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.: |