31P chemical shift anisotropy in solid nucleic acids

Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems

With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.

Microscopic structure of the polymer-induced liquid precursor for calcium carbonate

Many biomineral crystals form complex non-equilibrium shapes, often via transient amorphous precursors. Also in vitro crystals can be grown with non-equilibrium morphologies, such as thin films or nanorods. In many cases this involves charged polymeric additives that form a polymer-induced liquid precursor (PILP). Here, we investigate the CaCO3 based PILP process with a variety of techniques including cryoTEM and NMR. The initial products are 30-50 nm amorphous calcium carbonate (ACC) nanoparticles with ~2 nm nanoparticulate texture. We show the polymers strongly interact with ACC in the early stages, and become excluded during crystallization, with no liquid-liquid phase separation detected during the process. Our results suggest that "PILP" is actually a polymer-driven assembly of ACC clusters, and that its liquid-like behavior at the macroscopic level is due to the small size and surface properties of the assemblies. We propose that a similar biopolymer-stabilized nanogranular phase may be active in biomineralization.

Orientation and specific interactions of nucleotides and nucleolipids inside monoolein-based liquid crystals

The entrapment of AMP, GMP, CMP, and UMP nucleotides along with two different AMP-based nucleolipids (hydrophobically functionalized nucleotides) inside the liquid crystalline phases of the monoolein/water system is investigated through optical microscopy, small-angle X-ray diffraction (SAXRD), and nuclear magnetic resonance (NMR) techniques. As ascertained mainly through (31)P NMR experiments, when included within the cubic phase, the various nucleotides undergo a slow hydrolysis of the sugar-phosphate ester bond, induced by specific interactions at the monoolein-water interface. Upon aging, the degradation of the nucleotides causes a cubic-to-hexagonal phase transition. Differently, neither hydrolysis nor alterations of the monoolein self-assembly are observed when the nucleotides are included as lipid derivatives within the cubic liquid crystalline phase. A model that explains both the hydrolysis and the consequent phase transition is presented.

RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis

We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample. In order to interpret the (31)P relaxation data (R (1), R (2)), we measured the (31)P chemical shift anisotropy (CSA) by solid-state NMR spectroscopy under various salt and hydration conditions. A value of 178.5 ppm for the (31)P CSA in the static state (S (2) = 1) could be determined. In order to obtain information about fast time scale dynamics we performed a modelfree analysis on the basis of our relaxation data. The results show that subnanosecond dynamics detected around the phosphodiester backbone are more pronounced than the dynamics detected for the ribofuranosyl and nucleobase moieties of the individual nucleotides (Duchardt and Schwalbe, J Biomol NMR 32:295-308, 2005; Ferner et al., Nucleic Acids Res 36:1928-1940, 2008). Furthermore, the dynamics of the individual phosphate groups seem to be correlated to the 5' neighbouring nucleobases.

Relationships between 31P chemical shift tensors and conformation of nucleic acid backbone: a DFT study

Density functional theory (DFT) has been applied to study the conformational dependence of 31P chemical shift tensors in B-DNA. The gg and gt conformations of backbone phosphate groups representing BI- and BII-DNA have been examined. Calculations have been carried out on static models of dimethyl phosphate (dmp) and dinucleoside-3',5'-monophosphate with bases replaced by hydrogen atoms in vacuo as well as in an explicit solvent. Trends in 31P chemical shift anisotropy (CSA) tensors with respect to the backbone torsion angles alpha, zeta, beta, and epsilon are presented. Although these trends do not change qualitatively upon solvation, quantitative changes result in the reduction of the chemical shift anisotropy. For alpha and zeta in the range from 270 degrees to 330 degrees and from 240 degrees to 300 degrees , respectively, the delta22 and delta33 principal components vary within as much as 30 ppm, showing a marked dependence on backbone conformation. The calculated 31P chemical shift tensor principal axes deviate from the axes of O-P-O bond angles by at most 5 degrees . For solvent models, our results are in a good agreement with experimental estimates of relative gg and gt isotropic chemical shifts. Solvation also brings the theoretical deltaiso of the gg conformation closer to the experimental gg data of barium diethyl phosphate.

Heteronuclear NMR studies of cobalt corrinoids. 20. 31P chemical shift anisotropy of aquacobalamin and its complex with a haptocorrin from chicken serum

Static light scattering measurements have been used to determine the molecular mass (65.3 kDa) and second virial coefficient (3.66 x 10(-4) mol mL g-2) for the complex between chicken serum haptocorrin (HC) and aquacobalamin (H2OCbl). Dynamic light scattering measurements have also been used to determine the translational diffusion coefficient of the H2OCbl-HC complex as a function of concentration. From the diffusion coefficient at infinite dilution (4.71 x 10(-7) cm2 s-1), the hydrodynamic radius (45.5 A) and rotational correlation time (85.4 ns) have been calculated. Using the latter, and measured values of the 31P NMR linewidths of the H2OCbl-HC complex at several field strengths, a detailed analysis of the 31P nuclear relaxation is possible. The chemical shift anisotropy term from the transverse relaxation equation is determined to be 95.7 ppm, and the average phosphorus-proton internuclear distance is 2.05 A. For comparison to protein-free H2OCbl, the chemical shift anisotropy of the phosphorus atom was studied by solid state NMR spectroscopy and the 31P relaxation by solution T1 measurements. These studies give values of 110.3 ppm for the chemical shift anisotropy term and 2.45 A for the average phosphorus-proton internuclear distance. The results are consistent with a significant change in the conformation of the H2OCbl phosphodiester upon binding to haptocorrin which could be due to a shortening of the axial Co-N bond.

Determination of spin parameters reflected in the nuclear magnetic resonance powder patterns for two equivalent 31P nuclei in Lawesson's reagent

The nuclear magnetic resonance (NMR) powder patterns observed for the 31P spin pair in Lawesson's reagent (1) were analyzed. Using an efficient procedure, wide ranges of the spin parameters were examined to determine whether they might reproduce the experimental one-dimensional (1D) spectrum of the present A2 spin system. It was demonstrated that the parameters were not uniquely determined from the 1D powder pattern only, but a significant reduction of their uncertainties was realized using the two-dimensional (2D) powder pattern. The molecular structure of 1 was discussed in terms of the refined spin parameters.

31P-NMR studies of NADPH, NADP+ and the complex of NADPH and methotrexate with Lactobacillus casei dihydrofolate reductase in the solid state

31P-NMR spectra on solid samples of NADP+, NADPH and NADPH bound to Lactobacillus casei dihydrofolate reductase have been recorded using the techniques of cross polarisation, magic angle spinning and high power proton decoupling. The isotropic chemical shifts, the principal components of the shielding tensors and the asymmetry parameters for the 31P nuclei in the 2'-phosphate and pyrophosphate groups have been measured. The isotropic shifts show similar trends to the chemical shifts measured in solution. The isotropic shifts and the shielding tensors for the dianionic and monoanionic states of the 2'-phosphate group have been determined and the presence of both ionisation states has been detected in a solid sample of the lyophilised complex of L. casei dihydrofolate reductase with NADPH and methotrexate. This contrasts with the behaviour in solution, where only the dianionic form is bound to the enzyme. The signals from the two pyrophosphates 31P nuclei in bound NADPH were resolved and identified. The asymmetry parameters in the different ionisation states and the orientations of the shielding tensors within the molecular framework are considered in the context of previous 31P studies on phosphate-containing compounds.

Solid state 31P cross-polarization/magic angle sample spinning nuclear magnetic resonance of crystalline glycogen phosphorylase b

(31)P cross-polarization/magic angle sample spinning nuclear magnetic resonance spectra have been obtained for pyridoxal 5'-phosphate (PLP) bound to glycogen phosphorylase b (GPb) in two different crystalline forms, monoclinic and tetragonal. Analysis of the intensities of the spinning sidebands in the nuclear magnetic resonance spectra has enabled estimates of the principal values of the (31)P chemical shift tensors to be obtained. Differences between the two sets of values suggest differences in the environment of the phosphate moiety of the pyridoxal phosphate in the two crystalline forms. The tensor for the tetragonal crystalline form, T state GPb, is fully consistent with those found for dianionic phosphate groups in model compounds. The spectrum for the monoclinic crystalline form, R state GPb, although closer to that of dianionic than monoanionic model phosphate compounds, deviates significantly from that expected for a simple dianion or monoanion. This is likely to result from specific interactions between the PLP phosphate group and residues in its binding site in the protein. A possible explanation for the spectrum of the monoclinic crystals is that the shift tensor is averaged by a proton exchange process between different ionization states of the PLP associated with the presence of a sulfate ion bound in the vicinity of the PLP.

A solid-state 31P-NMR investigation of the allosteric transition in glycogen phosphorylase b

The catalytic role of the cofactor phosphate moiety at the active site of glycogen phosphorylase has been the subject of many investigations including solution-state high-resolution 31P-NMR studies. In this study the pyridoxal phosphate moiety in both the inactive and active forms of microcrystalline phosphorylase b has been investigated by high-resolution 31P magic-angle spinning NMR. The symmetry of the shielding tensor in model compounds at varying degrees of ionization is investigated and the results indicate a marked difference between the dianionic and monoanionic model compounds. Consequently the observed similarity in the principal tensor components describing the shielding tensor of the phosphorus nuclei present at the active site of both the R- and T-state conformations suggests that there is no change in ionization site upon activation in contrast to suggestions based upon isotropic shifts. Since previous relaxation measurements have pointed to the need to consider motional influences in such systems, several plausible models are considered. Subject to the assumption of congruency between the principal axis system describing the shielding interaction and molecular frame determined by the molecular symmetry axes, we conclude that the phosphate cofactor is dianionic in both forms.

The presence of the 30 nm filament structure of chromatins in intact chicken erythrocytes observed by 31P NMR

A 31P NMR spectrum of chicken erythrocyte chromatins in vivo was obtained. The spectrum was characterized by examining the spectra of isolated nuclei and nondigested chromatins under various conditions. The results have shown that most chromatins in chicken erythrocyte nuclei assume the 30 nm filament structure as a second step of condensation of DNA in vivo.

Phosphorus-31 NMR as a probe for phosphoproteins

Nuclear magnetic resonance methodology continues to advance such that phosphorus-31 NMR experiments can be profitably applied to elucidate some aspects of proteins which are covalently phosphorylated. This review introduces NMR spectral parameters pertinent to using phosphorus-31 NMR for investigation of structure and dynamics. The techniques of two-dimensional NMR, solid state NMR, and isotopic substitution are also introduced. Characteristics of phosphorylated amino acids and peptides, as revealed by phosphorus-31 NMR, are described. Studies of phosphorylated containing phosphomonoesters, phosphoramidates, acyl phosphates, and disubstituted phosphorus bridges are discussed. Among these phosphoproteins are several examples where phosphorus residues evidently play a role as polyelectrolytes, in enzyme catalysis, and in regulation of protein function.

NMR studies of conformational states and dynamics of DNA

The application of high resolution NMR techniques to the investigation of DNA double helices in solution is currently in a rapid state of change as a result of advances in three different fields. First, new methods (cloning, enzymatic degradation, sonication, and chemical synthesis) have been developed for producing large quantities of short DNA suitable for NMR studies. Second, there have been major advances in the field of NMR in terms of the introduction of new pulse techniques and improvements in instrumentation. Finally, as a result of recent X-ray diffraction studies on short DNA helices and the discovery of left-handed Z-DNA there is heightened interest in the study of DNA structures in solution and the effect of sequence on structure. In the present review, we discuss the way in which NMR techniques have been used to probe various aspects of the DNA properties, including base pairing structure, dynamics of breathing, effect of sequence on DNA structure, internal molecular motions, the effect of environment on the DNA, and the interaction of DNA with small ligands.

Deoxyribonucleic acid dynamics from phosphorus-31 nuclear magnetic resonance

31P NMR of native high molecular weight DNA shows that the phosphodiester backbone undergoes reorientation with a rotational correlation time of about 2 X 10(-6) s at 30 degrees C. This rate is consistent with the flexibility of the polymer and does not require the presence of internal phosphate motions. The line width of the phosphorus resonance of DNA is due to incompletely averaged 31P-1H dipolar couplings and 31P chemical shift anisotropy relaxation; high-power proton decoupling and magnetic field dependence experiments separate the two effects and allow the use of the line width for determination of the rotational correlation time. The line width is dependent on temperature, and an activation energy of 5-8 kcal/mol is calculated for the motion of DNA.

Phosphorus-31 nuclear magnetic resonance of fd virus

31P NMR experiments on the filamentous bacteriophage fd are used to characterize the viral DNA. Because fd is a 16.4 X 10(6) dalton rod-shaped particle, methods of high-resolution solid-state NMR including cross polarization, proton decoupling, and magic angle sample spinning are utilized. The 31P chemical shielding tensor of solid fd is indistinguishable from that of single-stranded or double-stranded DNA in the absence of proteins; therefore the 31P chemical shift does not show evidence of structural changes in DNA upon incorporation into the virus. fd in solution has a very broad 31P resonance line width. The line width is due to static chemical shift anisotropy that is not motionally averaged, as shown by the generation of sidebands with magic angle sample spinning and a linear dependence of line width on magnetic field strength. These results indicate that DNA packaged inside fd is immobilized by the coat proteins.

Nuclear magnetic resonance of the filamentous bacteriophage fd

The filamentous bacteriophage fd and its major coat protein are being studied by nuclear magnetic resonance (NMR) spectroscopy. 31P NMR shows that the chemical shielding tensor of the DNA phosphates of fd in solution is only slightly reduced in magnitude by motional averaging, indicating that DNA-protein interactions substantially immobilize the DNA packaged in the virus. There is no evidence of chemical interactions between the DNA backbone and the coat protein, since experiments on solid virus show the 31P resonances to have the same principle elements of its chemical shielding tensor as DNA. 1H and 13C NMR spectra of fd virus in solution indicate that the coat proteins are held rigidly in the structure except for some aliphatic side chains that undergo relatively rapid rotations. The presence of limited mobility in the viral coat proteins is substantiated by finding large quadrupole splittings in 2H NMR of deuterium labeled virions. The structure of the coat protein in a lipid environment differs significantly from that found for the assembled virus. Data from 1H and 13C NMR chemical shifts, amide proton exchange rates, and 13C relaxation measurements show that the coat protein in sodium dodecyl sulfate micelles has a native folded structure that varies from that of a typical globular protein or the coat protein in the virus by having a partially flexible backbone and some rapidly rotating aromatic rings.

Nonuniform backbone conformation of deoxyribonucleic acid indicated by phosphorus-31 nuclear magnetic resonance chemical shift anisotropy

31P nuclear magnetic resonance of highly oriented DNA fibers has been observed for three different conformations, namely, the A, B, and C forms of DNA. At a parallel orientation of the fiber axis with respect to the magnetic field, DNA fibers in both the A and B forms exhibit a single, abnormally broad resonance; in contrast, fibers in the C form show almost the full span of the chemical shift anisotropy (170 ppm). The spectra of the fibers oriented perpendicular indicate that the DNA molecules undergo a considerable rotational motion about the helical axis, with a rate of greater than 2 x 10(3) s-1 for the B-form DNA. Theoretical considerations indicate that the 31P chemical shift data for the B-form DNA fibers are consistent with the atomic coordinates of the phosphodiester group proposed by Langridge et al. [Langridge, R., Wilson, H. R. Hooper, C. W., Wilkins, M. H. F., & Hamilton, L. D. (1960) J. Mol. Biol. 2, 19--37] but not with the corresponding coordinates proposed by Arnott and Hukins [Arnott, S., & Hukins, D. W. L. (1972) Biochem. Biophys. Res. Coomun. 47, 1504--1509], and also lead to the conclusion that the phosphodiester orientation must vary significantly along the DNA molecule. The latter result suggests that DNA has significant variations in its backbone conformation along the molecule.