Kooperativer Bibliotheksverbund

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Format: 1 online resource (453 pages) : , illustrations

ISBN: 0-12-812516-0 , 0-12-812515-2

Note: Intro -- Title page -- Table of Contents -- Copyright -- Contributors -- Preface -- Chapter One: MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes -- Abstract -- 1 Introduction -- 2 Entry Cloning Into MacroBac Series 11 or 438 by LIC -- 3 Building Complexes by Restriction and Ligation: MacroBac Series 11 -- 4 Building Complexes by LIC: MacroBac Series 438 -- 5 Bacmid Preparation and Virus Production -- 6 Protein Expression and Viral Stock Maintenance -- 7 Trouble Shooting -- 8 Future Considerations -- Acknowledgments -- Chapter Two: Production and Assay of Recombinant Multisubunit Chromatin Remodeling Complexes -- Abstract -- 1 Introduction -- 2 Cloning -- 3 Case Studies -- 4 Nucleosome Sliding and Histone Exchange Kinetic Assays -- 5 Nucleosome Sliding by Recombinant hINO80 Chromatin Remodeling Complex -- 6 Histone Exchange by Recombinant ySWR1 Chromatin Remodeling Complex -- Chapter Three: Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR -- Abstract -- 1 Introduction -- 2 Small-Angle X-Ray Scattering -- 3 Nuclear Magnetic Resonance -- 4 Summary and Conclusion-Using SAX and NMR to Characterize Architectural Remodeling -- Chapter Four: Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair -- Abstract -- 1 Introduction -- 2 Generation of Defined Cysteine Variants -- 3 Cross-linking of Defined Cysteine Variants -- 4 Use of Single-Cysteine Variants to Study Conformational Changes in DNA Mismatch Repair -- 5 Concluding Remarks -- Acknowledgments -- Chapter Five: Expression and Structural Analyses of Human DNA Polymerase θ (POLQ) -- Abstract -- 1 Introduction -- 2 Purification and Structure Determination of Human Pol θ -- 3 Crystallization and Structure Determination of Human Pol θ -- 4 Conclusions -- Acknowledgments. , Chapter Six: Structural Studies of RNases H2 as an Example of Crystal Structure Determination of Protein-Nucleic Acid Complexes -- Abstract -- 1 Introduction -- 2 Purification of RNases H2 -- 3 Biochemical Assays for RNases H2 -- 4 General Considerations in the Crystallization of Protein-Nucleic Acid Complexes -- 5 Crystallization and Structure Determination of RNases H2 -- 6 Concluding Remarks -- Acknowledgment -- Chapter Seven: DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage -- Abstract -- 1 Introduction -- 2 Defining the Structure of DNA-PKcs -- 3 Exploiting Multiple Se-Met Substitutions -- 4 Using Se-Met Sites to Check Sequence Registration -- 5 DNA-PKcs as a Stage for the Assembly of the Actors in NHEJ -- Acknowledgments -- Chapter Eight: Single-Particle Electron Microscopy Analysis of DNA Repair Complexes -- Abstract -- 1 Introduction -- 2 Sample Preparation -- 3 Grid Preparation -- 4 Data Collection -- 5 Data Processing -- Acknowledgments -- Chapter Nine: Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair -- Abstract -- 1 Introduction -- 2 Methods to Study DNA Repair Complexes With AFM -- 3 Image Analysis -- 4 DREEM Imaging -- 5 Complementary Techniques -- 6 Conclusions -- Acknowledgments -- Chapter Ten: Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time -- Abstract -- 1 Introduction -- 2 Preparation of Defined Lesion Substrates for AFM and DNA Tightrope Assay -- 3 Atomic Force Microscopy -- 4 Single-Molecule DNA Tightrope Assay -- 5 Conclusions -- Acknowledgments -- Chapter Eleven: Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination -- Abstract -- 1 Introduction -- 2 Methods -- 3 Applications -- 4 Notes. , Acknowledgments -- Chapter Twelve: Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography -- Abstract -- 1 Introduction -- 2 DNA Polymerase η -- 3 Ribonuclease H1 -- 4 Endonuclease V -- 5 X-Ray Data Processing -- 6 Applications and Future Prospects -- Acknowledgments -- Chapter Thirteen: Analyzing the Catalytic Activities and Interactions of Eukaryotic Translesion Synthesis Polymerases -- Abstract -- 1 Introduction -- 2 Purification and Structures of Nonclassical Polymerases -- 3 Catalytic Activities of Nonclassical Polymerases -- 4 Interactions of Nonclassical Polymerases -- 5 Conclusions -- Acknowledgments -- Chapter Fourteen: Kinetic Methods for Studying DNA Glycosylases Functioning in Base Excision Repair -- Abstract -- 1 Introduction -- 2 Kinetic Methods to Study Catalysis by DNA Glycosylases -- 3 Analytical Methods for Monitoring DNA Glycosylase Activity -- 4 Determining Rate Constants From Kinetics Experiments -- Acknowledgment -- Chapter Fifteen: Transient Kinetic Methods for Mechanistic Characterization of DNA Binding and Nucleotide Flipping -- Abstract -- 1 Introduction -- 2 General Considerations for Monitoring Binding -- 3 Association Kinetics -- 4 Comparison of Binding and Flipping Mechanisms for AAG and AlkA -- 5 Use of Berkeley Madonna for Evaluating Kinetic Models -- 6 Useful Equations for Kinetic Analysis -- Acknowledgments -- Chapter Sixteen: What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses -- Abstract -- 1 Introduction -- 2 Metabolic Signaling: NAD and DDR by PARP, PARG, and AIF -- 3 DNA Double-Strand Break Responses -- 4 Taking Structural Mechanisms Into Cells by Advanced Imaging -- 5 What's Ahead -- Acknowledgments -- Author Index -- Subject Index.

Language: English