Residual Dipolar Couplings in Structure Determination of Biomolecules

NMRPipe: A multidimensional spectral processing system based on UNIX pipes

Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J., & Bax, A. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197809 · Cited by 15,965

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,715

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995) · Computer Physics Communications · doi:10.1016/0010-4655(95)00041-d · Cited by 3,124

Torsion angle dynamics for NMR structure calculation with the new program Dyana

Güntert, P., Mumenthaler, C., & Wüthrich, K. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1284 · Cited by 2,782

Attenuated T 2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution

Pervushin, K., Riek, R., Wider, G., & Wüthrich, K. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.23.12366 · Cited by 2,445

The Xplor-NIH NMR molecular structure determination package

Schwieters, C. D., Kuszewski, J. J., Tjandra, N., & Marius Clore, G. (2003) · Journal of Magnetic Resonance · doi:10.1016/s1090-7807(02)00014-9 · Cited by 2,369

Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium

Tjandra, N., & Bax, A. (1997) · Science · doi:10.1126/science.278.5340.1111 · Cited by 1,719

Measurement ofJand Dipolar Couplings from Simplified Two-Dimensional NMR Spectra

Ottiger, M., Delaglio, F., & Bax, A. (1998) · Journal of Magnetic Resonance · doi:10.1006/jmre.1998.1361 · Cited by 967

Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.

Tolman, J. R., Flanagan, J. M., Kennedy, M. A., & Prestegard, J. H. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.20.9279 · Cited by 837

Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions

Hansen, M. R., Mueller, L., & Pardi, A. (1998) · Nature Structural Biology · doi:10.1038/4176 · Cited by 703

Prediction of Sterically Induced Alignment in a Dilute Liquid Crystalline Phase: Aid to Protein Structure Determination by NMR

Zweckstetter, M., & Bax, A. (2000) · Journal of the American Chemical Society · doi:10.1021/ja0000908 · Cited by 702

Alignment of Biological Macromolecules in Novel Nonionic Liquid Crystalline Media for NMR Experiments

Rückert, M., & Otting, G. (2000) · Journal of the American Chemical Society · doi:10.1021/ja001068h · Cited by 632

Order Matrix Analysis of Residual Dipolar Couplings Using Singular Value Decomposition

Losonczi, J. A., Andrec, M., Fischer, M. W. F., & Prestegard, J. H. (1999) · Journal of Magnetic Resonance · doi:10.1006/jmre.1999.1754 · Cited by 573

Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution

Tjandra, N., Omichinski, J. G., Gronenborn, A. M., Clore, G. M., & Bax, A. (1997) · Nature Structural Biology · doi:10.1038/nsb0997-732 · Cited by 481

NMR structures of biomolecules using field oriented media and residual dipolar couplings

Prestegard, J. H., Al-Hashimi, H. M., & Tolman, J. R. (2000) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583500003656 · Cited by 439

Dipolar Couplings in Macromolecular Structure Determination

Bax, A., Kontaxis, G., & Tjandra, N. (2001) · Methods in Enzymology · doi:10.1016/s0076-6879(01)39313-8 · Cited by 418

Weak alignment offers new NMR opportunities to study protein structure and dynamics

Bax, A. (2003) · Protein Science · doi:10.1110/ps.0233303 · Cited by 400

Glycosyltransferase structure and mechanism

Ünligil, U. M., & Rini, J. M. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00124-x · Cited by 361

Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses

Clore, G. M., Starich, M. R., & Gronenborn, A. M. (1998) · Journal of the American Chemical Society · doi:10.1021/ja982592f · Cited by 316

Evaluation of Backbone Proton Positions and Dynamics in a Small Protein by Liquid Crystal NMR Spectroscopy

Ulmer, T. S., Ramirez, B. E., Delaglio, F., & Bax, A. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0350684 · Cited by 301

Structural Evaluation of Phospholipid Bicelles for Solution-State Studies of Membrane-Associated Biomolecules

Glover, K. J., Whiles, J. A., Wu, G., Yu, N.-J., Deems, R., Struppe, J. O., Stark, R. E., Komives, E. A., & Vold, R. R. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)75864-x · Cited by 297

Magnetic Field Dependence of Nitrogen−Proton J Splittings in 15N-Enriched Human Ubiquitin Resulting from Relaxation Interference and Residual Dipolar Coupling

Tjandra, N., Grzesiek, S., & Bax, A. (1996) · Journal of the American Chemical Society · doi:10.1021/ja960106n · Cited by 285

Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules

Ottiger, M., & Bax, A. (1998) · Journal of Biomolecular NMR · doi:10.1023/a:1008366116644 · Cited by 273

Determination of Relative N−HN, N−C‘, Cα−C‘, and Cα−Hα Effective Bond Lengths in a Protein by NMR in a Dilute Liquid Crystalline Phase

Ottiger, M., & Bax, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja9826791 · Cited by 254

Protein Structure Determination Using Molecular Fragment Replacement and NMR Dipolar Couplings

Delaglio, F., Kontaxis, G., & Bax, A. (2000) · Journal of the American Chemical Society · doi:10.1021/ja993603n · Cited by 251

A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles*

Chou, J. J., Gaemers, S., Howder, B., Louis, J. M., & Bax, A. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1013336502594 · Cited by 243

A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings

Dosset, P., Hus, J.-C., Marion, D., & Blackledge, M. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1011206132740 · Cited by 228

Lanthanide-Induced Pseudocontact Shifts for Solution Structure Refinements of Macromolecules in Shells up to 40 Å from the Metal Ion

Allegrozzi, M., Bertini, I., Janik, M. B. L., Lee, Y.-M., Liu, G., & Luchinat, C. (2000) · Journal of the American Chemical Society · doi:10.1021/ja993691b · Cited by 215

Model-Free Analysis of Protein Backbone Motion from Residual Dipolar Couplings

Peti, W., Meiler, J., Brüschweiler, R., & Griesinger, C. (2002) · Journal of the American Chemical Society · doi:10.1021/ja011883c · Cited by 207

Quaternary structure of hemoglobin in solution

Lukin, J. A., Kontaxis, G., Simplaceanu, V., Yuan, Y., Bax, A., & Ho, C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.232715799 · Cited by 204

The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase

Tjandra, N., Tate, S.-I., Ono, A., Kainosho, M., & Bax, A. (2000) · Journal of the American Chemical Society · doi:10.1021/ja000324n · Cited by 202

REDCAT: a residual dipolar coupling analysis tool

Valafar, H., & Prestegard, J. H. (2004) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2003.12.012 · Cited by 186

Micelle-Induced Curvature in a Water-Insoluble HIV-1 Env Peptide Revealed by NMR Dipolar Coupling Measurement in Stretched Polyacrylamide Gel

Chou, J. J., Kaufman, J. D., Stahl, S. J., Wingfield, P. T., & Bax, A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja017875d · Cited by 184

High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium

Bax, A., & Tjandra, N. (1997) · Journal of Biomolecular NMR · doi:10.1023/a:1018308717741 · Cited by 184

De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta

Rohl, C. A., & Baker, D. (2002) · Journal of the American Chemical Society · doi:10.1021/ja016880e · Cited by 179

Structural Characterization of Proteins with an Attached ATCUN Motif by Paramagnetic Relaxation Enhancement NMR Spectroscopy

Donaldson, L. W., Skrynnikov, N. R., Choy, W.-Y., Muhandiram, D. R., Sarkar, B., Forman-Kay, J. D., & Kay, L. E. (2001) · Journal of the American Chemical Society · doi:10.1021/ja011241p · Cited by 175

Molecular Basis for Synergistic Transcriptional Activation by Oct1 and Sox2 Revealed from the Solution Structure of the 42-kDa Oct1·Sox2·Hoxb1-DNA Ternary Transcription Factor Complex

Williams, D. C., Cai, M., & Clore, G. M. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309790200 · Cited by 164

Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein

Mueller, G. A., Choy, W. Y., Yang, D., Forman-Kay, J. D., Venters, R. A., & Kay, L. E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3842 · Cited by 163

NMR dipolar couplings for the structure determination of biopolymers in solution

de Alba, E., & Tjandra, N. (2002) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/s0079-6565(01)00042-5 · Cited by 159

Variation of Molecular Alignment as a Means of Resolving Orientational Ambiguities in Protein Structures from Dipolar Couplings

Al‐Hashimi, H. M., Valafar, H., Terrell, M., Zartler, E. R., Eidsness, M. K., & Prestegard, J. H. (2000) · Journal of Magnetic Resonance · doi:10.1006/jmre.2000.2049 · Cited by 150

Evaluation of Cross-Correlation Effects and Measurement of One-Bond Couplings in Proteins with Short Transverse Relaxation Times

Kontaxis, G., Clore, G. M., & Bax, A. (2000) · Journal of Magnetic Resonance · doi:10.1006/jmre.1999.1979 · Cited by 149

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings 1 1Edited by M. F. Summers

Al‐Hashimi, H. M., Gosser, Y. Q., Gorin, A. A., Hu, W., Majumdar, A. K., & Patel, D. J. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5235 · Cited by 141

Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy

Evenäs, J., Tugarinov, V., Skrynnikov, N. R., Goto, N. K., Muhandiram, R., & Kay, L. E. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4695 · Cited by 135

SANS Study of the Structural Phases of Magnetically Alignable Lanthanide-Doped Phospholipid Mixtures

Nieh, M., Glinka, C. J., Krueger, S., Prosser, R. S., & Katsaras, J. (2001) · Langmuir · doi:10.1021/la001567w · Cited by 133

NMR Spectroscopy of Glycoconjugates

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TROSY-based HNCO pulse sequences for the measurement of 1HN-15N, 15N-13CO, 1HN-13CO, 13CO-13Cα and 1HN-13Cα dipolar couplings in 15N, 13C, 2H-labeled proteins

Yang, D., Venters, R. A., Mueller, G. A., Choy, W., & Kay, L. E. (1999) · Journal of Biomolecular NMR · doi:10.1023/a:1008314803561 · Cited by 128

Docking of Protein−Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1 H N / 15 N Chemical Shift Mapping and Backbone 15 N− 1 H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics

Clore, G. M., & Schwieters, C. D. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028893d · Cited by 122

A Dipolar Coupling Based Strategy for Simultaneous Resonance Assignment and Structure Determination of Protein Backbones

Tian, F., Valafar, H., & Prestegard, J. H. (2001) · Journal of the American Chemical Society · doi:10.1021/ja011806h · Cited by 114

Conformational Analysis of a Flexible Oligosaccharide Using Residual Dipolar Couplings

Tian, F., Al‐Hashimi, H. M., Craighead, J. L., & Prestegard, J. H. (2000) · Journal of the American Chemical Society · doi:10.1021/ja002900l · Cited by 113

A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings

Cordier, F., Dingley, A. J., & Grzesiek, S. (1999) · Journal of Biomolecular NMR · doi:10.1023/a:1008301415843 · Cited by 112

Paramagnetism-based versus classical constraints: An analysis of the solution structure of Ca Ln calbindin D9k

Bertini, I., Donaire, A., Jiménez, B., et al. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1012422402545 · Cited by 110

Determination of the Interface of a Large Protein Complex by Transferred Cross-saturation Measurements

Nakanishi, T., Miyazawa, M., Sakakura, M., Terasawa, H., Takahashi, H. K., & Shimada, I. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00018-9 · Cited by 110

A set of HNCO-based experiments for measurement of residual dipolar couplings in 15N, 13C, (2H)-labeled proteins

Permi, P., Rosevear, P. R., & Annila, A. (2000) · Journal of Biomolecular NMR · doi:10.1023/a:1008372624615 · Cited by 105

Quantitative NMR Studies of High Molecular Weight Proteins: Application to Domain Orientation and Ligand Binding in the 723 Residue Enzyme Malate Synthase G

Tugarinov, V., & Kay, L. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00238-9 · Cited by 105

Improved Sensitivity and Resolution in 1H−13C NMR Experiments of RNA

Brutscher, B., Boisbouvier, J., Pardi, A., Marion, D., & Simorre, J. (1998) · Journal of the American Chemical Society · doi:10.1021/ja982853l · Cited by 104

Observation of Long-Range 1H−1H Distances in Solution by Dipolar Coupling Interactions

Hansen, M. R., Rance, M., & Pardi, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja9829665 · Cited by 103

Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel

Ishii, Y., Markus, M. A., & Tycko, R. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1012417721455 · Cited by 99

Structure and Orientation of a G Protein Fragment in the Receptor Bound State from Residual Dipolar Couplings

Koenig, B. W., Kontaxis, G., Mitchell, D. C., Louis, J. M., Litman, B. J., & Bax, A. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00745-3 · Cited by 98

What is the average conformation of bacteriophage T4 lysozyme in solution? a domain orientation study using dipolar couplings measured by solution NMR 1 1Edited by P. E. Wright

Goto, N. K., Skrynnikov, N. R., Dahlquist, F. W., & Kay, L. E. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4614 · Cited by 89

Residual dipolar coupling derived orientational constraints on ligand geometry in a 53 kDa protein-ligand complex

Bolon, P. J., Al‐Hashimi, H. M., & Prestegard, J. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3133 · Cited by 80

The Southeast Collaboratory for Structural Genomics: A High-Throughput Gene to Structure Factory

Adams, M. W. W., Dailey, H. A., DeLucas, L. J., et al. (2003) · Accounts of Chemical Research · doi:10.1021/ar0101382 · Cited by 77

Measurement of Methyl 2H Quadrupolar Couplings in Oriented Proteins. How Uniform Is the Quadrupolar Coupling Constant?

Mittermaier, A., & Kay, L. E. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9925047 · Cited by 73

Single-Step Determination of Protein Substructures Using Dipolar Couplings: Aid to Structural Genomics

Zweckstetter, M., & Bax, A. (2001) · Journal of the American Chemical Society · doi:10.1021/ja016496h · Cited by 70

Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings

Azurmendi, H. F., Martín‐Pastor, M., & Bush, C. A. (2002) · Biopolymers · doi:10.1002/bip.10015 · Cited by 70

Measurement of Homonuclear Proton Couplings from Regular 2D COSY Spectra

Delaglio, F., Wu, Z., & Bax, A. (2001) · Journal of Magnetic Resonance · doi:10.1006/jmre.2001.2297 · Cited by 69

Simultaneous Measurement of 1H−15N, 1H−13C‘, and 15N−13C‘ Dipolar Couplings in a Perdeuterated 30 kDa Protein Dissolved in a Dilute Liquid Crystalline Phase

Wang, Y., Marquardt, J. L., Wingfield, P. T., Stahl, S. J., Lee‐Huang, S., Torchia, D. A., & Bax, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja980862o · Cited by 66

Using Conjoined Rigid Body/Torsion Angle Simulated Annealing to Determine the Relative Orientation of Covalently Linked Protein Domains from Dipolar Couplings

Clore, G. M., & Bewley, C. A. (2002) · Journal of Magnetic Resonance · doi:10.1006/jmre.2001.2489 · Cited by 63

Refined Solution Structure of the Iron-responsive Element RNA Using Residual Dipolar Couplings

McCallum, S. A., & Pardi, A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01431-6 · Cited by 60

How Tetrahedral Are Methyl Groups in Proteins? A Liquid Crystal NMR Study

Ottiger, M., & Bax, A. (1999) · Journal of the American Chemical Society · doi:10.1021/ja984484z · Cited by 59

The Global Conformation of the Hammerhead Ribozyme Determined Using Residual Dipolar Couplings

Bondensgaard, K., Mollova, E. T., & Pardi, A. (2002) · Biochemistry · doi:10.1021/bi012167q · Cited by 59

An HNCO-based Pulse Scheme for the Measurement of 13Cα-1Hα One-bond Dipolar couplings in 15N, 13C Labeled Proteins

Yang, D., Tolman, J. R., Goto, N. K., & Kay, L. E. (1998) · Journal of Biomolecular NMR · doi:10.1023/a:1008223017233 · Cited by 57

Conformational Differences in Liganded and Unliganded States of Galectin-3

Umemoto, K., Leffler, H., Venot, A. P., Valafar, H., & Prestegard, J. H. (2003) · Biochemistry · doi:10.1021/bi026671m · Cited by 57

Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: an application to maltose binding protein

Choy, W., Tollinger, M., Mueller, G. A., & Kay, L. E. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1011933020122 · Cited by 55

Determination of the Glycosidic Bond Angle χ in RNA from Cross-Correlated Relaxation of CH Dipolar Coupling and N Chemical Shift Anisotropy

Duchardt, E., Richter, C. P., Ohlenschläger, O., Görlach, M., Wöhnert, J., & Schwalbe, H. (2004) · Journal of the American Chemical Society · doi:10.1021/ja0367041 · Cited by 39

Measurement of Five Dipolar Couplings from a Single 3D NMR Multiplet Applied to the Study of RNA Dynamics

O’Neil-Cabello, E., Bryce, D. L., Nikonowicz, E. P., & Bax, A. (2003) · Journal of the American Chemical Society · doi:10.1021/ja038314k · Cited by 36

Accurate Measurement of HN–Hα Residual Dipolar Couplings in Proteins

Cai, M., Wang, H., Olejniczak, E. T., et al. (1999) · Journal of Magnetic Resonance · doi:10.1006/jmre.1999.1819 · Cited by 35

Residual dipolar couplings: Synergy between NMR and structural genomics

Al‐Hashimi, H. M., & Patel, D. J. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1013801714041 · Cited by 29

Solution structure determination of the two DNA-binding domains in the Shizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints

Kikuchi, J., Iwahara, J., Kigawa, T., Murakami, Y., Okazaki, T., & Yokoyama, S. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1014977808170 · Cited by 15

Perspectives on NMR in drug discovery: a technique comes of age

Pellecchia, M., Bertini, I., Cowburn, D., Dalvit, C., Giralt, E., Jahnke, W., James, T. L., Homans, S. W., Kessler, H., Luchinat, C., et al. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2606 · Cited by 414

The Magic of Bicelles Lights Up Membrane Protein Structure

Dürr, U. H. N., Gildenberg, M., & Ramamoorthy, A. (2012) · Chemical Reviews · doi:10.1021/cr300061w · Cited by 362

Relation between native ensembles and experimental structures of proteins

Best, R. B., Lindorff-Larsen, K., DePristo, M. A., & Vendruscolo, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511156103 · Cited by 152

NMR Structures of Damaged DNA

Lukin, M., & de los Santos, C. (2006) · Chemical Reviews · doi:10.1021/cr0404646 · Cited by 158

Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance

Delaforge, E., Cordeiro, T. N., Bernadó, P., & Sibille, N. (2018) · Modern Magnetic Resonance · doi:10.1007/978-3-319-28388-3_52 · Cited by 7