Gibbs-Helmholtz Curves = ΔG Versus Temperature -- 2.Analysis of ΔG Versus Temperature in Protein Folding -- 3.Using Stability Curves to Compare Mesophilic and Thermophilic Protein Pairs -- 4.Temperature Dependence of Folding Enthalpies and Entropies -- 5.Analysis of ΔG Versus Temperature Data in Macromolecular Interactions -- 6.Fitting ΔH and ΔG Versus Temperature for a ΔΔCp -- 7.Examples of Potential Consequences of a Small ΔΔCp -- References -- 10.Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases / Burki Rajendar -- 1.Introduction -- 2.Single-Turnover Fluorescence Stopped-Flow Method to Monitor Polypeptide Translocation -- 3.Application of the Sequential n-Step Mechanism -- 4.Concluding Remarks -- Acknowledgments -- References -- 11.A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics / Karolin Luger -- 1.Introduction -- 2.Salt-Mediated Nucleosome (Dis)Assembly -- 3.A Chaperone-Mediated Coupled Approach to Nucleosome Thermodynamics -- 4.Experimental Setup and Considerations -- 5.Data Analysis and Theory -- 6.Summary and Implications -- References -- 12.Quantitative Methods for Measuring DNA Flexibility In Vitro and In Vivo / L. James Maher III -- 1.Introduction -- 2.DNA Polymer Theory -- 3.Ligase-Catalyzed DNA Cyclization Kinetics In Vitro -- 4.In Vivo Analysis of E. coli lac Repression Loops -- Acknowledgments -- References.
Summary
RNA-Ligand Interactions, Part A focuses on structural biology methods. Major topics covered include semisynthetic methodologies (RNA synthetic methods and derivatization of RNA); RNA structure determination (X-ray crystallography, NMR, EM); techniques for monitoring RNA conformation and dynamics (solution methods and electrophoretic and spectroscopic methods); and modeling tertiary structure: Part B, its companion Volume 318 of Methods in Enzymology, focuses on molecular biology methods. The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the Series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.
Subject(s)
Genre(s)
ISBN
0121822184 (electronic bk.)
9780121822187 (electronic bk.)
Note
AVAILABLE ONLINE TO AUTHORIZED PSU USERS.
Bibliography Note
Includes bibliographical references and indexes.
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