Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplings in the solution state. By combining a number of different types of couplings, (1)D(CH), (2)D(CH), and D(HH), an order matrix is solved for each ring of the trimannoside. The resulting order parameters indicate the internal motion at the alpha (1,3) linkage to be limited, while significant motion is suggested at the alpha (1,6) linkage. Two structures for the trimannoside were determined by aligning the order tensor principal axes obtained from two different orienting media, bicelles and phage. The very similar conformations at the alpha (1,3) linkage of these two structures confirm that the internal motion at the alpha (1,3) linkage is small and the conformation is a good representation of a single preferred structure. The different conformations at the alpha (1,6) linkage suggest that the motional amplitudes are large and the conformations must be viewed as virtual conformers. Compared with traditional NMR methods, data acquisition is easy and data analysis is straightforward.     

Conformation and orientation of tetraalanine in a lyotropic liquid crystal studied by nuclear magnetic resonance

The (1)H NMR spectra of two isotopomers of tetraalanine deuterated on the two external methyl groups and on the two internal ones, respectively, were recorded in the lyotropic solvent cesium pentadecafluorooctanoate (CsPFO)/water. Eight dipolar couplings could be estimated from the spectra. The set of dipolar couplings was fitted assuming that one rigid conformer is present. Of the four major conformers considered, selected on the basis of theoretical calculations, the one characterized by the two couples of internal dihedral angles in the Ramachandran region of PPII resulted to be the only one to fit the set of couplings within experimental error. The data indicate that the molecule is oriented with the long molecular axis tilted with respect to the surface of the micelles formed by CsPFO.     

PITANSEMA, a low-power PISEMA solid-state NMR experiment

A low radio frequency power polarization inversion spin exchange at the magic angle (PISEMA) pulse sequence is described for the measurement of heteronuclear dipolar couplings from solids. The method employs a time averaged nutation concept to significantly reduce the rf power required to spin-lock low gamma nuclear spins in PISEMA experiments. The efficacy of the 2D method is demonstrated on a single crystal of n-acetyl-L-(15)N-valyl-L-(15)N-leucine dipeptide to measure (1)H-(15)N dipolar couplings and a liquid crystal sample to measure (1)H-(13)C dipolar couplings.     

Molecules with large-amplitude torsional motion partially oriented in a nematic liquid crystal: ethane and isotopomers

An NMR study on ethane and five isotopomers dissolved in the nematic liquid crystal Merck ZLI 1132 is performed. A consistent set of dipolar and quadrupolar couplings is obtained. The dipolar couplings are corrected for harmonic vibrational effects, while the contribution from the torsional motion is incorporated classically. The corrected dipolar couplings cannot be understood in terms of a reasonable molecular structure unless effects of the reorientation-vibration interaction are taken into account. Assuming that the reorientation-vibration contributions that are known for the methyl group in methyl fluoride are transferable to ethane, excellent agreement between observed and calculated dipolar couplings is obtained on the basis of the ethane gas-phase structure. The observed and calculated deuterium quadrupolar couplings show discrepancies supporting the notion that average electric field gradients are important in liquid-crystal solvents. An important consequence of the transferability of the reorientation-vibration correlation is that in other molecules with a methyl group the same procedure as for ethane can be followed. Inclusion of this effect generally removes the need to interpret changes in observed dipolar couplings in terms of elusive chemical effects.     

Comparison of methyl rotation axis order parameters derived from model-free analyses of (2)H and (13)C longitudinal and transverse relaxation rates measured in the same protein sample.

Recombinant HIV-1 protease was obtained from bacteria grown on a 98% D(2)O medium containing 3-(13)C pyruvic acid as the sole source of (13)C and (1)H. The purified protein is highly deuterated at non-methyl carbons, but contains significant populations of (13)CHD(2) and (13)CH(2)D methyl isotopomers. This pattern of isotope labeling permitted measurements of (1)H and (13)C relaxation rates of (13)CHD(2) isotopomers and (2)H (D) relaxation rates of (13)CH(2)D isotopomers using a single sample. The order parameters S(axis)(2), which characterize the motions of the methyl rotation axes, were derived from model-free analyses of R(1) and R(2) data sets measured for (13)C and (2)H spins. Our primary goal was to compare the S(axis)(2) values derived from the two independent types of data sets to test our understanding of the relaxation mechanisms involved. However, S(axis)(2) values derived from the analyses depend strongly on the geometry of the methyl group, the sizes of the quadrupolar and dipolar couplings, and the effects of bond vibrations and librations on these couplings. Therefore uncertainties in these basic physical parameters complicate comparison of the order parameters. This problem was circumvented by using an experimental relationship, between the methyl quadrupolar, (13)C-(13)C and (13)C-(1)H dipolar couplings, derived from independent measurements of residual static couplings of weakly aligned proteins by Ottiger and Bax (J. Am. Chem. Soc. 1999, 121, 4690-4695) and Mittermaier and Kay (J. Am. Chem. Soc. 1999, 121, 10608-10613). This approach placed a tight experimental restraint on the values of the (2)H quadrupolar and (13)C-(1)H dipolar interactions and greatly facilitated the accurate comparison of the relative values of the order parameters. When applied to our data this approach yielded satisfactory agreement between the S(axis)(2) values derived from the (13)C and (2)H data sets.     

Determination of natural abundance 15N-1H and 13C-1H dipolar couplings of molecules in a strongly orienting media using two-dimensional inverse experiments

NMR spectra of molecules oriented in liquid crystals provide homo- and heteronuclear dipolar couplings and thereby the geometry of the molecules. Several inequivalent dilute spins such as 13C and 15N coupled to protons form different coupled spin systems in their natural abundance and appear as satellites in the proton spectra. Identification of transitions belonging to each spin system is essential to determine heteronuclear dipolar couplings, which is a formidable task. In the present study, using 15N-1H and 13C-1H HSQC, and HMQC experiments we have selectively detected spectra of each rare spin coupled to protons. The 15N-1H and 13C-1H dipolar couplings have been determined in the natural abundance of 13C and 15N for the molecules pyrazine, pyrimidine and pyridazine oriented in a thermotropic liquid crystal.     

Proton evolved local field solid-state nuclear magnetic resonance using Hadamard encoding: theory and application to membrane proteins

NMR anisotropic parameters such as dipolar couplings and chemical shifts are central to structure and orientation determination of aligned membrane proteins and liquid crystals. Among the separated local field experiments, the proton evolved local field (PELF) scheme is particularly suitable to measure dynamically averaged dipolar couplings and give information on local molecular motions. However, the PELF experiment requires the acquisition of several 2D datasets at different mixing times to optimize the sensitivity for the complete range of dipolar couplings of the resonances in the spectrum. Here, we propose a new PELF experiment that takes the advantage of the Hadamard encoding (HE) to obtain higher sensitivity for a broad range of dipolar couplings using a single 2D experiment. The HE scheme is obtained by selecting the spin operators with phase switching of hard pulses. This approach enables one to detect four spin operators, simultaneously, which can be processed into two 2D spectra covering a broader range of dipolar couplings. The advantages of the new approach are illustrated for a U-(15)N NAL single crystal and the U-(15)N labeled single-pass membrane protein sarcolipin reconstituted in oriented lipid bicelles. The HE-PELF scheme can be implemented in other multidimensional experiments to speed up the characterization of the structure and dynamics of oriented membrane proteins and liquid crystalline samples.     

应用相敏HMQC和HSQC谱准确测定异核碳-氢偶合常数

准确测定各种同核和异核偶合常数是核磁共振（NMR）方法研究的一个非常跃的领域。首先,各种三键偶合常数通过Karplus关系式^[1]反映了相应二面角的大小,因此,多键偶合常数的准确测定直接影响分子结构确定的精确性。其次,由于稀液晶溶剂体系NMR方法的发展^[2],准确测定各种异核键偶合常数也显得非常重要,特别是应用场相关偶合常数研究分子在磁场中的取向时,对异核－键偶合常数测定的准确性要求更加严格^[3]。异核－键偶合常数的最准确的测定方法是异核偶合调制的HSQC（Heteronuclear Single-Quantum Coherence)实验^[3],它通过测定一系列异核耦合调制的二维HSQC谱,对交叉峰的强度进行分析来精确确定相应的异核－键偶合常数。这一方法的缺点是比较费时。作者在异核多键偶合常数的准确测定方面也做了一些有意义的工作^[4-6 α]。在前文^[5]工作的基础上,本文提出了二维相敏HMQC（Heteronuclear Multiple-Quantum Coherence)和HSQC（Heteronuclear Single-Quantum Coherence)实验,用于准确测定异核－键偶合常数。     

Magnetic field induced dipolar couplings in the pretransitional region of a nematic liquid crystal

13C and 1H NMR spectroscopy have been used to study the orientational order which develops when a nematogenic compound, 4-pentyl-4'-cyanobiphenyl (5CB), approaches the transition from the isotropic to the nematic phase at T(NI). The experiments yield values of field induced dipolar couplings, (1), between all of the directly bonded carbon and hydrogen nuclei in the molecule, and 2D(HH)B, the geminal dipolar coupling between protons in the first methylene group in the alkyl chain. The temperature dependence of these couplings shows that in each case they follow a divergence behavior governed by (T - T*)(-1),where T* is a temperature determined from the experimental data and which is close to but less than T(NI). Experiments performed at spectrometer field strengths of 11.75 and 18.79 T confirm the prediction that the induced couplings should depend on the square of the applied field strength. It was found that, within experimental error, T* is the same for each field-induced coupling, and that T(NI) - T* is the same at 11.75 and 18.79 T. It is shown that the set of field-induced couplings 1D(CHi)B obtained at a temperature close to T(NI) can be used to derive a conformer distribution for 5CB in the isotropic phase.     

The D Parameter (EPR Zero-Field Splitting) of Localized 1,3-Cyclopentanediyl Triplet Diradicals as a Measure of Electronic Substituent Effects on the Spin Densities in Para-Substituted Benzyl-Type Radicals

The zero-field splitting parameters D of the symmetrically disubstituted and unsymmetrically monosubstituted 1,3-diaryl-1,3-cyclopentanediyl triplet diradicals 1, 2 (X = p-MeO, p-Me, p-Cl, p-NH(2), p-CO(2)Me, p-CN, p-NO(2)), and 5 were determined in 2-methyltetrahydrofuran glass at 77 K. The linear plot (m = 0.558, r(2) = 0.993) of the experimental D values for the symmetrically disubstituted derivatives versus the corresponding monosubstituted ones reveals that the electronic substituent effects are additive and implies (except for the magnetic dipolar interaction) that each benzyl-type radical site acts independently in the localized diradicals. This additivity permits us to view these triplet diradicals as a composite of the two separate monoradical components and allows us to assess valuable electronic properties of benzyl-type monoradicals from the D parameter of the triplet diradical species. A theoretical analysis shows that the D parameter is a measure of the spin density rho at the benzylic positions and the inter-radical distance d in localized diradicals. A good correlation exists between the D parameter of these triplet diradicals (constant inter-radical distance d) and the EPR hyperfine coupling constants of the corresponding benzyl-type monoradicals, which establishes that the observed electronic substituent effects reflect changes in the spin densities at the radical sites. The novel DeltaD scale allows us to quantify spectroscopically the para substituent effect on the spin delocalization at the benzylic position.     

Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.

We present a new NMR procedure for determining the three-dimensional fold of C2-symmetric nucleic acid homodimers that relies on long-range orientational constraints derived from the measurement of two independent sets of residual dipolar couplings under two alignment conditions. The application is demonstrated on an (15)N/(13)C-enriched deoxyoligonucleotide sequence, d(G-G-G-T-T-C-A-G-G), shown previously to dimerize into a quadruplex in solution and form a pair of G.(C-A) triads and G-G-G-G tetrads (G-tetrad) motifs. One-bond (1)H-(15)N ((1)D(NH)) and (1)H-(13)C ((1)D(CH)) residual dipolar couplings have been measured between nuclei in the bases of these motifs using bacteriophage as an ordering medium, and under direct magnetic field alignment (800 MHz). By combining the two dipolar data sets in an order matrix analysis, the orientation of the G.(C-A) triad relative to the G-tetrad within a contiguous monomeric unit can directly be determined, even in the presence of interstrand/intrastrand NOE ambiguity. We further demonstrate that the orientation of the C2-axis of molecular symmetry in the homodimer relative to the G.(C-A) triad and G-tetrad motifs can unambiguously be determined using the two sets of independent dipolar coupling measurements. The three-dimensional fold of the homodimer determined using this procedure is very regular and in excellent agreement with a previously determined high-resolution NOE-based NMR structure, where interstrand/intrastrand NOEs were treated as ambiguous and where noncrystallographic symmetry constraints were implicitly imposed during the structure calculation.     

Measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in (15)N,(13)C,(2)H-labeled proteins: application to domain orientation in maltose binding protein.

TROSY-based HN(CO)CA 2D and 3D pulse schemes are presented for measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in high molecular weight (15)N,(13)C,(2)H-labeled proteins. In one approach, (13)C(alpha)-(13)C(beta) dipolar couplings are obtained directly from the time modulation of cross-peak intensities in a set of 2D (15)N-(1)HN correlated spectra recorded in both the presence and absence of aligning media. In a second approach 3D data sets are recorded with (13)C(alpha)-(13)C(beta) couplings encoded in a frequency dimension. The utility of the experiments is demonstrated with an application to an (15)N,(13)C,(2)H-labeled sample of the ligand free form of maltose binding protein. A comparison of experimental dipolar couplings with those predicted from the X-ray structure of the apo form of this two-domain protein establishes that the relative orientation of the domains in solution and in the crystal state are very similar. This is in contrast to the situation for maltose binding protein in complex with beta-cyclodextrin where the solution structure can be generated from the crystal state via a 11 degrees domain closure.     

Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study

This paper describes an analysis of NMR dipolar couplings in a bilayer formed by dimyristoylphosphatidylcholine (DMPC). The couplings are calculated from a trajectory generated in a molecular dynamics (MD) simulation based on a realistic atom-atom interaction potential. The analysis is carried out employing a recently developed approach that focuses on the construction of the conformational distribution function. This approach is a combination of two models, the additive potential (AP) model and the maximum entropy (ME) method, and is therefore called APME. In contrast to the AP model, the APME procedure does not require an intuition-based choice of the functional form of the torsional potential and is, unlike the ME method, applicable to weakly ordered systems. The conformational distribution function for the glycerol moiety of the DMPC molecule derived from the APME analysis of the dipolar couplings is in reasonable agreement with the "true" distributions calculated from the trajectory. Analyses of dipolar couplings derived from MD trajectories can, in general, serve as guidelines for experimental investigations of bilayers and other complex biological systems.     

Conformational analysis of 2,2'-bithiophene: a (1)H liquid crystal NMR study using the (13)C satellite spectra

We have obtained a very large data set of spectral parameters from the analysis of (1)H NMR and (13)C satellite spectra of 2,2'-bithiophene dissolved in anisotropic, partially orienting mesophases. In particular, this parameter set includes 33 dipolar couplings, which are directly related to the interatomic distances, the dihedral angle phi between the two thiophenic rings, and the anisotropic solute-solvent interaction potential. This allows an exhaustive investigation of the conformational equilibrium of 2,2'-bithiophene in a liquidlike phase. Comparison with the predictions of high-level theoretical calculations for the isolated molecule provides evidence of a strong flattening as well as the sharpening effect of the medium on the conformer population. The approximations needed to apply vibrational corrections to flexible molecules are discussed in detail and some general conclusions concerning their effect on structure and conformational equilibria are proposed.     

The structure and conformation of a mesogenic compound between almost zero and almost complete orientational order

The conformational distributions in molecules that form liquid crystalline phases are predicted to depend strongly on orientational order. Results are presented here to test this hypothesis. The mesogen 4-hexyloxy-4'-cyanobiphenyl (6OCB) has been studied by NMR spectroscopy in the isotropic phase and in the nematic phase. In the isotropic phase the field-induced orientational ordering produces small dipolar couplings between ¹³C and ¹H nuclei, which were determined from the ¹³C spectra. Couplings between ¹H nuclei were also obtained using 2D selective refocusing experiments. In the nematic phase, both ¹H-¹H dipolar couplings and quadrupolar splittings for deuterium nuclei were measured for partially-deuterated samples. Both proton and deuterium spectra were also obtained for 6OCB in an equimolar mixture with 4-(ethoxybenzylidene)-4'-butylaniline (EBBA). This mixture exhibits SmA and SmB phases. The data obtained from these experiments has been analysed to yield the probability distribution of the conformations in this molecule generated by rotations about bonds. It is found that there is a substantial influence of the orientational order of the molecules on these distributions.     

NMR studies of molecular conformations in alpha-cyclodextrin

A new approach for analysis of NMR parameters is proposed. The experimental data set includes scalar couplings, NOEs, and residual dipolar couplings. The method, which aims at construction of the conformational distribution function, is applied to alpha-cyclodextrin in isotropic solution and dissolved in a dilute liquid crystal. An attempt to analyze the experimental data using an average molecular conformation resulted in unacceptable errors. Our approach rests on the maximum entropy method (ME), which gives the flattest possible distribution, consistent with the experimental data. Very good agreement between experimental and calculated NMR parameters was observed. In fact, two conformational states were required in order to obtain a satisfactory agreement between calculated and experimental data. In addition, good agreement with Langevin dynamics computer simulations was obtained.     

Conformational thermodynamic and kinetic parameters of methyl-substituted 1,3-butadienes

The s-trans/s-cis conformational equilibria of 10 methyl-substituted 1,3-butadienes [(E)- and (Z)-1,3-pentadiene; 2-methyl-1,3-butadiene; (E)-2-methyl-1,3-pentadiene; 2,3-dimethyl-1,3-butadiene; (E,E)-, (E,Z)-, and (Z,Z)-2,4-hexadiene; 2,5-dimethyl-2,4-hexadiene; and (E,E)-2,4-dimethyl-2,4-hexadiene] were explored by trapping high-temperature conformational equilibria by cryogenic deposition. The vapor state enthalpy differences of these s-trans/s-cis conformers, DeltaH(t equilibrium c), were determined by varying the equilibrating temperature and integrating the resulting matrix isolated IR spectra. The results obtained are in good agreement with ab initio calculations at the G3 level. From these thermodynamic parameters, methyl group nonbonded interactions in conjugated 1,3-butadienes were delineated. Rates of decay of s-cis conformers to their s-trans rotamers were obtained in the solid-state by warming up trapped high-temperature equilibrated samples formed from neat depositions. These data were analyzed in terms of dispersive kinetics with matrix site effects in the solid-state modeled by a Gaussian distribution of activation energies. The activation barriers thus obtained were compared with G3 calculations of the enthalpies of activation.     

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.     

PAH formation under single collision conditions: reaction of phenyl radical and 1,3-butadiene to form 1,4-dihydronaphthalene

The crossed beam reactions of the phenyl radical (C(6)H(5), X(2)A(1)) with 1,3-butadiene (C(4)H(6), X(1)A(g)) and D6-1,3-butadiene (C(4)D(6), X(1)A(g)) as well as of the D5-phenyl radical (C(6)D(5), X(2)A(1)) with 2,3-D2-1,3-butadiene and 1,1,4,4-D4-1,3-butadiene were carried out under single collision conditions at collision energies of about 55 kJ mol(-1). Experimentally, the bicyclic 1,4-dihydronaphthalene molecule was identified as a major product of this reaction (58 ± 15%) with the 1-phenyl-1,3-butadiene contributing 34 ± 10%. The reaction is initiated by a barrierless addition of the phenyl radical to the terminal carbon atom of the 1,3-butadiene (C1/C4) to form a bound intermediate; the latter underwent hydrogen elimination from the terminal CH(2) group of the 1,3-butadiene molecule leading to 1-phenyl-trans-1,3-butadiene through a submerged barrier. The dominant product, 1,4-dihydronaphthalene, is formed via an isomerization of the adduct by ring closure and emission of the hydrogen atom from the phenyl moiety at the bridging carbon atom through a tight exit transition state located about 31 kJ mol(-1) above the separated products. The hydrogen atom was found to leave the decomposing complex almost parallel to the total angular momentum vector and perpendicularly to the rotation plane of the decomposing intermediate. The defacto barrierless formation of the 1,4-dihydronaphthalene molecule involving a single collision between a phenyl radical and 1,3-butadiene represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated counterparts in combustion and interstellar chemistry.