scholarly journals Multiple Alignment of Membrane Proteins for Measuring Residual Dipolar Couplings Using Lanthanide Ions Bound to a Small Metal Chelator

2007 ◽  
Vol 129 (7) ◽  
pp. 1846-1847 ◽  
Author(s):  
Douglas E. Kamen ◽  
Sean M. Cahill ◽  
Mark E. Girvin
Keyword(s):  
Membrane Proteins ◽  
Residual Dipolar Couplings ◽  
Multiple Alignment ◽  
Dipolar Couplings ◽  
Lanthanide Ions ◽  
Metal Chelator

scholarly journals TITANIA: Model Free Interpretation of Residual Dipolar Couplings in the context of Organic Compounds

2021 ◽  
Author(s):  
Felix Roth ◽  
Volker Schmidts ◽  
Christina Thiele
Keyword(s):  
Organic Compounds ◽  
Iterative Procedure ◽  
Residual Dipolar Couplings ◽  
Multiple Alignment ◽  
Dipolar Couplings ◽  
Data Sets ◽  
Joint Determination ◽  
Model Free ◽  
Direct Use

The direct use of RDCs as restraint to construct structures based on RDCs is proposed for organic compounds. It uses the vector and dynamics information available in multi alignment data sets directly for the joint determination of conformation and configuration of organic compounds. We show that employing these data even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. <br>

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).

scholarly journals TITANIA: Model Free Interpretation of Residual Dipolar Couplings in the context of Organic Compounds

2021 ◽  
Author(s):  
Felix Roth ◽  
Volker Schmidts ◽  
Christina Thiele
Keyword(s):  
Organic Compounds ◽  
Iterative Procedure ◽  
Residual Dipolar Couplings ◽  
Multiple Alignment ◽  
Dipolar Couplings ◽  
Data Sets ◽  
Joint Determination ◽  
Model Free ◽  
Direct Use

The direct use of RDCs as restraint to construct structures based on RDCs is proposed for organic compounds. It uses the vector and dynamics information available in multi alignment data sets directly for the joint determination of conformation and configuration of organic compounds. We show that employing these data even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. <br>

scholarly journals Phage-Induced Alignment of Membrane Proteins Enables the Measurement and Structural Analysis of Residual Dipolar Couplings with Dipolar Waves and λ-Maps

2009 ◽  
Vol 131 (40) ◽  
pp. 14140-14141 ◽  
Author(s):  
Sang Ho Park ◽  
Woo Sung Son ◽  
Rishi Mukhopadhyay ◽  
Homayoun Valafar ◽  
Stanley J. Opella
Keyword(s):  
Structural Analysis ◽  
Membrane Proteins ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings
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