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

Abstract

1. Introduction 372

1.1 Residual dipolar couplings as a route to structure and dynamics 372

1.2 A brief history of oriented phase high resolution NMR 374

2. Theoretical treatment of dipolar interactions 376

2.1 Anisotropic interactions as probes of macromolecular structure and dynamics 376

2.1.1 The dipolar interaction 376

2.1.2 Averaging in the solution state 377

2.2 Ordering of a rigid body 377

2.2.1 The Saupe order tensor 378

2.2.2 Orientational probability distribution function 380

2.2.3 The generalized degree of order 380

2.3 Molecular structure and internal dynamics 381

3. Inducing molecular order in high resolution NMR 383

3.1 Tensorial interactions between the magnetic field and anisotropic magnetic susceptibilities 383

3.2 Dilute liquid crystal media: a tunable source of order 384

3.2.1 Bicelles : from membrane mimics to aligning media 385

3.2.2 Filamentous phage 387

3.2.3 Transfer of alignment from ordered media to macromolecules 388

3.3 Magnetic field alignment 389

3.3.1 Paramagnetic assisted alignment 389

3.3.2 Advantages of using magnetic alignment 389

4. The measurement of residual dipolar couplings 391

4.1 Introduction 391

4.2 Frequency based methods 392

4.2.1 Coupling enhanced pulse schemes 392

4.2.2 In phase anti-phase methods (IPAP): ¹D_NH couplings in proteins 393

4.2.3 Exclusive correlated spectroscopy (E-COSY): ¹D_NH, ¹D_NC′ and ²D_HN_C′ 395

4.2.4 Extraction of splitting values from the frequency domain 396

4.3 Intensity based experiments 397

4.3.1 J-Modulated experiments: the measurement of ¹D_C^αH^α in proteins 397

4.3.2 Phase modulated methods 399

4.3.3 Constant time COSY – the measurement of D_HH couplings 399

4.3.4 Systematic errors in intensity based experiments 400

5. Interpretation of residual dipolar coupling data 401

5.1 Structure determination protocols utilizing orientational constraints 401

5.1.1 The simulated annealing approach 401

5.1.2 Order matrix analysis of dipolar couplings 402

5.1.3 A discussion of the two approaches 402

5.2 Reducing orientational degeneracy 403

5.2.1 Multiple alignment media in the simulated annealing approach 404

5.2.2 Multiple alignment media in the order matrix approach 405

5.3 Simplifying effects arising due to molecular symmetry 406

5.4 Database approaches for determining protein structure 407

6. Applications to the characterization of macromolecular systems 408

6.1 Protein structure refinement 408

6.2 Protein domain orientation 409

6.3 Oligosaccharides 413

6.4 Biomolecular complexes 415

6.5 Exchanging systems 416

7. Acknowledgements 418

8. References 419

Within 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).