Dipolar couplings as a probe of molecular dynamics and structure in solution

The introduction of residual dipolar coupling methodology has increased the scope of structural biological problems that can be addressed by NMR spectroscopy. Conformational changes, the relative orientation of domains, and intermolecular complexes can now be characterized accurately and rapidly using NMR. The development of residual dipolar coupling methodology for the rapid recognition of homologous protein folds and for studies of submillisecond timescale dynamics has also seen considerable progress.

Cross-correlated chemical shift modulation: a signature of slow internal motions in proteins

A novel NMR experiment allows one to characterize slow motion in macromolecules. The method exploits the fact that motions, such as rotation about dihedral angles, induce correlated fluctuations of the isotropic chemical shifts of the nuclei in the vicinity. The relaxation of two-spin coherences involving C(alpha) and Cbeta nuclei in proteins provides information about correlated fluctuations of the isotropic chemical shifts of C(alpha) and Cbeta. The difference between the relaxation rates of double- and zero-quantum coherences and is shown to be affected by cross-correlated chemical shift modulation. In ubiquitin, evidence for slow motion is found in loops or near the ends of beta-strands and alpha-helices.

Structural and dynamic analysis of residual dipolar coupling data for proteins

The measurement of residual dipolar couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual dipolar coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual dipolar coupling measurements. We also illustrate this new methodology using an extensive set of residual dipolar coupling measurements made on (15)N,(13)C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the X-ray structure (Vijay-Kumar, et al., J. Mol. Biol. 1987, 194, 531--544) for the protein core. However, the data are also consistent with a dynamic model of ubiquitin, exhibiting variable amplitudes, and anisotropy, of internal motions. This work suggests the possibility of primary use of residual dipolar couplings in characterizing both structure and anisotropic internal motions of proteins in the solution state.

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

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): 1DNH couplings in proteins 393

4.2.3 Exclusive correlated spectroscopy (E-COSY): 1DNH, 1DNC′ and 2DHNC′ 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 1DCαHα in proteins 397

4.3.2 Phase modulated methods 399

4.3.3 Constant time COSY – the measurement of DHH 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).

Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin

Protein function is often regulated by conformational changes that occur in response to ligand binding or covalent modification such as phosphorylation. In many multidomain proteins these conformational changes involve reorientation of domains within the protein. Although X-ray crystallography can be used to determine the relative orientation of domains, the crystal-state conformation can reflect the effect of crystal packing forces and therefore may differ from the physiologically relevant form existing in solution. Here we demonstrate that the solution-state conformation of a multidomain protein can be obtained from its X-ray structure using an extensive set of dipolar couplings measured by triple-resonance multidimensional NMR spectroscopy in weakly aligning solvent. The solution-state conformation of the 370-residue maltodextrin-binding protein (MBP) loaded with beta-cyclodextrin has been determined on the basis of one-bond (15)N-H(N), (15)N-(13)C', (13)C(alpha)-(13)C', two-bond (13)C'-H(N), and three-bond (13)C(alpha)-H(N) dipolar couplings measured for 280, 262, 276, 262, and 276 residues, respectively. This conformation was generated by applying hinge rotations to various X-ray structures of MBP seeking to minimize the difference between the experimentally measured and calculated dipolar couplings. Consistent structures have been derived in this manner starting from four different crystal forms of MBP. The analysis has revealed substantial differences between the resulting solution-state conformation and its crystal-state counterpart (Protein Data Bank accession code 1DMB) with the solution structure characterized by an 11(+/-1) degrees domain closure. We have demonstrated that the precision achieved in these analyses is most likely limited by small uncertainties in the intradomain structure of the protein (ca 5 degrees uncertainty in orientation of internuclear vectors within domains). In addition, potential effects of interdomain motion have been considered using a number of different models and it was found that the structures derived on the basis of dipolar couplings accurately represent the effective average conformation of the protein.

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

A triple resonance pulse scheme is presented for recording 13Cα-1Hα one-bond dipolar couplings in 15N, 13C labeled proteins. HNCO correlation maps are generated where the carbonyl chemical shift is modulated by the 13Cα-1Hα coupling, with the two doublet components separated into individual data sets. The experiment makes use of recently described methodology whereby the protein of interest is dissolved in a dilute solution of bicelles which orient above a critical temperature, thus permitting measurement of significant couplings (Tjandra and Bax, 1997a). An application to the protein ubiquitin is described.

NMR evidence for slow collective motions in cyanometmyoglobin

Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic and well correlated within a given helix of this highly alpha-helical protein. These observations can be explained by invoking collective motion and small displacements of representative helices from their reported average positions in the solid state. Thus, the measurements appear to be capable of providing important insights into slower, collective protein motions, which are likely to be important for function, and which have been difficult to study using established experimental techniques.

A quantitative J-correlation experiment for the accurate measurement of one-bond amide 15N-1H couplings in proteins

Very precise measurements of 1JNH couplings have been made for approximately 40% of the amide sites in cyanometmyoglobin using two different experimental approaches. The first approach is a previously described frequency-based method in which the couplings are observed as splittings in the frequency-domain spectrum. The second is a new approach, along the lines of quantitative J-correlation spectroscopy, in which the coupling is encoded in the resonance intensity. Measurements obtained from the two experimental techniques are in agreement to a high degree of precision (s.d. of 0.17 Hz) and residual deviations appear to be largely random. The new method offers substantial time savings when resonances are widely dispersed in the frequency domain and may offer improved precision in these instances.

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

The measurement of dipolar contributions to the splitting of 15N resonances of 1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported. The splittings appear as small field-dependent perturbations of normal scalar couplings. Assignment of more than 90 resonances to specific sequential sites in the protein allows correlation of the dipolar contributions with predictions based on the known susceptibility and known structure of the protein. Implications as an additional source of information for protein structure determination in solution are discussed.