Structure computation and dynamics in protein NMR:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
New York [u.a.]
Kluwer Acad., Plenum Publ.
1999
|
| Series: | Biological magnetic resonance
17 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Einzelaufn. eines Zs.-Bds. |
| Physical Description: | XXI, 554 S. graph. Darst. |
| ISBN: | 0306459531 |
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| 245 | 1 | 0 | |a Structure computation and dynamics in protein NMR |c ed. by N. Rama Krishna ... |
| 264 | 1 | |a New York [u.a.] |b Kluwer Acad., Plenum Publ. |c 1999 | |
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| 490 | 0 | |a Biological magnetic resonance |v 17 | |
| 500 | |a Einzelaufn. eines Zs.-Bds. | ||
| 650 | 4 | |a Nuclear magnetic resonance | |
| 650 | 4 | |a Proteins - Analysis | |
| 650 | 4 | |a Magnetic Resonance Spectroscopy | |
| 650 | 4 | |a Nuclear Magnetic Resonance, Biomolecular | |
| 650 | 4 | |a Nuclear magnetic resonance spectroscopy | |
| 650 | 4 | |a Protein Structure | |
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| 700 | 1 | |a Krishna, N. Rama |e Sonstige |0 (DE-588)122639707 |4 oth | |
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Record in the Search Index
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|---|---|
| adam_text | Contents
Section I. Computational Methods
Chapter 1
Aspects of Modeling Biomolecular Structure on the Basis of Spectroscopic
or Diffraction Data
Wilfred F. van Gunsteren, Alexandre M. J. J. Bonvin,
Xavier Daura, and Lorna J. Smith
1. Introduction 3
2. The Molecular Modeling Approach 5
3. Generating Ensembles Consistent with Experimental Data 6
4. Six Aspects of Structure Determination Based on Experimental
Data 7
4.1. Choice of Degrees of Freedom r for Generating an Ensemble
and for Calculating q{r) 8
4.2. Choice of Physical Force Field VPhys(r) 9
4.3. Choice of (Empirical) Function q(r) for Calculating the
Quantity q Using r 12
4.4. Choice of Penalty Function V9 «g(r))r; 7°bs) to Restrain
(q(r))rtoq°hs 13
4.5. Quality of the Experimental Data ^obs to Guide the
Restraining 19
4.6. Choice of Method and Extent of Boltzmann Sampling of the
Configurational Space 21
5. Assessing the Quality of the Obtained Ensemble of Structures ... 29
xiii
xiv Contents
6. Pitfalls That Can Be Avoided 31
References 32
Chapter 2
Combined Automated Assignment of NMR Spectra and Calculation of
Three Dimensional Protein Structures
Yuan Xu, Catherine H. Schein, and Werner Braun
1. Introduction 37
2. Computational Methods for Sequence Specific Resonance
Assignments 40
2.1. Graph Theory 41
2.2. Genetic Algorithms and Mutual Information Method .... 50
2.3. Neural Networks 52
2.4. Matching Rungs on a Ladder: Automated Sequential
Assignment Using Isotopically Labeled Proteins 56
2.5. Combinatorial Optimization and Monte Carlo Simulated
Annealing of Score Functions 59
2.6. Real Space Assignment 61
3. Automated Stereospecific Assignments 62
3.1. Concepts 62
3.2. Tests, Applications, and Assessment 65
4. Combined Automated NOESY Spectra Assignment and
3D Structure Calculation 67
4.1. Molecular Dynamics Calculations with Ambiguous
Restraints 67
4.2. Self Correcting Distance Geometry Method 68
5. Future Improvements and Outlook 75
References 76
Chapter 3
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,
and Diane E. Zimmerman
1. Introduction 81
2. Systems for Automated Analysis of Resonance Assignments from
Triple Resonance NMR Spectra 82
Contents xv
3. Autoassign 85
3.1. The Algorithm 85
3.2. The Philosophy of AUTOASSIGN 87
3.3. Generic Spin System Objects 87
3.4. Constraint Propagation 87
3.5. Representative Results 90
4. Practical Considerations in Data Collection and
Processing 97
4.1. General Considerations 97
4.2. Peak Picking of NMR Spectra 99
4.3. Validation of Input Files 100
5. Experiments for Automated Analysis of Backbone
Resonance Assignments 100
5.1. HSQC 101
5.2. HNCO 104
5.3. HN(CA)CO 104
5.4. HNCA 108
5.5. HACA(CO)NH 109
5.6. HACANH 114
5.7. C C and C H Phase Information in HACA(CO)NH and
HACANH Experiments 115
5.8. CBCA(CO)NH 121
5.9. CBCANH 121
5.10. C C and C H Phase Information in CBCA(CO)NH and
CBCANH Experiments 126
6. Future Developments 127
References 128
Chapter 4
Calculation of Symmetric Oligomer Structures from NMR Data
Sedn I. O Donoghue and Michael Nilges
1. Summary 131
2. Introduction 132
2.1. Symmetry in Macromolecular Aggregates 132
2.2. The Problem: Symmetry Degeneracy in NMR Spectra ... 136
2.3. Reducing Symmetry Degeneracy with
Asymmetric Labeling 137
3. The Symmetry ADR Calculation Method 138
3.1. Symmetry Restraint Terms 138
xvi Contents
3.2. Ambiguous Distance Restraints (ADRs) 140
3.3. Annealing Protocols 142
3.4. Iterative Structure Calculation and Explicit Assignment
of ADRs 145
3.5. Other Restraint Terms 146
4. Experiences with the Symmetry ADR Method 147
4.1. Initial Test Calculations 147
4.2. ssDBPDimer 149
4.3. Leucine Zipper Homodimers 149
4.4. p53 Tetramerization Domain 151
5. Symmetric Oligomers Solved by NMR 152
6. Discussion 155
6.1. Problems of the Symmetry ADR Method 155
6.2. Should Symmetry Restraint Terms Be Used? 156
6.3. Alternatives to the Symmetry ADR Method 157
Symbols 157
References 158
Chapter 5
Hybrid Hybrid Matrix Method for 3D NOESY NOESY Data Refinements
Elliott K. Gozansky, Varatharasa Thiviyanathan, Nishantha Illangasekare,
Bruce A. Luxon, and David G. Gorenstein
1. Introduction 163
2. Simulation Studies Describing 3D NOESY NOESY Cross Peaks,
Approximate versus Exact Methods 167
3. Hybrid Hybrid Relaxation Matrix Method for 3D
NOESY NOESY Data Analysis 171
3.1. Theory and Methods: Deconvolution of 2D NOESY
Volumes from 3D NOESY NOESY Volumes 173
3.2. Three Dimensional Simulation Test and Effect of Added
Noise 176
3.3. Hybrid Hybrid Relaxation Matrix Structural Refinement
of Duplex DNA from Simulated 3D NOESY NOESY
Data 177
4. Hybrid Hybrid Matrix: Experimental Refinement Test on a DNA
Three Way Junction 190
5. Conclusions 194
References 198
Contents xvii
Chapter 6
Conformational Ensemble Calculations: Analysis of Protein and Nucleic
Acid NMR Data
Anwer Mujeeb, Nikolai B. Ulyanov, Todd M. Billed, Shauna Farr Jones,
and Thomas L. James
1. Introduction 201
2. Determination of Structural Restraints 203
2.1. Interproton Distance Restraints 203
2.2. Coupling Constants and Torsion Angle Restraints 207
2.3. Other Types of Restraints 209
2.4. Indices of Agreement 209
3. Assessment of Conformational Flexibility 210
4. Ensemble Calculations 212
4.1. Overview 212
4.2. Relaxation Rate Based Probability Calculations 213
5. Experimental Examples 214
5.1. w Conotoxin MVIIC 214
5.2. Nucleic Acid Example 216
6. Conclusions 219
References 220
Chapter 7
Complete Relaxation and Conformational Exchange Matrix (CORCEMA)
Analysis of NOESY Spectra of Reversibly Forming Ligand Receptor
Complexes
Application to Transferred NOESY
N. Rama Krishna and Hunter N. B. Moseley
1. Introduction 223
1.1. Molecular Complexes and Conformational Exchange .... 224
1.2. Reversible Binding and Transferred NOESY 225
2. CORCEMA Theory 230
2.1. Basic Formulation 230
2.2. Two State Model of Ligand Receptor Interactions 233
2.3. Treatment for More than Two States 240
2.4. Intermolecular Transferred NOESY 244
2.5. Treatment of Nonspecific Binding 244
3. Methods 246
3.1. The CORCEMA Program 246
3.2. Calculation of Concentrations 247
xviii Contents
3.3. Methods for Suppressing or Identifying Protein Mediated
Effects 249
3.4. Methods for Observing Intermolecular Transferred NOESY
Contacts 255
3.5. Structure Refinement Calculations 261
4. Characterization of Some Critical Factors Using Simulated
Transferred NOESY Data 267
4.1. Finite Receptor Off Rates 268
4.2. Effect of Ligand Receptor Ratio on the Ligand Transferred
NOESY 270
4.3. Role of Ligand Protein Intermolecular
Dipolar Relaxation 272
4.4. Ligand Protein Intermolecular NOESY Intensity as a
Function of Off Rate 277
4.5. Effect of Motions in the Protein Ligand Complex on the
Transferred NOESY 278
5. Experimental Examples 281
5.1. Thrombin Bound Structures of Human Fibrinopeptide
Analogs 282
5.2. Studies on Blood Group A Trisaccharide Bound to Dolichos
biflorus Lectin 283
5.3. Transferred NOESY Studies on the Forssman Pentasaccharide
Complexed to Dolichos biflorus 285
5.4. Interaction of Sialyl Lewis Tetrasaccharide
with E selectin 290
5.5. Reversible Binding of Corepressor Tryptophan with
Repressor Operator Complex 297
6. Final Comments 301
References 302
Section II. Structure and Dynamics
Chapter 8
Protein Structure and Dynamics from Field Induced Residual Dipolar
Couplings
James H. Prestegard, Joel R. Tolman, Hashim M. Al Hashimi, and
Michael Andrec
1. Introduction 311
Contents xix
2. Theory 314
2.1. Anisotropic Spin Interactions in Solution State NMR .... 314
2.2. The Dipolar Hamiltonian 315
2.3. Residual Dipolar Couplings under Magnetic
Field Alignment 316
3. Early History of Observation 320
4. Application to Protein Systems 322
5. Measurement of Residual Dipolar Couplings 328
5.1. Frequency Domain Experiments 328
5.2. Intensity Based Experiments 333
6. Other Contributions to Multiplet Splittings 336
6.1. Effects of Transverse Relaxation 336
6.2. Dynamic Frequency Shifts 337
7. Structure Determination Protocols 339
8. The Effects of Molecular Motion and Their Separation 344
8.1. The Cone and Arc Model 344
8.2. Order Matrix Analysis: A Test for Rigid Model Validity ... 348
References 353
Chapter 9
Recent Developments in Studying the Dynamics of Protein Structures from
15N and 13C Relaxation Time Measurements
Jan Engelke and Heinz Ruterjans
1. Introduction 357
1.1. General Features of Dynamics 357
1.2. Microdynamic Motional Parameters 359
2. Methods 361
2.1. Theory of Relaxation in Proteins 361
2.2. Experiments for the Determination of Relaxation Rates . . . 365
3. Backbone Dynamics Derived from 15N Relaxation Rates 370
3.1. Experimental Details 370
3.2. Processing of Spectra and Determination of Relaxation
Rates 376
3.3. Calculation of Microdynamical Parameters 377
3.4. Interpretation of Microdynamical Parameters 381
4. Backbone Dynamics Derived from 13C Relaxation Rates 385
4.1. Analysis of the Multispin Relaxation of 13Ca 386
4.2. Experiments to Determine the 13C° Relaxation Rates .... 391
xx Contents
4.3. Microdynamical Parameters Derived from 13C Relaxation
Rates 394
5. Side Chain Dynamics Derived from 13C^ Relaxation Rates .... 395
5.1. Dynamical Parameters Derived from 7 Relaxation Times
and Steady State NOE 396
5.2. SIIS Cross Relaxation 402
6. Determination of Protein Dynamics in the Microsecond Time
Window 406
7. Determination of Protein Dynamics in the Millisecond Time
Window 409
8. Concluding Remarks 414
References 414
Chapter 10
Multinuclear Relaxation Dispersion Studies of Protein Hydration
Bertil Halle, Vladimir P. Denisov, and Kandadai Venu
1. Introduction 419
2. Methodology of Water NMRD 421
2.1. Conventional Field Variation 421
2.2. Fast Field Cycling 424
2.3. NMR Properties of the Water Nuclei 429
3. Relaxation Mechanisms 432
3.1. Quadrupolar Relaxation 433
3.2. Dipolar Relaxation 437
3.3. Relaxation due to Isotropic Couplings 442
4. Molecular Motions 444
4.1. Spatial Resolution 446
4.2. Temporal Resolution 451
4.3. Water Relaxation in Semisolid Proteins 457
5. Quantitative Analysis of NMRD Data 462
5.1. Parametrization of the NMRD Profile 462
5.2. Correlation Time 465
5.3. Dispersion Amplitude 466
5.4. High Frequency Plateau 470
5.5. NMRD Time Scales 471
5.6. Stretched Dispersions 474
5.7. Labile Hydrogens 477
6. Outlook 480
References 481
Contents xxi
Chapter 11
Hydration Studies of Biological Macromolecules by Intermolecular
Water Solute NOEs
Gottfried Otting
1. Introduction 485
2. Theoretical Background for Intermolecular NOEs 487
2.1. NOE between Two Rigidly Bound Protons 488
2.2. NOE between Solute Proton and Bound but Locally
Reorientating Water 489
2.3. NOE with Rapidly Diffusing Water Molecules 490
3. Assignments of Water Solute Cross peaks 493
4. NMR Experiments for the Detection of Intermolecular NOEs
with Water 494
4.1. Water Suppression 494
4.2. Selective Water Excitation 496
4.3. Nonselective Experiments 508
4.4. Dipolar Field Effects 511
5. Applications 511
5.1. Studies of Protein Hydration 511
5.2. Studies of DNA and RNA Hydration 516
6. Summary of the Results 519
6.1. Residence Times 519
6.2. Structural Relevance 521
6.3. Future Perspectives 523
7. Conclusion 523
References 524
Contents of Previous Volumes 529
Index 545
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| indexdate | 2024-07-09T18:42:04Z |
| institution | BVB |
| isbn | 0306459531 |
| language | English |
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| physical | XXI, 554 S. graph. Darst. |
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| spelling | Structure computation and dynamics in protein NMR ed. by N. Rama Krishna ... New York [u.a.] Kluwer Acad., Plenum Publ. 1999 XXI, 554 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biological magnetic resonance 17 Einzelaufn. eines Zs.-Bds. Nuclear magnetic resonance Proteins - Analysis Magnetic Resonance Spectroscopy Nuclear Magnetic Resonance, Biomolecular Nuclear magnetic resonance spectroscopy Protein Structure Proteins Structure Krishna, N. Rama Sonstige (DE-588)122639707 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009013980&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Structure computation and dynamics in protein NMR Nuclear magnetic resonance Proteins - Analysis Magnetic Resonance Spectroscopy Nuclear Magnetic Resonance, Biomolecular Nuclear magnetic resonance spectroscopy Protein Structure Proteins Structure |
| title | Structure computation and dynamics in protein NMR |
| title_auth | Structure computation and dynamics in protein NMR |
| title_exact_search | Structure computation and dynamics in protein NMR |
| title_full | Structure computation and dynamics in protein NMR ed. by N. Rama Krishna ... |
| title_fullStr | Structure computation and dynamics in protein NMR ed. by N. Rama Krishna ... |
| title_full_unstemmed | Structure computation and dynamics in protein NMR ed. by N. Rama Krishna ... |
| title_short | Structure computation and dynamics in protein NMR |
| title_sort | structure computation and dynamics in protein nmr |
| topic | Nuclear magnetic resonance Proteins - Analysis Magnetic Resonance Spectroscopy Nuclear Magnetic Resonance, Biomolecular Nuclear magnetic resonance spectroscopy Protein Structure Proteins Structure |
| topic_facet | Nuclear magnetic resonance Proteins - Analysis Magnetic Resonance Spectroscopy Nuclear Magnetic Resonance, Biomolecular Nuclear magnetic resonance spectroscopy Protein Structure Proteins Structure |
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