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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:9780121822408
9 7 8 - 0 - 1 2 - 1 8 2 2 4 0 - 8
eBook ISBN:9780080496894
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.
Biochemists, biophysicists, molecular biologists, and cell biologists.
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
No. of pages: 454
Language: English
Published: June 29, 2001
Imprint: Academic Press
Hardback ISBN: 9780121822408
eBook ISBN: 9780080496894
TJ
Thomas L. James
Affiliations and expertise
School of Pharmacy, University of California, San Francisco, U.S.A.
VD
Volker Dotsch
Affiliations and expertise
University of California, San Francisco, U.S.A.
US
Uli Schmitz
Affiliations and expertise
Gemlabs Technologies, Inc., Redwood City, California, U.S.A.