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Nuclear Magnetic Resonance of Biological Macromolecules, Part B

1st Edition - June 29, 2001

Editors: Thomas L. James, Volker Dotsch, Uli Schmitz

Hardback ISBN:

9 7 8 - 0 - 1 2 - 1 8 2 2 4 0 - 8

eBook ISBN:

9 7 8 - 0 - 0 8 - 0 4 9 6 8 9 - 4

This volume and its companion, Volume 338, supplement Volumes 176, 177, 239, and 261. Chapters are written with a "hands-on" perspective. That is, practical applications with… Read more

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This volume and its companion, Volume 338, supplement Volumes 176, 177, 239, and 261. Chapters are written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules.

Contributors to Volume 339
Preface
Methods in Enzymology
Section I: Proteins A. Techniques for proteins
- [1]: Physiological Conditions and Practicality for Protein Nuclear Magnetic Resonance Spectroscopy: Experimental Methodologies and Theoretical Background
  - Natural Environment of Proteins
  - Buffers for NMR Spectroscopy
  - Native Structure of Protein: Methodology
- [2]: Optimization of Protein Solubility and Stability for Protein Nuclear Magnetic Resonance
  - Introduction
  - Polypeptide Constructs: Defining Domain Boundaries and Segmental Isotope Labeling
  - Polypeptide Folding
  - Aggregation State of Polypeptide
  - Folded Polypeptides: Optimization of Solubility and Stability
  - Polypeptides: Not Folded; Folded, but Not Soluble
  - Perspective
- [3]: Segmental Isotopic Labeling Using Expressed Protein Ligation
  - Illustrative Example: Segmental Labeling of Abl SH(32)
  - Acknowledgment
- [4]: High-Resolution Nuclear Magnetic Resonance of Encapsulated Proteins Dissolved in Low Viscosity Fluids
  - Introduction
  - Reduced Macromolecular Tumbling
  - Reverse Micelle Technology
  - Definition of Sample Composition
  - NMR Sample Preparation
  - NMR Spectroscopy
  - Assessment of Reverse Micelle Preparations
  - Validation of Sample Preparation
  - Optimal Use of Cryogenic Probe Technology in NMR Studies of Macromolecules
  - Application to Membrane Proteins
  - Acknowledgments
- [5]: Automated Assignment of Ambiguous Nuclear Overhauser Effects with ARIA
  - Introduction
  - Program Flow
  - NOE Peak Lists in ARIA
  - Iterative Assignment and Structure Calculation
  - Use of Additional Information
  - Practical Experiences with ARIA
  - Acknowledgments
- [6]: Automatic Determination of Protein Backbone Resonance Assignments from Triple Resonance Nuclear Magnetic Resonance Data
  - Introduction
  - Methodology of AutoAssign
  - Description of Input Data for AutoAssign
  - Quality Control Issues of Input Data for AutoAssign
  - Using AutoAssign
  - Testing AutoAssign
  - Conclusions and Future Prospects
  - Acknowledgments
- [7]: Nuclear Magnetic Resonance Relaxation in Determination of Residue-Specific ¹⁵N Chemical Shift Tensors in Proteins in Solution: Protein Dynamics, Structure, and Applications of Transverse Relaxation Optimized Spectroscopy
  - Introduction
  - Analytical Approaches to Chemical Shift Determination from Relaxation Measurements
  - Practical Example: ¹⁵N Chemical Shift Tensors in Ubiquitin
  - Implications for Protein Dynamics
  - Relating These Results to Protein Structure
  - Implications for TROSY
  - ¹⁵N CSA Determination in Solution: Analysis of Possible Sources of Errors
  - Summary
  - Acknowledgments
- [8]: Dipolar Couplings in Macromolecular Structure Determination
  - 1 Introduction
  - 2 Theory
  - 3 Measurement of Dipolar Couplings
  - 4 Alignment Media for Macromolecules
  - 5 Relation between Alignment and Shape
  - 6 Use of Multiple Alignment Media
  - 7 Structure Validation
  - 8 Use of Dipolar Couplings in Structure Calculation
- [9]: Nuclear Magnetic Resonance Methods for High Molecular Weight Proteins: A Study Involving a Complex of Maltose Binding Protein and β-Cyclodextrin
  - Introduction
  - Labeling Strategy Used for MBP
  - Backbone and Side-Chain Assignments of MBP
  - TROSY-Based Triple Resonance 4D Spectroscopy of MBP at Low Temperature
  - Structural Studies of MBP
  - Orienting Domains in MBP: A Study Based on Combined NMR and X-Ray Data
  - A Global Fold of MBP Based on a Limited Set of NOEs and Dipolar Couplings
  - Concluding Remarks
  - Acknowledgments
- [10]: Nuclear Magnetic Resonance Methods for Quantifying Microsecond-to-Millisecond Motions in Biological Macromolecules
  - Introduction
  - Theoretical Description of Chemical Exchange
  - Experimental Methods for Quantifying Chemical Exchange
  - Conclusions
  - Acknowledgments
Section I: Proteins B. Classes of proteins
- [11]: Characterizing Protein-Protein Complexes and Oligomers by Nuclear Magnetic Resonance Spectroscopy
  - Introduction
  - Isotope-Edited NMR Experiments
  - Development of Low-Pass J Filter
  - Development of Half-Filter Experiments
  - Use of 3D and 4D ¹⁵N/¹³C-edited NOESY Experiments to Observe Intermolecular NOE Interactions
  - Characterizing Protein Complexes by Using Selective Deuteration
  - Asymmetric Deuteration to Characterize Homodimers
  - Production of Highly (>98%) Deuterated Sample
  - Producing Heterodimers
  - Obtaining Intermolecular NOEs from Asymmetrically Deuterated Heterodimer
  - Application to PUT3 (31–100)
  - Applications to GAL4 Dimerization Domain
  - Application to UmuD′ dimer
  - Selective Deuteration to Characterize Trimeric Proteins
  - Application to Ii 118–192
  - Computational Approaches to Solving Structures of Protein Oligomers
  - Production of Single-Chain Proteins to Study Protein Complexes
  - Application of Single-Chain Proteins
  - Advancements to Study Large Protein Complexes
  - Perspectives
- [12]: Nuclear Magnetic Resonance Methods for Elucidation of Structure and Dynamics in Disordered States
  - Functional Relevance of Disordered States
  - Resonance Assignments
  - NMR Parameters
  - Measurement of Dynamics
  - Outlook
  - Acknowledgments
- [13]: Micellar Systems as Solvents in Peptide and Protein Structure Determination
  - IA Introduction
  - IB Studies of Peptides and Proteins in Micellar Systems
  - IIA Traditional Biomembrane Mimetic Solvents
  - IIB Bicelles: Discoidal Phospholipid Aggregates
  - III Structure Determination from NMR Data
  - IV Positioning of Peptide Relative to Micelle Surface
  - V Dynamics
  - VI Practical Considerations
  - VII Future Directions
  - Acknowledgment
- [14]: Nuclear Magnetic Resonance of Membrane-Associated Peptides and Proteins
  - Introduction
  - Expression of Membrane Proteins
  - Solution NMR of Membrane Proteins in Lipid Micelles
  - Solid-State NMR of Membrane Proteins in Lipid Bilayers
  - Structure of Acetylcholine M2 Segment in Lipid Micelles and Bilayers
  - Discussion
  - Acknowledgments
- [15]: Paramagnetic Probes in Metalloproteins
  - 1 Introduction: Solving Solution Structures of Paramagnetic Proteins
  - 2 Use of Nonconventional Constraints for Structure Calculations
  - 3 Paramagnetic Probes and Orientation Constraints
  - 4 Cross Correlation and Hyperfine Interaction
  - 5 Experimental Techniques
Section II: Macromolecular complexes
- [16]: Protein–DNA Interactions
  - Introduction
  - I Structure Determination of Protein in Protein–DNA Complex
  - II DNA Assignment
  - III Assignment of Interface
  - IV Refinement of Protein–DNA Complexes
  - V Concluding Remarks
  - Acknowledgments
- [17]: Nuclear Magnetic Resonance Methods to Study Structure and Dynamics of RNA–Protein Complexes
  - Introduction
  - Obtaining Spectral Assignments in RNA–Protein Complexes
  - Mapping Interaction Surfaces by NMR
  - Structure Determination of Large RNAs and RNA–Protein Complexes
  - Strategies for Efficient and Reliable Structure Calculations
  - Conformational Dynamics in Protein–RNA Interaction
  - Conclusions and Perspectives
- [18]: Protein–protein interactions probed by nuclear magnetic resonance spectroscopy
  - Introduction
  - Structure Determination of Protein Complexes
  - Mapping Protein Binding Interfaces
  - Probing Conformation of Small Peptides Weakly Bound to Target Proteins
  - Perspective
  - Acknowledgments
- [19]: Solid-State Nuclear Magnetic Resonance Techniques for Structural Studies of Amyloid Fibrils
  - Introduction
  - Peptide Backbone Conformations in Amyloid Fibrils
  - Supramolecular Organization of Amyloid Fibrils
  - Conclusion
  - Acknowledgments
Author Index
Subject Index