A novel PH-cT-COSY methodology for measuring JPH coupling constants in unlabeled nucleic acids. application to HIV-2 TAR RNA

A quantitative analysis of JPH scalar couplings in nucleic acids is difficult due to small couplings to phosphorus, the extreme overlap of the sugar protons and the fast relaxation of the spins involved in the magnetization transfer. Here we present a new methodology that relies on heteronuclear Constant Time Correlation Spectroscopy (CT-COSY). The three vicinal 3JPH3', 3JPHS' and 3JPHS" scalar couplings can be obtained by monitoring the intensity decay of the P1-H3'(i-1) peak as a function of the constant time T in a 2D correlation map. The advantage of the new method resides in the possibility of measuring the two 3JPH5' and 3JPH5" scalar couplings even in the presence of overlapped H5'/H5" resonances, since the quantitative information is extracted from the intensity decay of the P-H3' peak. Moreover, the relaxation of the H3' proton is considerably slower than that of the H5'/H5" geminal protons and the commonly populated conformations of the phosphate backbone are associated with large 3JPH3' couplings and relatively small 3JPH5'/H5". These two facts lead to optimal signal-to-noise ratio for the P-H3' correlation compared to the P-H5'/H5" correlation. The heteronuclear CT-COSY experiment is suitable for oligonucleotides in the 10-15 kDa molecular mass range and has been applied to the 30mer HIV-2 TAR RNA. The methodology presented here can be used to measure P-H dipolar couplings (DPH) as well. We will present qualitative results for the measurement of P-Hbase and P-H2' dipolar couplings in the HIV-2 TAR RNA and will discuss the reasons that so far precluded the quantification of the DPHS for the 30mer RNA.

Determination of aliphatic side-chain conformation using cross-correlated relaxation: application to an extraordinarily stable 2'-aminoethoxy-modified oligonucleotide triplex

The structural basis for the extraordinary stability of a triple-stranded oligonucleotide in which the third strand contains 2'-aminoethoxy-substituted riboses is investigated by NMR spectroscopy. The enhanced stability of the modified triplex in comparison to the unmodified DNA triplex of the same sequence can be attributed to strong interactions of the aminoethoxy groups of the third strand with the phosphate groups of the purine strand. In molecular dynamics calculations the aminoethoxy side chain was found to be rather flexible, allowing for the presence of hydrogen bonds between the aminoethoxy group of the third strand and two different phosphates of the backbone of the second strand. To investigate the conformational preference of the aminoethoxy side chain a new NMR method has been developed which relies on CH-CH dipolar-dipolar cross-correlated relaxation rates. The results indicate that the aminoethoxy side chains adopt mainly a gauche(+) conformation, for which only one of the two hydrogen bonds inferred by NMR and molecular dynamics simulations is possible. This demonstrates a highly specific interaction between the amino group of the third strand and one of the phosphate groups of the purine strand.

Errors in the measurement of cross-correlated relaxation rates and how to avoid them

Cross-correlated relaxation rates Gamma are commonly obtained from constant time experiments by measuring the effect of the desired cross-correlated relaxation on an appropriate coherence during the constant time T. These measurements are affected by systematic errors, which derive from undesired cross-correlated relaxation effects taking place before and after the constant time period T. In this paper we discuss the sources and the size of these errors in an example of two pulse sequences. Higher accuracy of the measured data can be obtained by recording a set of experiments with different T values. Cross-correlated relaxation rates are measured in constant time experiments either from the differential relaxation of multiple components (J-resolved Gamma experiments) or from the efficiency of magnetization transfer between two coherences (quantitative Gamma experiments). In this paper we calculate analytically the statistical errors in both J-resolved and quantitative Gamma experiments. These formulae provide the basis for the choice of the most efficient experimental approach and parameters for a given measurement time and size of the rate. The optimal constant time T for each method can be calculated and depends on the relaxation properties of the molecule under investigation. Moreover, we will show how to optimize the relative duration of cross and reference experiments in a quantitative Gamma approach.

A new method for the simultaneous measurement of magnitude and sign of 1DCH and 1DHH dipolar couplings in methylene groups

Heteronuclear dipolar couplings of the protein backbone have proven to have a big impact on the accuracy of protein NMR structures. H,H dipolar couplings might have the same impact on side chains. Here we present a method that combines both heteronuclear and homonuclear dipolar couplings to investigate the local conformation of methylene groups. A new pulse sequence (SPITZE-HSQC) is presented, that allows to measure the two C,H and the H,H dipolar couplings at the same time, using spin state selective transfers. The new method has been applied to the methylene groups of glycines in the protein ubiquitin. The C,H and the H,H dipolar couplings might have a key role in fast stereospecific assignment of protons in CH2 groups.

New methylene specific experiments for the measurement of scalar spin-spin coupling constants between protons attached to 13C

New two- and three-dimensional NMR methods are proposed for the measurement of 3J(H, H) coupling constants between two adjacent methylene moieties. The new experiment, which is based on a combination of the E.COSY principle and double/zero quantum heteronuclear spectroscopy, has been applied to diaceton-glucose and to the protein rhodniin. The coupling constants of CH-CH2 groups have been compared with those obtained from a HCCH-E.COSY experiment to check the reliability of the results. An analysis of the coupling constants derived by comparison between experimental and simulated spectra is presented. Simulations were done with the program wtest considering fully correlated dipolar relaxation. Side-chain conformations in amino acids with adjacent methylene groups can be determined by the new experiment.

"Kin " HEHAHA Sequences, Heteronuclear Hartmann-Hahn Transfer with Different Bandwidths for Spins I and S

A new class of heteronuclear Hartmann-Hahn experiments that is based on the simultaneous irradiation of two different multiple-pulse sequences is introduced. For these "kin " HEHAHA sequences, the scaling properties of the effective heteronuclear coupling constants are analyzed. Four kin sequences are presented with a ratio of the active bandwidths DeltanuI /DeltanuS ranging between 1/2 and 1/10. The offset dependence of the polarization-transfer efficiency is examined experimentally and with the help of numerical simulations.

Resonance assignment and secondary structure determination and stability of the recombinant human uteroglobin with heteronuclear multidimensional NMR

Human uteroglobin (h-UG) or Clara cell 10kDa (cc10kDa) is a steroid-dependent, 17 kDa homodimeric, secretory protein with potent anti-inflammatory/immunomodulatory properties. However, the exact physiological role still remains to be determined. It has been hypothesised that its activity is exerted through the binding of a specific target represented by a small molecule (still unknown), and that the binding is regulated by the formation/disruption of two cysteine bonds. The binding properties of the reduced UG have been proved in vitro for several different molecules, but no in vivo data are available to date. However, binding has been observed between reduced rabbit UG and a protein of an apparent molecular mass of 90 kDa and, more recently, we found an h-UG-binding protein

PLUSH TACSY: Homonuclear planar TACSY with two-band selective shaped pulses applied to C(α),C' transfer and C (β),C (aromatic) correlations

A new homonuclear Hartmann-Hahn-type mixing scheme is introduced that effects coherence transfer between resonances in two separated frequency bands. The mixing scheme relies on the irradiation of two-band selective shaped pulses that are expanded in an MLEV-16 supercycle. Similar to heteronuclear Hartmann-Hahn experiments, a planar effective coupling tensor is created. This novel mixing scheme is applied to C(α),C' transfer and to the transfer between C(β) and aromatic carbon spins.

Conformational analysis of dolastatin 10: an NMR and theoretical approach

A solution conformational analysis of dolastatin 10, a powerful antineoplastic agent, has been carried out by means of nmr techniques and theoretical calculations. 1H mono- and bidimensional nmr experiments, as well as 1H-13C heterocorrelated spectra, have been performed on CD2Cl2 solutions. The most interesting nmr data is a huge shielding of the aCH(25) proton of the Dov residue, suggesting the presence of an interaction between the N-terminal and the aromatic C-terminal ends of the molecule. The possibility of a head-to-tail intermolecular association having been discarded, the presence of a series of preferred folded conformation has been hypothesized. Conformational theoretical analysis supports the nmr hypothesis of a folded peptide-like molecule, and a series of possible conformers in good agreement with the experimental data have been analyzed.