New techniques in structural NMR--anisotropic interactions

Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble

Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.

Zinc finger structure determination by NMR: Why zinc fingers can be a handful

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.

Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'

We present a systematic investigation into the attainable accuracy and precision of protein structures determined by heteronuclear magic angle spinning solid-state NMR for a set of four proteins of varied size and secondary structure content. Structures were calculated using synthetically generated random sets of C-C distances up to 7 Å at different degrees of completeness. For single-domain proteins, 9-15 restraints per residue are sufficient to derive an accurate model structure, while maximum accuracy and precision are reached with over 15 restraints per residue. For multi-domain proteins and protein assemblies, additional information on domain orientations, quaternary structure and/or protein shape is needed. As demonstrated for the HIV-1 capsid protein assembly, this can be accomplished by integrating MAS NMR with cryoEM data. In all cases, inclusion of TALOS-derived backbone torsion angles improves the accuracy for small number of restraints, while no further increases are noted for restraint completeness above 40%. In contrast, inclusion of TALOS-derived torsion angle restraints consistently increases the precision of the structural ensemble at all degrees of distance restraint completeness.

Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR

NMR approaches using nucleotide-specific deuterium labeling schemes have enabled structural studies of biologically relevant RNAs of increasing size and complexity. Although local structure is well-determined using these methods, definition of global structural features, including relative orientations of independent helices, remains a challenge. Residual dipolar couplings, a potential source of orientation information, have not been obtainable for large RNAs due to poor sensitivity resulting from rapid heteronuclear signal decay. Here we report a novel multiple quantum NMR method for RDC determination that employs flip angle variation rather than a coupling evolution period. The accuracy of the method and its utility for establishing interhelical orientations are demonstrated for a 36-nucleotide RNA, for which comparative data could be obtained. Applied to a 78 kDa Rev response element from the HIV-1 virus, which has an effective rotational correlation time of ca. 160 ns, the method yields sensitivity gains of an order of magnitude or greater over existing approaches. Solution-state access to structural organization in RNAs of at least 230 nucleotides is now possible.

Alignment of 17O-enriched water-endofullerene H2O@C60 in a liquid crystal matrix

We present a 17O and 1H NMR study of molecular endofullerene H2O@C60 dissolved in the nematic liquid crystal N-(4-methoxybenzylidene)-4-butylaniline (MBBA). The 17O NMR peak is split into five components by the 17O residual quadrupolar coupling, each of which is split into a triplet by the 1H-17O residual dipolar coupling and scalar coupling. The splittings are analysed in terms of the partial alignment of the encapsulated water molecules. Order parameters describing the alignment are estimated. It is found that the preferential orientation of the endohedral water molecule has the molecular plane perpendicular to the liquid crystal director.

Mapping the Binding Modes of Hemilabile Pincer-Crown Ether Ligands in Solution Using Diamagnetic Anisotropic Effects on NMR Chemical Shift

A protocol for identifying ligand binding modes in a series of iridium pincer complexes bearing hemilabile aza-crown ether ligands has been developed using readily accessible NMR methods. The approach was tested on a collection of 13 structurally diverse pincer-crown ether complexes that include several newly characterized species. New synthetic routes enable facile interconversion of coordination modes and supporting ligands. Detailed structural assignments of five complexes reveal that the difference in chemical shift (Δδ) between geminal protons in the crown ether is influenced by diamagnetic anisotropy arising from halides and other ligands in the primary coordination sphere. The average difference in chemical shift between diastereotopic geminal protons in the crown ether macrocycle (Δδ_avg), as determined through a single ¹H-¹³C HSQC experiment, provides information on the pincer ligand binding mode by establishing whether the macrocycle is in close proximity to the metal center. The Δδ_avg values for binding modes that involve chelating ether(s) bound to iridium are roughly 2-fold larger than those for tridentate complexes with no Ir-O bonds.

Magnetic susceptibility anisotropy outside the central nervous system

Magnetic-susceptibility-based MRI has made important contributions to the characterization of tissue microstructure, chemical composition, and organ function. This has motivated a number of studies to explore the link between microstructure and susceptibility in organs and tissues throughout the body, including the kidney, heart, and connective tissue. These organs and tissues have anisotropic magnetic susceptibility properties and cellular organizations that are distinct from the lipid organization of myelin in the brain. For instance, anisotropy is traced to the epithelial lipid orientation in the kidney, the myofilament proteins in the heart, and the collagen fibrils in the knee cartilage. The magnetic susceptibility properties of these and other tissues are quantified using specific MRI tools: susceptibility tensor imaging (STI), quantitative susceptibility mapping (QSM), and individual QSM measurements with respect to tubular and filament directions determined from diffusion tensor imaging. These techniques provide complementary and supplementary information to that produced by traditional MRI methods. In the kidney, STI can track tubules in all layers including the cortex, outer medulla, and inner medulla. In the heart, STI detected myofibers throughout the myocardium. QSM in the knee revealed three unique layers in articular cartilage by exploiting the anisotropic susceptibility features of collagen. While QSM and STI are promising tools to study tissue susceptibility, certain technical challenges must be overcome in order to realize routine clinical use. This paper reviews essential experimental findings of susceptibility anisotropy in the body, the underlying mechanisms, and the associated MRI methodologies. Copyright © 2016 John Wiley & Sons, Ltd.

NMR of molecular endofullerenes dissolved in a nematic liquid crystal

We report the NMR of the molecular endofullerenes H₂@C₆₀, H₂O@C₆₀ and HF@C₆₀ dissolved in the nematic liquid crystal N-(4-methoxybenzylidene)-4-butylaniline (MBBA).

Pf1 filamentous phage as an alignment tool for generating local and global structural information in nucleic acids

Abstract Pf1 filamentous phage represent a simple versatile method for generating partially ordered macromolecules in solution. The phage allow tunable degrees of alignment of macromolecules under a wide range of temperature and solvent conditions. The negatively charged phage are ideal for aligning negatively charged nucleic acids and these phage-nucleic acid solutions are stable indefinitely. We have used Pf1 phage to align various DNA and RNA molecules in solution for measurement of dipolar coupling interactions. These dipolar couplings can be used to improve the local structure of nucleic acids. More importantly they also contain information on the global structure, such as DNA bending, which presently cannot be obtained by standard NMR methods. The principles involved in using Pf1 phage to generate solutions of partially order macromolecules will be discussed. The use of (1)H-(1)H, (1)H-(13)C and (1)H-(15)N dipolar couplings for generating angle constraints for structure refinement of nucleic acids will also be discussed.

Ensembles of a small number of conformations with relative populations

In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assigning relative populations to protein ensembles could significantly improve their quality. To demonstrate that ESP indeed is an excellent alternative to represent protein native states, in this work we compare the quality of two ESP ensembles of Ubiquitin with several well-known regular ensembles or average structure representations. Extensive amount of significant experimental data are employed to achieve a thorough assessment. Our results demonstrate that ESP ensembles, though much smaller in size comparing to regular ensembles, perform equally or even better sometimes in all four different types of experimental data used in the assessment, namely, the residual dipolar couplings, residual chemical shift anisotropy, hydrogen exchange rates, and solution scattering profiles. This work further underlines the significance of having relative populations in describing the native states.

Enhancing the quality of protein conformation ensembles with relative populations

The function and dynamics of many proteins are best understood not from a single structure but from an ensemble. A high quality ensemble is necessary for accurately delineating protein dynamics. However, conformations in an ensemble are generally given equal weights. Few attempts were made to assign relative populations to the conformations, mainly due to the lack of right experimental data. Here we propose a method for assigning relative populations to ensembles using experimental residue dipolar couplings (RDC) as constraints, and show that relative populations can significantly enhance an ensemble's ability in representing the native states and dynamics. The method works by identifying conformation states within an ensemble and assigning appropriate relative populations to them. Each of these conformation states is represented by a sub-ensemble consisting of a subset of the conformations. Application to the ubiquitin X-ray ensemble clearly identifies two key conformation states, with relative populations in excellent agreement with previous work. We then apply the method to a reprotonated ERNST ensemble that is enhanced with a switched conformation, and show that as a result of population reweighting, not only the reproduction of RDCs is significantly improved, but common conformational features (particularly the dihedral angle distributions of ϕ 53 and ψ 52) also emerge for both the X-ray ensemble and the reprotonated ERNST ensemble.

Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings

Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N--H , C(α)--H(α), and C--N vectors of 1BRF, 1F53, 110M, and 3LAY proteins, with up to ±1 Hz error in three alignment media, and was able to produce structures with less than 1.9 Å of the original structures. DynaFold was then tested using experimental data, obtained from the Biological Magnetic Resonance Bank, for proteins PDBID:1P7E and 1D3Z using RDC data from two alignment media. This exercise yielded structures within 1.0 Å of their respective published structures in segments with high data density, and less than 1.9 Å over the entire protein. The same sets of RDC data were also used in comparisons with traditional methods for analysis of RDCs, which failed to match the accuracy of DynaFold's approach to structure determination.

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy.

DNA nanotubes for NMR structure determination of membrane proteins

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

REFINEMENT OF NMR-DETERMINED PROTEIN STRUCTURES WITH DATABASE DERIVED DISTANCE CONSTRAINTS

The protein structures determined by NMR (Nuclear Magnetic Resonance Spectroscopy) are not as detailed and accurate as those by X-ray crystallography and are often underdetermined due to the inadequate distance data available from NMR experiments. The uses of NMR-determined structures in such important applications as homology modeling and rational drug design have thus been severely limited. Here we show that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures. We show through a survey on 462 NMR structures that, in fact, many inter-atomic distances in these structures deviate considerably from their database distributions and based on the refinement results on 10 selected NMR structures that these structures can actually be improved significantly when a selected set of distances are constrained within their high probability ranges in their database distributions.

Magnetic susceptibility anisotropy of human brain in vivo and its molecular underpinnings

Frequency shift of gradient-echo MRI provides valuable information for assessing brain tissues. Recent studies suggest that the frequency and susceptibility contrast depend on white matter fiber orientation. However, the molecular underpinning of the orientation dependence is unclear. In this study, we investigated the orientation dependence of susceptibility of human brain in vivo and mouse brains ex vivo. The source of susceptibility anisotropy in white matter is likely to be myelin as evidenced by the loss of anisotropy in the dysmyelinating shiverer mouse brain. A biophysical model is developed to investigate the effect of the molecular susceptibility anisotropy of myelin components, especially myelin lipids, on the bulk anisotropy observed by MRI. This model provides a consistent interpretation of the orientation dependence of macroscopic magnetic susceptibility in normal mouse brain ex vivo and human brain in vivo and the microscopic origin of anisotropic susceptibility. It is predicted by the theoretical model and illustrated by the experimental data that the magnetic susceptibility of the white matter is least diamagnetic along the fiber direction. This relationship allows an efficient extraction of fiber orientation using susceptibility tensor imaging. These results suggest that anisotropy on the molecular level can be observed on the macroscopic level when the molecules are aligned in a highly ordered manner. Similar to the utilization of magnetic susceptibility anisotropy in elucidating molecular structures, imaging magnetic susceptibility anisotropy may also provide a useful tool for elucidating the microstructure of ordered biological tissues.

Simultaneous measurement of ¹H-¹⁵N and methyl ¹Hm-¹³Cm residual dipolar couplings in large proteins

A two-dimensional TROSY-based SIM-(13)C(m)-(1)H(m)/(1)H-(15)N NMR experiment for simultaneous measurements of methyl (1) D (CH) and backbone amide (1) D (NH) residual dipolar couplings (RDC) in {U-[(15)N,(2)H]; Ileδ1-[(13)CH(3)]; Leu,Val-[(13)CH(3)/(12)CD(3)]}-labeled samples of large proteins is described. Significant variation in the alignment tensor of the 82-kDa enzyme Malate synthase G is observed as a function of only slight changes in experimental conditions. The SIM-(13)C(m)-(1)H(m)/(1)H-(15)N data sets provide convenient means of establishing the alignment tensor characteristics via the measurement of (1) D (NH) RDCs in the same protein sample.

Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins

Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.

The structural and topological analysis of membrane-associated polypeptides by oriented solid-state NMR spectroscopy: established concepts and novel developments

Solid-state NMR spectroscopy is a powerful technique for the investigation of membrane-associated peptides and proteins as well as their interactions with lipids, and a variety of conceptually different approaches have been developed for their study. The technique is unique in allowing for the high-resolution investigation of liquid disordered lipid bilayers representing well the characteristics of natural membranes. Whereas magic angle solid-state NMR spectroscopy follows approaches that are related to those developed for solution NMR spectroscopy the use of static uniaxially oriented samples results in angular constraints which also provide information for the detailed analysis of polypeptide structures. This review introduces this latter concept theoretically and provides a number of examples. Furthermore, ongoing developments combining solid-state NMR spectroscopy with information from solution NMR spectroscopy and molecular modelling as well as exploratory studies using dynamic nuclear polarization solid-state NMR will be presented.

Sensitivity enhancement of separated local field experiments: application to membrane proteins

Separated local field (SLF) experiments have been used for almost three decades to obtain structural information in solid-state NMR. These experiments resolve chemical shift anisotropy (CSA) from dipole-dipole interactions (dipolar couplings, DC) in isolated spin systems. Both CSA and DC data can be converted into orientational constraints to elucidate the secondary structure and topology of membrane proteins in oriented lipid bilayers. Here, we propose a new suite of sensitivity enhanced SLF pulse sequences to measure CSA and DC for aligned membrane proteins and liquid crystalline molecules that will decrease the time needed for data acquisition. We demonstrate the efficacy of these new sensitivity enhanced experiments using both a single crystal of N-acetyl leucine and a single pass membrane protein sarcolipin reconstituted in aligned lipid bicelles. These results lay the groundwork for the routine application of this methodology for studying the structure and topology of membrane proteins.

How different are diastereomorphous orientations of enantiomers in the liquid crystalline phases of PBLG and PBDG: a case study

The orientational properties of the two enantiomers of an example compound, namely isopinocampheol [(+)- and (-)-IPC] in the two enantiomers of a liquid crystalline phase, namely Poly-gamma-benzyl-L/D-glutamate (PBLG/PBDG) with the organic cosolvent CDCl(3), were investigated. The interactions can be either enantiomorphous, leading to equal orientations and residual dipolar couplings (RDCs), or diastereomorphous, leading to different orientations and RDCs. The difference between the two diastereomorphous orientations was determined to be rather small (5 degrees in the Euler angle beta). Furthermore, we investigated whether one of the two diastereomorphous interactions is favored.

Structural glycobiology: a game of snakes and ladders

Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate-protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate-protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate-protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate-protein structures, and (5) Current challenges in structural glycoscience.

Recent advances in RNA structure determination by NMR

Despite recent advances in the solution of NMR structures of RNA and RNA-ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J-coupling data with the measurement of dipolar couplings and cross-correlated relaxation rates in high-resolution NMR spectroscopy.

A unifying probabilistic framework for analyzing residual dipolar couplings

Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.

BioMagResBank

The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pK(a) values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.

J-ONLY-TOCSY: efficient suppression of RDC-induced transfer in homonuclear TOCSY experiments using JESTER-1-derived multiple pulse sequences

The main purpose of homonuclear Hartmann-Hahn or TOCSY experiments is the assignment of spin systems based on efficient coherence transfer via scalar couplings. In partially aligned samples, however, magnetization is also transferred via residual dipolar couplings (RDCs) and therefore through space correlations can be observed in COSY and TOCSY experiments that make the unambiguous assignment of covalently bound spins impossible. In this article, we show that the JESTER-1 multiple pulse sequence, originally designed for broadband heteronuclear isotropic Hartmann-Hahn transfer, efficiently suppresses the homonuclear dipolar coupling Hamiltonian. This suppression can be enhanced even further by variation of the supercycling scheme. The application of the resulting element in homonuclear TOCSY periods results in coherence transfer via J-couplings only. As a consequence, the assignment of scalar coupled spin systems is also possible in partially aligned samples. The bandwidth of coherence transfer for the JESTER-1-derived sequences is comparable to existing TOCSY multiple pulse sequences. Results are demonstrated in theory and experiment.

Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis

(15)N-(1)H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement.

An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange

A series of experiments are presented that provide an exchange-free measure of dipole-dipole (15)N transverse relaxation, R(dd), that can then be substituted for (15)N R(1rho) or R(2) rates in the study of internal protein dynamics. The method is predicated on the measurement of a series of relaxation rates involving (1)H-(15)N longitudinal order, anti-phase (1)H and (15)N single-quantum coherences, and (1)H-(15)N multiple quantum coherences; the relaxation rates of all coherences are measured under conditions of spin-locking. Results from detailed simulations and experiments on a number of protein systems establish that R(dd) values are independent of exchange and systematic errors from dipolar interactions with proximal protons are calculated to be less than 1-2%, on average, for applications to perdeuterated proteins. Simulations further indicate that the methodology is rather insensitive to the exact level of deuteration so long as proteins are reasonably highly deuterated (>50%). The utility of the methodology is demonstrated with applications involving protein L, ubiquitin, and a stabilized folding intermediate of apocytochrome b(562) that shows large contributions to (15)N R(1rho) relaxation from chemical exchange.

Determining the topology of integral membrane peptides using EPR spectroscopy

This paper reports on the development of a new structural biology technique for determining the membrane topology of an integral membrane protein inserted into magnetically aligned phospholipid bilayers (bicelles) using EPR spectroscopy. The nitroxide spin probe, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC), was attached to the pore-lining transmembrane domain (M2delta) of the nicotinic acetylcholine receptor (AChR) and incorporated into a bicelle. The corresponding EPR spectra revealed hyperfine splittings that were highly dependent on the macroscopic orientation of the bicelles with respect to the static magnetic field. The helical tilt of the peptide can be easily calculated using the hyperfine splittings gleaned from the orientational dependent EPR spectra. A helical tilt of 14 degrees was calculated for the M2delta peptide with respect to the bilayer normal of the membrane, which agrees well with previous 15N solid-state NMR studies. The helical tilt of the peptide was verified by simulating the corresponding EPR spectra using the standardized MOMD approach. This new method is advantageous because: (1) bicelle samples are easy to prepare, (2) the helical tilt can be directly calculated from the orientational-dependent hyperfine splitting in the EPR spectra, and (3) EPR spectroscopy is approximately 1000-fold more sensitive than 15N solid-state NMR spectroscopy; thus, the helical tilt of an integral membrane peptide can be determined with only 100 microg of peptide. The helical tilt can be determined more accurately by placing TOAC spin labels at several positions with this technique.

Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor

In solution NMR spectroscopy the residual dipolar coupling (RDC) is invaluable in improving both the precision and accuracy of NMR structures during their structural refinement. The RDC also provides a potential to determine protein structure de novo. These procedures are only effective when an accurate estimate of the alignment tensor has already been made. Here we present a top-down approach, starting from the secondary structure elements and finishing at the residue level, for RDC data analysis in order to obtain a better estimate of the alignment tensor. Using only the RDCs from N-H bonds of residues in alpha-helices and CA-CO bonds in beta-strands, we are able to determine the offset and the approximate amplitude of the RDC modulation-curve for each secondary structure element, which are subsequently used as targets for global minimization. The alignment order parameters and the orientation of the major principal axis of individual helix or strand, with respect to the alignment frame, can be determined in each of the eight quadrants of a sphere. The following minimization against RDC of all residues within the helix or strand segment can be carried out with fixed alignment order parameters to improve the accuracy of the orientation. For a helical protein Bax, the three components A(xx), A(yy) and A(zz), of the alignment order can be determined with this method in average to within 2.3% deviation from the values calculated with the available atomic coordinates. Similarly for beta-sheet protein Ubiquitin they agree in average to within 8.5%. The larger discrepancy in beta-strand parameters comes from both the diversity of the beta-sheet structure and the lower precision of CA-CO RDCs. This top-down approach is a robust method for alignment tensor estimation and also holds a promise for providing a protein topological fold using limited sets of RDCs.

Protein backbone dynamics through 13C'-13Calpha cross-relaxation in NMR spectroscopy

Internal dynamics of proteins are usually characterized by the analysis of (15)N relaxation rates that reflect the motions of NH(N) vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C'C(alpha) vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2N(z)() and 2N(z)(). This amounts to "anchoring" the and operators to the N(z)() term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C'C(alpha) vector appear more restricted than those of the NH(N) vector.

Assessment of solvent effects: do weak alignment media affect the structure of the solute?

Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions.

Analyses, extensions and comparison of three experimental schemes for measuring ((n)J(CH)+D(CH))-couplings at natural abundance

Three types of experiments for measuring (n)J(CH) heteronuclear long-range coupling constants are examined and extended with state-of-the-art pulse sequence building-blocks: The use of a HMBC with corresponding reference-HSQC for accurate coupling determination is combined with the constant time technique and the conversion of antiphase magnetization into ZQ/DQ-coherences; CPMG-based LR-CAHSQC and BIRD(r,X)-HSQMBC experiments are examined in detail with respect to their coherence transfer properties; finally, the HSQC-TOCSY-IPAP experiment is introduced, a sequence derived from previously published alpha and beta selective HSQC-TOCSYs using a different spin state selection technique and a recently developed ZQ-suppression method. The experiments are characterized with their advantages and disadvantages and compared using strychnine and menthol as standard molecules.

J-GFT NMR for precise measurement of mutually correlated nuclear spin-spin couplings

G-matrix Fourier transform (GFT) NMR spectroscopy is presented for accurate and precise measurement of chemical shifts and nuclear spin-spin couplings correlated according to spin system. The new approach, named "J-GFT NMR", is based on a largely extended GFT NMR formalism and promises to have a broad impact on projection NMR spectroscopy. Specifically, constant-time J-GFT (6,2)D (HA-CA-CO)-N-HN was implemented for simultaneous measurement of five mutually correlated NMR parameters, that is, 15N backbone chemical shifts and the four one-bond spin-spin couplings 13Calpha-1Halpha, 13Calpha-13C', 15N-13C', and 15N-1HNu. The experiment was applied for measuring residual dipolar couplings (RDCs) in an 8 kDa protein Z-domain aligned with Pf1 phages. Comparison with RDC values extracted from conventional NMR experiments reveals that RDCs are measured with high precision and accuracy, which is attributable to the facts that (i) the use of constant time evolution ensures that signals do not broaden whenever multiple RDCs are jointly measured in a single dimension and (ii) RDCs are multiply encoded in the multiplets arising from the joint sampling. This corresponds to measuring the couplings multiple times in a statistically independent manner. A key feature of J-GFT NMR, i.e., the correlation of couplings according to spin systems without reference to sequential resonance assignments, promises to be particularly valuable for rapid identification of backbone conformation and classification of protein fold families on the basis of statistical analysis of dipolar couplings.

J-Spectroscopy in the presence of residual dipolar couplings: determination of one-bond coupling constants and scalable resolution

The access to weak alignment media has fuelled the development of methods for efficiently and accurately measuring residual dipolar couplings (RDCs) in NMR-spectroscopy. Among the wealth of approaches for determining one-bond scalar and RDC constants only J-modulated and J-evolved techniques retain maximum resolution in the presence of differential relaxation. In this article, a number of J-evolved experiments are examined with respect to the achievable minimum linewidth in the J-dimension, using the peptide PA4 and the 80-amino-acid-protein Saposin C as model systems. With the JE-N-BIRDd,X-HSQC experiment, the average full-width at half height could be reduced to approximately 5 Hz for the protein, which allows the additional resolution of otherwise unresolved peaks by the active (J+D)-coupling. Since RDCs generally can be scaled by the choice of alignment medium and alignment strength, the technique introduced here provides an effective resort in cases when chemical shift differences alone are insufficient for discriminating signals. In favorable cases even secondary structure elements can be distinguished.

Two new chiral EDTA-based metal chelates for weak alignment of proteins in solution

[structure: see text] A short synthesis of EDTA-based metal chelates that can be attached to the cysteine residue of a protein via a disulfide bond is described. The complexes were used after coordination of lanthanides to align trigger factor and apo-calmodulin in solution to yield residual dipolar couplings and pseudocontact shifts. Alignment tensors for the new tags are linearly independent compared to those of previously published tags.

"Four-dimensional" protein structures: examples from metalloproteins

The fact that an object, for example, a protein, possesses a three-dimensional structure seems an obvious concept. However, when the object is flexible, the concept is less obvious. Growing experimental data over several decades show that proteins are not rigid objects, but they may sample more or less wide ranges of different conformations. To stress this concept, we propose to call the range of sampled conformations the "fourth dimension" of the protein structure. Nuclear magnetic resonance is a precious technique to define this fourth dimension. Examples of conformational heterogeneity taken from the realm of metalloproteins and their functional implications are discussed.

Atomic structures of peptide self-assembly mimics

Although the beta-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the beta-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer beta-sheet located between two globular domains consists of two beta-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular beta-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular beta-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of beta-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.