Structure computation and dynamics in protein NMR

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Structure computation and dynamics in protein NMR / edited by N. Rama Krishna and Lawrence J. Berliner

資料種別:

図書

出版情報:

New York : Kluwer Academic/Plenum Publishers, c1999

形態:

xxi, 554 p ; 24 cm

シリーズ名:

Biological magnetic resonance / edited by Lawrence J. Berliner and Jacques Reuben ; v. 17 <BA00368883>

著者名:

ISBN:

9780306459535 [0306459531]

書誌ID:

BA43691665

子書誌情報

フルテキスト

所蔵情報

他の版・巻

書誌詳細

注記:

Includes bibliographical references and index

主題:

Nuclear magnetic resonance; Proteins--Analysis; Proteins--Structure

言語:

英語

目次情報:

Computational Methods / Section I.：

Aspects of Modeling Biomolecular Structure on the Basis of Spectroscopic or Diffraction Data / Wilfred F. van Gunsteren ; Alexandre M. J. J. Bonvin ; Xavier Daura ; Lorna J. SmithChapter 1：

Introduction / 1.：

The Molecular Modeling Approach / 2.：

Generating Ensembles Consistent with Experimental Data / 3.：

Six Aspects of Structure Determination Based on Experimental Data / 4.：

Choice of Degrees of Freedom r for Generating an Ensemble and for Calculating q(r) / 4.1.：

Choice of Physical Force Field V[superscript phys](r) / 4.2.：

Choice of (Empirical) Function q(r) for Calculating the Quantity q Using r / 4.3.：

Choice of Penalty Function V[superscript qr] ([q(r)][subscript r]; q[superscript obs]) to Restrain [q(r)][subscript r] to q[superscript obs] / 4.4.：

Quality of the Experimental Data q[superscript obs] to Guide the Restraining / 4.5.：

Choice of Method and Extent of Boltzmann Sampling of the Configurational Space / 4.6.：

Assessing the Quality of the Obtained Ensemble of Structures / 5.：

Pitfalls That Can Be Avoided / 6.：

References

Combined Automated Assignment of NMR Spectra and Calculation of Three-Dimensional Protein Structures / Yuan Xu ; Catherine H. Schein ; Werner BraunChapter 2：

Computational Methods for Sequence-Specific Resonance Assignments

Graph Theory / 2.1.：

Genetic Algorithms and Mutual Information Method / 2.2.：

Neural Networks / 2.3.：

Matching Rungs on a Ladder: Automated Sequential Assignment Using Isotopically Labeled Proteins / 2.4.：

Combinatorial Optimization and Monte Carlo Simulated Annealing of Score Functions / 2.5.：

Real-Space Assignment / 2.6.：

Automated Stereospecific Assignments

Concepts / 3.1.：

Tests, Applications, and Assessment / 3.2.：

Combined Automated NOESY Spectra Assignment and 3D Structure Calculation

Molecular Dynamics Calculations with Ambiguous Restraints

Self-Correcting Distance Geometry Method

Future Improvements and Outlook

NMR Pulse Sequences and Computational Approaches for Automated Analysis of Sequence-Specific Backbone Resonance Assignments of Proteins / Gaetano T. Montelione ; Carlos B. Rios ; G. V. T. Swapna ; Diane E. ZimmermanChapter 3：

Systems for Automated Analysis of Resonance Assignments from Triple-Resonance NMR Spectra

Autoassign

The Algorithm

The Philosophy of AUTOASSIGN

Generic Spin System Objects / 3.3.：

Constraint Propagation / 3.4.：

Representative Results / 3.5.：

Practical Considerations in Data Collection and Processing

General Considerations

Peak Picking of NMR Spectra

Validation of Input Files

Experiments for Automated Analysis of Backbone Resonance Assignments

HSQC / 5.1.：

HNCO / 5.2.：

HN(CA)CO / 5.3.：

HNCA / 5.4.：

HACA(CO)NH / 5.5.：

HACANH / 5.6.：

C-C and C-H Phase Information in HACA(CO)NH and HACANH Experiments / 5.7.：

CBCA(CO)NH / 5.8.：

CBCANH / 5.9.：

C-C and C-H Phase Information in CBCA(CO)NH and CBCANH Experiments / 5.10.：

Future Developments

Calculation of Symmetric Oligomer Structures from NMR Data / Sean I. O'Donoghue ; Michael NilgesChapter 4：

Summary

Symmetry in Macromolecular Aggregates

The Problem: Symmetry Degeneracy in NMR Spectra

Reducing Symmetry Degeneracy with Asymmetric Labeling

The Symmetry-ADR Calculation Method

Symmetry Restraint Terms

Ambiguous Distance Restraints (ADRs)

Annealing Protocols

Iterative Structure Calculation and Explicit Assignment of ADRs

Other Restraint Terms

Experiences with the Symmetry-ADR Method

Initial Test Calculations

ssDBP Dimer

Leucine Zipper Homodimers

p53 Tetramerization Domain

Symmetric Oligomers Solved by NMR

Discussion

Problems of the Symmetry-ADR Method / 6.1.：

Should Symmetry Restraint Terms Be Used? / 6.2.：

Alternatives to the Symmetry-ADR Method / 6.3.：

Symbols

Hybrid-Hybrid Matrix Method for 3D NOESY-NOESY Data Refinements / Elliott K. Gozansky ; Varatharasa Thiviyanathan ; Nishantha Illangasekare ; Bruce A. Luxon ; David G. GorensteinChapter 5：

Simulation Studies Describing 3D NOESY-NOESY Cross Peaks, Approximate versus Exact Methods

Hybrid-Hybrid Relaxation Matrix Method for 3D NOESY-NOESY Data Analysis

Theory and Methods: Deconvolution of 2D NOESY Volumes from 3D NOESY-NOESY Volumes

Three-Dimensional Simulation Test and Effect of Added Noise

Hybrid-Hybrid Relaxation Matrix Structural Refinement of Duplex DNA from Simulated 3D NOESY-NOESY Data

Hybrid-Hybrid Matrix: Experimental Refinement Test on a DNA Three-Way Junction

Conclusions

Conformational Ensemble Calculations: Analysis of Protein and Nucleic Acid NMR Data / Anwer Mujeeb ; Nikolai B. Ulyanov ; Todd M. Billeci ; Shauna Farr-Jones ; Thomas L. JamesChapter 6：

Determination of Structural Restraints

Interproton Distance Restraints

Coupling Constants and Torsion-Angle Restraints

Other Types of Restraints

Indices of Agreement

Assessment of Conformational Flexibility

Ensemble Calculations

Overview

Relaxation-Rate-Based Probability Calculations

Experimental Examples

[omega]-Conotoxin MVIIC

Nucleic Acid Example

Complete Relaxation and Conformational Exchange Matrix (CORCEMA) Analysis of NOESY Spectra of Reversibly Forming Ligand-Receptor Complexes / Chapter 7：

Application to Transferred NOESY / N. Rama Krishna ; Hunter N. B. Moseley

Molecular Complexes and Conformational Exchange / 1.1.：

Reversible Binding and Transferred NOESY / 1.2.：

CORCEMA Theory

Basic Formulation

Two-State Model of Ligand-Receptor Interactions

Treatment for More than Two States

Intermolecular Transferred NOESY

Treatment of Nonspecific Binding

Methods

The CORCEMA Program

Calculation of Concentrations

Methods for Suppressing or Identifying Protein-Mediated Effects

Methods for Observing Intermolecular Transferred NOESY Contacts

Structure Refinement Calculations

Characterization of Some Critical Factors Using Simulated Transferred NOESY Data

Finite Receptor Off-Rates

Effect of Ligand-Receptor Ratio on the Ligand Transferred NOESY

Role of Ligand-Protein Intermolecular Dipolar Relaxation

Ligand-Protein Intermolecular NOESY Intensity as a Function of Off-Rate

Effect of Motions in the Protein-Ligand Complex on the Transferred NOESY

Thrombin-Bound Structures of Human Fibrinopeptide Analogs

Studies on Blood Group A Trisaccharide Bound to Dolichos biflorus Lectin

Transferred NOESY Studies on the Forssman Pentasaccharide Complexed to Dolichos biflorus

Interaction of Sialy1 Lewis[superscript x] Tetrasaccharide with E-selectin

Reversible Binding of Corepressor Tryptophan with Repressor-Operator Complex

Final Comments

Structure and Dynamics / Section II.：

Protein Structure and Dynamics from Field-Induced Residual Dipolar Couplings / James H. Prestegard ; Joel R. Tolman ; Hashim M. Al-Hashimi ; Michael AndrecChapter 8：

Theory

Anisotropic Spin Interactions in Solution-State NMR

The Dipolar Hamiltonian

Residual Dipolar Couplings under Magnetic Field Alignment

Early History of Observation

Application to Protein Systems

Measurement of Residual Dipolar Couplings

Frequency-Domain Experiments

Intensity-Based Experiments

Other Contributions to Multiplet Splittings

Effects of Transverse Relaxation

Dynamic Frequency Shifts

Structure Determination Protocols / 7.：

The Effects of Molecular Motion and Their Separation / 8.：

The Cone-and-Arc Model / 8.1.：

Order Matrix Analysis: A Test for Rigid Model Validity / 8.2.：

Recent Developments in Studying the Dynamics of Protein Structures from [superscript 15]N and [superscript 13]C Relaxation Time Measurements / Jan Engelke ; Heinz RuterjansChapter 9：

General Features of Dynamics

Microdynamic Motional Parameters

Theory of Relaxation in Proteins

Experiments for the Determination of Relaxation Rates

Backbone Dynamics Derived from [superscript 15]N Relaxation Rates

Experimental Details

Processing of Spectra and Determination of Relaxation Rates

Calculation of Microdynamical Parameters

Interpretation of Microdynamical Parameters

Backbone Dynamics Derived from [superscript 13]C[superscript alpha] Relaxation Rates

Analysis of the Multispin Relaxation of [superscript 13]C[superscript alpha]

Experiments to Determine the [superscript 13]C[superscript alpha] Relaxation Rates

Microdynamical Parameters Derived from [superscript 13]C[superscript alpha] Relaxation Rates

Side-Chain Dynamics Derived from [superscript 13]C[superscript beta] Relaxation Rates

Dynamical Parameters Derived from T[subscript 1] Relaxation Times and Steady-State NOE

SIIS Cross Relaxation

Determination of Protein Dynamics in the Microsecond Time Window

Determination of Protein Dynamics in the Millisecond Time Window

Concluding Remarks

Multinuclear Relaxation Dispersion Studies of Protein Hydration / Bertil Halle ; Vladimir P. Denisov ; Kandadai VenuChapter 10：

Methodology of Water NMRD

Conventional Field Variation

Fast Field Cycling

NMR Properties of the Water Nuclei

Relaxation Mechanisms

Quadrupolar Relaxation

Dipolar Relaxation

Relaxation due to Isotropic Couplings

Molecular Motions

Spatial Resolution

Temporal Resolution

Water Relaxation in Semisolid Proteins

Quantitative Analysis of NMRD Data

Parametrization of the NMRD Profile

Correlation Time

Dispersion Amplitude

High-Frequency Plateau

NMRD Time Scales

Stretched Dispersions

Labile Hydrogens

Outlook

Hydration Studies of Biological Macromolecules by Intermolecular Water-Solute NOEs / Gottfried OttingChapter 11：

Theoretical Background for Intermolecular NOEs

NOE between Two Rigidly Bound Protons

NOE between Solute Proton and Bound but Locally Reorientating Water

NOE with Rapidly Diffusing Water Molecules

Assignments of Water-Solute Cross Peaks

NMR Experiments for the Detection of Intermolecular NOEs with Water

Water Suppression

Selective Water Excitation

Nonselective Experiments

Dipolar Field Effects

Applications

Studies of Protein Hydration

Studies of DNA and RNA Hydration

Summary of the Results

Residence Times

Structural Relevance

Future Perspectives

Conclusion

Contents of Previous Volumes

Index

Computational Methods / Section I.：

Aspects of Modeling Biomolecular Structure on the Basis of Spectroscopic or Diffraction Data / Wilfred F. van Gunsteren ; Alexandre M. J. J. Bonvin ; Xavier Daura ; Lorna J. SmithChapter 1：

Introduction / 1.：

The Molecular Modeling Approach / 2.：

Generating Ensembles Consistent with Experimental Data / 3.：

Six Aspects of Structure Determination Based on Experimental Data / 4.：

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