Determining Stoichiometry in Homomultimeric Nucleic Acid Complexes Using Magnetic Field Induced Residual Dipolar Couplings

2001 ◽  
Vol 123 (24) ◽  
pp. 5806-5807 ◽  
Author(s):  
Hashim M. Al-Hashimi ◽  
Joel R. Tolman ◽  
Ananya Majumdar ◽  
Andrey Gorin ◽  
Dinshaw J. Patel
Keyword(s):  
Magnetic Field ◽  
Nucleic Acid ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings

HERMES – A Software Tool for the Prediction and Analysis of Magnetic‐Field‐Induced Residual Dipolar Couplings in Nucleic Acids

ChemPlusChem ◽  
2020 ◽  
Vol 85 (9) ◽  
pp. 2177-2185
Author(s):  
Ilektra‐Chara Giassa ◽  
Andrea Vavrinská ◽  
Jiří Zelinka ◽  
Jakub Šebera ◽  
Vladimír Sychrovský ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Nucleic Acids ◽  
Residual Dipolar Couplings ◽  
Software Tool ◽  
Dipolar Couplings

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

2004 ◽  
Vol 30 (3) ◽  
pp. 287-301 ◽  
Author(s):  
Jérôme Boisbouvier ◽  
David L. Bryce ◽  
Erin O’Neil-Cabello ◽  
Edward P. Nikonowicz ◽  
Ad Bax
Keyword(s):  
Nucleic Acid ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Nucleic Acid Bases

scholarly journals NMR Spectroscopic Determination of the Solution Structure of a Branched Nucleic Acid from Residual Dipolar Couplings by Using Isotopically Labeled Nucleotides

2004 ◽  
Vol 43 (2) ◽  
pp. 187-192 ◽  
Author(s):  
Bernd N. M. van Buuren ◽  
Jürgen Schleucher ◽  
Valentin Wittmann ◽  
Christian Griesinger ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Spectroscopic Determination

Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field

2007 ◽  
Vol 39 (2) ◽  
pp. 91-96 ◽  
Author(s):  
Jinfa Ying ◽  
Alexander Grishaev ◽  
Michael P. Latham ◽  
Arthur Pardi ◽  
Ad Bax
Keyword(s):  
Magnetic Field ◽  
Nucleic Acids ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings

scholarly journals NMR Spectroscopic Determination of the Solution Structure of a Branched Nucleic Acid from Residual Dipolar Couplings by Using Isotopically Labeled Nucleotides

2004 ◽  
Vol 116 (2) ◽  
pp. 189-194 ◽  
Author(s):  
Bernd N. M. van Buuren ◽  
Jürgen Schleucher ◽  
Valentin Wittmann ◽  
Christian Griesinger ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Spectroscopic Determination

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

2000 ◽  
Vol 33 (4) ◽  
pp. 371-424 ◽  
Author(s):  
J. H. Prestegard ◽  
H. M. Al-Hashimi ◽  
J. R. Tolman
Keyword(s):  
Magnetic Field ◽  
Simulated Annealing ◽  
Protein Structure ◽  
High Resolution ◽  
Residual Dipolar Couplings ◽  
Multiple Alignment ◽  
Dipolar Couplings ◽  
Structure And Dynamics ◽  
High Resolution Nmr

1. Introduction 3721.1 Residual dipolar couplings as a route to structure and dynamics 3721.2 A brief history of oriented phase high resolution NMR 3742. Theoretical treatment of dipolar interactions 3762.1 Anisotropic interactions as probes of macromolecular structure and dynamics 3762.1.1 The dipolar interaction 3762.1.2 Averaging in the solution state 3772.2 Ordering of a rigid body 3772.2.1 The Saupe order tensor 3782.2.2 Orientational probability distribution function 3802.2.3 The generalized degree of order 3802.3 Molecular structure and internal dynamics 3813. Inducing molecular order in high resolution NMR 3833.1 Tensorial interactions between the magnetic field and anisotropic magnetic susceptibilities 3833.2 Dilute liquid crystal media: a tunable source of order 3843.2.1 Bicelles : from membrane mimics to aligning media 3853.2.2 Filamentous phage 3873.2.3 Transfer of alignment from ordered media to macromolecules 3883.3 Magnetic field alignment 3893.3.1 Paramagnetic assisted alignment 3893.3.2 Advantages of using magnetic alignment 3894. The measurement of residual dipolar couplings 3914.1 Introduction 3914.2 Frequency based methods 3924.2.1 Coupling enhanced pulse schemes 3924.2.2 In phase anti-phase methods (IPAP): 1DNH couplings in proteins 3934.2.3 Exclusive correlated spectroscopy (E-COSY): 1DNH, 1DNC′ and 2DHNC′ 3954.2.4 Extraction of splitting values from the frequency domain 3964.3 Intensity based experiments 3974.3.1 J-Modulated experiments: the measurement of 1DCαHα in proteins 3974.3.2 Phase modulated methods 3994.3.3 Constant time COSY – the measurement of DHH couplings 3994.3.4 Systematic errors in intensity based experiments 4005. Interpretation of residual dipolar coupling data 4015.1 Structure determination protocols utilizing orientational constraints 4015.1.1 The simulated annealing approach 4015.1.2 Order matrix analysis of dipolar couplings 4025.1.3 A discussion of the two approaches 4025.2 Reducing orientational degeneracy 4035.2.1 Multiple alignment media in the simulated annealing approach 4045.2.2 Multiple alignment media in the order matrix approach 4055.3 Simplifying effects arising due to molecular symmetry 4065.4 Database approaches for determining protein structure 4076. Applications to the characterization of macromolecular systems 4086.1 Protein structure refinement 4086.2 Protein domain orientation 4096.3 Oligosaccharides 4136.4 Biomolecular complexes 4156.5 Exchanging systems 4167. Acknowledgements 4188. References 419Within its relatively short history, nuclear magnetic resonance (NMR) spectroscopy has managed to play an important role in the characterization of biomolecular structure. However, the methods on which most of this characterization has been based, Nuclear Overhauser Effect (NOE) measurements for short-range distance constraints and scalar couplings measurements for torsional constraints, have limitations (Wüthrich, 1986). For extended structures, such as DNA helices, for example, propagation of errors in the short distance constraints derived from NOEs leaves the relative orientation of remote parts of the structures poorly defined. Also, the low density of observable protons in contact regions of molecules held together by factors other than hydrophobic packing, leads to poorly defined structures. This is especially true in carbohydrate containing complexes where hydrogen bonds often mediate contacts, and in multi-domain proteins where the area involved in domain–domain contact can also be small. Moreover, most NMR based structural applications are concerned with the characterization of a single, rigid conformer for the final structure. This can leave out important mechanistic information that depends on dynamic aspects and, when motion is present, this can lead to incorrect structural representations. This review focuses on one approach to alleviating some of the existing limitations in NMR based structure determination: the use of constraints derived from the measurement of residual dipolar couplings (D).

Periodicity in Residual Dipolar Couplings and Nucleic Acid Structures

2004 ◽  
Vol 126 (7) ◽  
pp. 1938-1939 ◽  
Author(s):  
Joseph D. Walsh ◽  
Javier Cabello-Villegas ◽  
Yun-Xing Wang
Keyword(s):  
Nucleic Acid ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Nucleic Acid Structures
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