Multiple-spin effects in fast magic angle spinning Lee–Goldburg cross-polarization experiments in uniformly labeled compounds

Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM)

In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in Z' value, from 2 to 1, as observed by variable-temperature ¹H-¹³C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional ¹³C-¹H and ¹H-¹H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two Z' = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.

Simple and accurate determination of X-H distances under ultra-fast MAS NMR

We demonstrate that a very simple experiment, Cross-Polarization with Variable Contact-time (CP-VC), is very efficient at ultra-fast MAS (νR ≥ 60 kHz) to measure accurately the C-H and N-H distances, and to analyze the dynamics of bio-molecules. This experiment can be performed with samples that are either (13)C or (15)N labeled or without any labeling. The method is very robust experimentally with respect to imperfect Hartman-Hahn setting, and presents a large scaling factor allowing a better dipolar determination, especially for long C-H or N-H distances, or for CH3 or NH3 moieties with three-site hopping. At ultra-fast MAS, it can be used quantitatively in a 2D way, because its scaling factor is then little dependent on the offsets. This robustness with respect to offset is related to the ultra-fast spinning speed, and hence to the related small rotor diameter. Indeed, these two specifications lead to efficient n = ±1 zero-quantum Hartman-Hahn CP-transfers with large RF-fields on proton and carbon or nitrogen channels, and large dipolar scaling factor.

Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A

Despite extensive study, the molecular structure of the chromophore-binding pocket of phytochrome A (phyA), the principal photoreceptor controlling photomorphogenesis in plants, has not yet been successfully resolved. Here, we report a series of two-dimensional (2-D) magic-angle spinning solid-state NMR experiments on the recombinant N-terminal, 65-kDa PAS-GAF-PHY light-sensing module of phytochrome A3 from oat (Avena sativa), assembled with uniformly 13C- and 15N-labeled phycocyanobilin (u-[13C,15N]-PCB-As.phyA3). The Pr state of this protein was studied regarding the electronic structure of the chromophore and its interactions with the proximal amino acids. Using 2-D 13C-13C and 1H-15N experiments, a complete set of 13C and 15N assignments for the chromophore were obtained. Also, a large number of 1H-13C distance restraints between the chromophore and its binding pocket were revealed by interfacial heteronuclear correlation spectroscopy. 13C doublings of the chromophore A-ring region and the C-ring carboxylate moiety, together with the observation of two Pr isoforms, Pr-I and Pr-II, demonstrate the local mobility of the chromophore and the plasticity of its protein environment. It appears that the interactions and dynamics in the binding pocket of phyA in the Pr state are remarkably similar to those of cyanobacterial phytochrome (Cph1). The N-terminus of the region modeled (residues 56-66 of phyA) is highly mobile. Differences in the regulatory processes involved in plant and Cph1 phytochromes are discussed.

Exploring Chromophore-Binding Pocket: High-Resolution Solid-State H-C Interfacial Correlation NMR Spectra with Windowed PMLG Scheme

High-resolution two-dimensional (2D) (1)H-(13)C heteronuclear correlation spectra are recorded for selective observation of interfacial 3-5.5 Å contacts of the uniformly (13)C-labeled phycocyanobilin (PCB) chromophore with its unlabeled binding pocket. The experiment is based on a medium- and long-distance heteronuclear correlation (MELODI-HETCOR) method. For improving (1)H spectral resolution, a windowed phase-modulated Lee-Goldburg (wPMLG) decoupling scheme is applied during the t(1) evolution period. Our approach allows for identification of chromophore-protein interactions, in particular for elucidation of the hydrogen-bonding networks and charge distributions within the chromophore-binding pocket. The resulting pulse sequence is tested on the cyanobacterial (Cph1) phytochrome sensory module (residues 1-514, Cph1Δ2) containing uniformly (13)C- and (15)N-labeled PCB chromophore (u-[(13)C,(15)N]-PCB-Cph1Δ2) at 17.6 T.

Magic Angle Spinning (MAS) NMR: a new tool to study the spatial and electronic structure of photosynthetic complexes

In the last two decades, Magic Angle Spinning (MAS) NMR has created its own niche in studies involving photosynthetic membrane protein complexes, owing to its ability to provide structural and functional information at atomic resolution of membrane proteins when in the membrane, in the natural environment. The light-harvesting two (LH2) transmembrane complex from Rhodopseudomonas acidophila is used to illustrate the procedure of the technique applicable in photosynthesis research. One- and two-dimensional solid-state NMR experiments involving (13)C- and (15)N-labeled LH2 complexes allow to make a sequence-specific assignment of NMR signals, which forms the basis for resolving structural details and the assessment of charge transfer, electronic delocalization effects, and functional strain in the ground state.

Homonuclear dipolar recoupling techniques for structure determination in uniformly 13C-labeled proteins

In solid-state NMR magic angle spinning is often used to remove line broadening associated with anisotropic interactions, such as chemical shift anisotropy and dipolar couplings. Dipolar recoupling refers to sequences of pulses designed to reintroduce dipolar interactions that are otherwise averaged by magic angle spinning. One of the key applications of homonuclear (and heteronuclear) dipolar recoupling is for the purpose of protein structure determination. Recoupling experiments, originally designed for applications in spin-pair labeled samples, have been revised in recent years for applications in samples with extensive or uniform incorporation of isotopic labels. In these samples multiple internuclear distances can in principle be probed simultaneously, but the dipolar truncation effects (i.e. attenuation of the effects of weak couplings by strong ones) circumvent such measurements. In this article we review some of the recent developments in homonuclear recoupling methods that allow overcoming this problem.

Solid-state NMR spectroscopy using the lost I spin magnetization in polarization transfer experiments

A variation of the cross polarization (CP) experiment is discussed. The method requires two scans where the difference signal is equivalent to the I spin magnetization that is transferred to the S spins. The acquired signal is equivalent to F1 sum projection of a two-dimensional (2D) heteronuclear correlation experiment and is obtained by just two scans without the need to increment the indirect time domain t(1). Any polarization transfer method and any kind of spin manipulations during the t(1) incrementation period of a 2D NMR experiment can be applied. The method allows fast measurements of the CP transfer, particularly if various S spins signal overlap and is good for spectral editing of I spin signals with contact to S spins. Various examples for biomaterials are presented. Most importantly, this novel approach is ideal for detailed investigations of organic-mineral interfaces in bone, here demonstrated for O-phospho-l-serine as simple model compound.

Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage

This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists of approximately 7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, S, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA-protein interface within a virus.

Structural analysis of pituitary adenylate cyclase-activating polypeptides bound to phospholipid membranes by magic angle spinning solid-state NMR

PACAP (pituitary adenylate cyclase-activating polypeptide) is a member of the VIP/secretin/glucagon family, which includes the ligands of class II G-protein coupled receptors. Since the recognition of PACAP by the receptor may involve the binding of PACAP to membranes, its membrane-bound structure should be important. We have carried out structural analysis of uniformly 13C,15N labeled PACAP27 and its C-terminal truncated form PACAP(1-21)NH2 (PACAP21) bound to membranes with high resolution solid-state NMR. Phosphatidylcholine bilayers and phosphatidylcholine/phosphatidylglycerol bilayers were used for PACAP27 and PACAP21, respectively. Most backbone signals were assigned for PACAP27 and PACAP21. TALOS analysis revealed that both peptides take on extended conformations on the membranes. Dilution of PACAP21 did not change the conformation of the major part. Selective polarization transfer experiment confirmed that PACAP27 is interacting with the membranes. It was concluded that the interaction of PACAP with the membrane surface causes their extended conformation. PACAP27 is reported to take an alpha-helical conformation in dodecylphosphocholine micelles and membrane-binding peptides usually take similar conformations in micelles and in membranes. Therefore, the property of PACAP27 changing its conformation in response to its environment is unique. Its conformational flexibility may be associated with its wide variety of functions.

(13)C-(13)C distance measurements in U-(13)C, (15)N-labeled peptides using rotational resonance width experiment with a homogeneously broadened matching condition

In this publication, we introduce a version of the rotational resonance width experiment with a homogeneously broadened matching condition. The increase in the bandwidth is achieved by the reduction of the proton decoupling power during mixing, which results in the reduction of zero-quantum relaxation, and broadens the rotational resonance condition. We show that one can achieve recoupling of the carbonyl-aliphatic side chain dipolar interactions band selectively, while avoiding the recoupling of strongly interacting C'-Calpha and C'-Cbeta spin pairs. The attenuation of the multi-spin effects in the presence of short zero-quantum relaxation enables a two-spin approximation to be employed for the analysis of the experimental data. The systematic error introduced by this approximation is estimated by comparing the results with a three-spin simulation. The experiment is demonstrated in [U-(13)C,(15)N]N-acetyl-L-Val-L-Leu dipeptide, where 11 distances, ranging from 2.5 to 6 A, were measured.

Order parameters based on (13)C(1)H, (13)C(1)H(2) and (13)C(1)H(3) heteronuclear dipolar powder patterns: a comparison of MAS-based solid-state NMR sequences

Order parameters describing conformational exchange processes on the nanosecond to microsecond timescale can be obtained from powder patterns in solid-state NMR (SSNMR) experiments. Extensions of these experiments to magic-angle spinning (MAS) based high-resolution experiments have been demonstrated, which show a great promise for site-specific probes of biopolymers. In this study, we present a detailed comparison of two pulse sequences, transverse Manfield-Rhim-Elleman-Vaughn (T-MREV) and Lee-Goldburg cross-polarization (LGCP), using experimental and simulation tools to explore their utility in the study of order parameters. We discuss systematic errors due to passively coupled (13)C or (1)H nuclei, as well as due to B(1) inhomogeneity. Both pulse sequences can provide quantitative measurements of the order parameter, but the LGCP experiment is capable of greater accuracy provided that the B(1) field is highly homogeneous. The T-MREV experiment is far better compensated for B(1) inhomogeneity, and it also performs better in situations with limited signal.

13C/15N distance determination by CPMAS NMR in uniformly 13C labeled molecules

The REDOR and CPMAS techniques are applied for measuring 13C-15N dipolar coupling constants in glycine. It is shown that the selective CP or SPECIFIC CP technique removes the coherent evolution of the spin system under homonuclear 13C-13C J couplings. While the large coupling constant (approximately 900 Hz) is readily determined because of the presence of large oscillations in the CPMAS dynamics, their absence precludes the measurement of the small coupling constant (approximately 200 Hz). The experimental results and numerical simulations demonstrate that the determination of 13C-15N coupling constants of medium size (<1 kHz) by the CPMAS technique is mainly limited by the strength of the 1H decoupling field and the size of the 13C and 15N chemical shift anisotropies.

1H/31P distance determination by solid state NMR in multiple-spin systems

The results of two techniques of dipolar recoupling, REDOR and CPMAS, are compared in the case of a coupled multiple-spin system. A fundamentally different behavior is observed for these two techniques. In REDOR, the terms associated with each interaction S-I(k) commute with each other and no truncation takes place so that each addition of spin I(k) causes a splitting with its dipolar frequency. In CPMAS, the flip-flop terms of the dipolar Hamiltonian do not commute with the dominant term from the strongly coupled spin pair so that the weak coupling terms from the neighboring spin I(k) are effectively truncated by the dominant pair interaction. Spin dynamics calculations are in agreement with the experimental data in a cubane shaped cluster.

Determining the geometry of strongly hydrogen-bonded silanols in a layered hydrous silicate by solid-state nuclear magnetic resonance

High-resolution solid-state NMR spectroscopy is exploited to obtain structural constraints involving strongly hydrogen-bonded silanols in octosilicate, a prominent member of the layered hydrous sodium silicates. Proton-silicon cross-polarization dynamics reveals that octosilicate contains two types of Q(3) silicons present in hydrogen-bonded -Si-O-Hcdots, three dots, centeredO-Si- and -Si-O(-)-type sites which can only be distinguished by their different abilities to cross polarize and the different mobilities of neighboring hydrous species. The theoretical analysis of the oscillating components of the polarization transfer buildup curves suggests that the model of heteronuclear pairs is an adequate description of the quantum spin system within hydrogen-bonded -Si-O-Hcdots, three dots, centeredO-Si- fragments. We also show that dipolar modulated, slow speed magic-angle (29)Si NMR spectrum provides unique geometric information on strongly hydrogen-bonded silanols. The dipolar modulated spinning sidebands contain all the information necessary to determine the internuclear Sicdots, three dots, centeredH distances as well as the magnitude and orientation of the principal elements of the (29)Si chemical shielding tensor in the molecular frame. The data provide definite proof of the intralayer character of strongly hydrogen-bonded silanol groups in a bridging, albeit not symmetric, position between neighboring tetrahedra. The approach developed in this work may be useful to obtain structural information on related layered alkali metal silicates, silica gels as well as on other classes of microporous materials.

Heteronuclear dipolar recoupling in solid-state nuclear magnetic resonance by amplitude-, phase-, and frequency-modulated Lee–Goldburg cross-polarization

This paper presents a theoretical, numerical, and experimental study of phase- and frequency-switched Lee-Goldburg cross-polarization (FSLG-CP) under magic-angle spinning conditions. It is shown that a well-defined amplitude modulation of one of the two radio-frequency (rf) fields in the FSLG-CP sequence results in highly efficient heteronuclear dipolar recoupling. The recoupled dipolar interaction is gamma-encoded and, under ideal conditions, the effective spin Hamiltonian is equivalent to that in continuous-wave Lee-Goldburg CP. In practice, however, FSLG-CP is less susceptible to rf field mismatch and inhomogeneity, and provides better suppression of (1)H spin diffusion. The performance of FSLG-CP is experimentally demonstrated on liquid-crystalline samples exhibiting motionally averaged dipolar couplings.

Band-selective carbonyl to aliphatic side chain 13C-13C distance measurements in U-13C,15N-labeled solid peptides by magic angle spinning NMR

We describe three-dimensional magic angle spinning NMR experiments that enable simultaneous band-selective measurement of the multiple distance constraints between carbonyl and side chain carbons in uniformly 13C,15N-labeled peptides. The approaches are designed to circumvent the dipolar truncation and to allow experimental separation of the multiple quantum (MQ) relaxation and dipolar effects. The pulse sequences employ the double quantum (DQ) rotational resonance in the tilted frame (R2TR) to perform selective polarization transfers that reintroduce the 13C'-13Cgamma,delta dipolar interactions. The scheme avoids recoupling of the strongly coupled C'-Calpha and C'-Cbeta spin pairs, therefore minimizing dipolar truncation effects. The experiment is performed in a constant time fashion as a function of the radio frequency irradiation intensity and measures the line shape of the DQ transition. The width and the intensity of this line shape are analyzed in terms of the DQ relaxation and dipolar coupling. The attenuation of the multispin effects in the presence of relaxation enables a two-spin approximation to be employed for the analysis of the experimental data. The systematic error introduced by this approximation is estimated by comparing the results with a three-spin simulation. The contributions of B1-inhomogeneity, CSA orientation effects, and the effects of inhomogeneous line broadening are also estimated. The experiments are demonstrated in model U-13C,15N-labeled peptides, N-acetyl-L-Val-L-Leu and N-formyl-L-Met-L-Leu-L-Phe, where 10 and 6 distances, ranging between 3 and 6 A, were measured, respectively.

Multiple-spin analysis of chemical-shift-selective (13C, 13C) transfer in uniformly labeled biomolecules

Chemical-shift-selective (13C, 13C) polarization transfer is analyzed in uniformly labeled biomolecules. It is shown that the spin system dynamics remain sensitive to the distance of interest and can be well reproduced within a quantum-mechanical multiple-spin analysis. These results lead to a general approach on how to describe chemical-shift-selective transfer in uniformly labeled systems. As demonstrated in the case of ubiquitin, this methodology can be used to detect long-range distance constraints in uniformly labeled proteins.

Heteronuclear dipolar recoupling in liquid crystals and solids by PISEMA-type pulse sequences

A pulse sequence is described for the recoupling of heteronuclear dipolar interactions under MAS. The method is similar to the PISEMA experiment, but employs a well-defined amplitude modulation of one of the two radio-frequency fields. The technique is used for measurements of 1H-13C dipolar couplings in unoriented solid and liquid-crystalline samples.