More line narrowing in TROSY by decoupling of long-range couplings: shift correlation and 1JNC' coupling constant measurements

Since the introduction of RDCs in high-resolution NMR studies of macromolecules, there is a growing interest in the development of accurate, and sensitive methods for determining coupling constants. Most methods for extracting these couplings are based on the measurement of the splitting between multiplet components in J-coupled spectra. However, these methods are often unreliable since undesired multiple-bond couplings can considerably broaden the multiplet components and consequently make accurate determination of their position difficult. To demonstrate one approach to this problem, G-BIRD((r)) decoupled TROSY sequences are proposed for the measurement of (1)J(NH) and (1)J(NC') coupling constants. Resolved or unresolved splittings due to remote protons are removed by a G-BIRD((r)) module employed during t(1) and as a result, spectra with narrow, well-resolved peaks are obtained from which heteronuclear one-bond couplings can be accurately measured. Moreover, introduction of a spin-state-selective alpha/beta-filter in the TROSY sequence allows the separation of the (1)J(NC') doublet components into two subspectra which contain the same number of peaks as the regular TROSY spectrum. The (1)J(NC') couplings are obtained from the displacement between the corresponding peaks in the subspectra.     

More line narrowing in TROSY by decoupling of long-range couplings: shift correlation and JNC′ coupling constant measurements

Since the introduction of RDCs in high-resolution NMR studies of macromolecules, there is a growing interest in the development of accurate, and sensitive methods for determining coupling constants. Most methods for extracting these couplings are based on the measurement of the splitting between multiplet components in J-coupled spectra. However, these methods are often unreliable since undesired multiple-bond couplings can considerably broaden the multiplet components and consequently make accurate determination of their position difficult. To demonstrate one approach to this problem, G-BIRD^(r) decoupled TROSY sequences are proposed for the measurement of ¹J_NH and ¹J_NC′ coupling constants. Resolved or unresolved splittings due to remote protons are removed by a G-BIRD^(r) module employed during t₁ and as a result, spectra with narrow, well-resolved peaks are obtained from which heteronuclear one-bond couplings can be accurately measured. Moreover, introduction of a spin-state-selective α/β-filter in the TROSY sequence allows the separation of the ¹J_NC′ doublet components into two subspectra which contain the same number of peaks as the regular TROSY spectrum. The ¹J_NC′ couplings are obtained from the displacement between the corresponding peaks in the subspectra.     

J-modulated TROSY experiment extends the limits of homonuclear coupling measurements for larger proteins.

This paper describes the use of a TROSY experimental scheme and its variant extended with a scaled J-modulation spin-echo sequence for accurate and sensitive measurement of homonuclear 3J(H(N)H(alpha)) coupling constants in larger proteins with uniform 15N labeling. Exclusive selection of the most slowly relaxing component of a 15N-1H multiplet by the TROSY approach leads to substantial improvement in resolution; this is a prerequisite for accurate measurement of couplings from the 1H multiplets directly along the 1H frequency dimension or from the J-scaled doublets along the 15N frequency dimension.     

Sensitivity-enhanced E.COSY-type HSQC experiments for accurate measurements of one-bond 15N-1H(N) and 15N-13C' and two-bond 13C'-1H(N) residual dipolar couplings in proteins

Novel E.COSY-type HSQC experiments are presented for the accurate measurement of one-bond 15N-1H(N) and 15N-13C(') and two-bond 13C(')-1H(N) residual dipolar couplings in proteins. Compared with existing experiments, the (delta,J)-E.COSY experiments described here are composed of fewer pulses and the resulting spectra exhibit 1.4 times the sensitivity of coupled HSQC spectra. Since residual dipolar couplings play increasingly important roles in structural NMR, the proposed methods should find wide spread application for structure determination of proteins and other biological macromolecules.     

Sensitivity-enhanced 2D IPAP,TROSY-anti-TROSY,and E.COSY experiments: alternatives for measuring dipolar 15N-1HN couplings

Sensitivity-enhanced versions of the IPAP, TROSY-anti-TROSY, and E.COSY experiments for measuring one-bond 15N-1HN couplings are presented. Together with the previously developed sensitivity-enhanced E.COSY-type HSQC experiment they comprise a suite of sensitivity-enhanced experiments that allows one to chose the optimal spectrum for accurate measurement of one-bond 15N-1HN residual dipolar couplings in proteins. Since one-bond 15N-1HN residual dipolar couplings play uniquely important roles in structural NMR, these additional methods provide further tools for improving structure determination of proteins and other biological macromolecules.     

3hJ coupling between C(alpha) and H(N) across hydrogen bonds in proteins

J couplings between (13)C(alpha) and (1)H(N) across hydrogen bonds in proteins are reported for the first time, and a two- or three-dimensional NMR technique for their measurement is presented. The technique exploits the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms, for sensitivity enhancement. The 2D or 3D spectra exhibit E.COSY patterns where the splittings in the (13)CO and (1)H(N) dimensions are (1)J((13)C(alpha), (13)CO) and the desired (3h)J((13)C(alpha), (1)H(N)), respectively. A demonstration of the new method is shown for the (15)N,(13)C-labeled protein chymotrypsin inhibitor 2 where 17 (3h)J((13)C(alpha), (1)H(N)) coupling constants ranging from 0 to 1.4 Hz where identified and all of positive sign.     

Accurate determination of small one-bond heteronuclear residual dipolar couplings by F1 coupled HSQC modified with a G-BIRD(r) module

We report a G-BIRD(r) modified coupled HSQC experiment for the accurate determination of one-bond heteronuclear residual dipolar couplings. The G-BIRD(r) module has been employed to refocus the long-range coupling evolution of the heteronucleus during the t1 frequency labeling period. As a result, the crosspeaks obtained are split by only the direct one-bond coupling that can be extracted by measuring simple frequency differences between singlet maxima. Additionally the decoupling of long-range multiple bond splittings leads to considerable sensitivity enhancement. The modification also has been applied in a TROSY sequence resulting in a significant sensitivity and resolution improvement.     

Efficient measurement of (3)J(N,Cgamma) and (3)J(C',Cgamma) coupling constants of aromatic residues in (13)C, (15)N-labeled proteins

An NMR pulse sequence is proposed for the simultaneous determination of side chain chi1 torsion-angle related (3)J(N,Cgamma) and (3)J(C', Cgamma) couplings in aromatic amino acid spin systems. The method is of the quantitative J correlation type and takes advantage of attenuated (15)N and (1)H transverse relaxation by means of the TROSY principle. Unlike previously developed schemes for the measurement of either of the two coupling types, spectra contain internal reference peaks that are usually recorded in separate experiments. Therefore, the desired information is extracted from a single rather than four data sets. The new method is demonstrated with uniformly (13)C/(15)N labeled Desulfovibrio vulgaris flavodoxin, which contains 14 aromatic out of 147 total amino acid residues.     

Measurement of homonuclear proton couplings from regular 2D COSY spectra

An interactive computer procedure is described which determines (1)H--(1)H couplings from fitting the cross-peak multiplets in regular phase-sensitive COSY spectra. The robustness and simplicity of the method rely on the fact that a given cross-peak intensity is not an independent variable in the fitting procedure, making it possible to measure couplings accurately even from individual cross peaks with unresolved multiplet structure.     

Pulse sequences for measurement of one-bond (15)N-(1)H coupling constants in the protein backbone.

A set of three improved two-dimensional (2D) NMR methods for measuring one-bond (15)N-(1)H coupling constants in the protein backbone is presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D spectra into two separate subspectra corresponding to the two possible spin states of the coupling partner. Cross talk between the two subspectra is a second order effect in the difference between the actual coupling constants and the one used in setting the pertinent delays of the pulse sequences. This relatively high degree of editing accuracy makes the methods useful for applications to molecules subjected to weak alignment where the one-bond coupling constants are linear combinations of a scalar J and a residual dipolar contribution containing important structural information. A demonstration of the new methods is shown for the (15)N-labeled protein chymotrypsin inhibitor 2 in a lipid bicelle mixture.     

Clean TROSY: compensation for relaxation-induced artifacts

TROSY pulse sequences for recording, e.g., (1)H-(15)N chemical shift correlation spectra of proteins are designed to select only one of four two-dimensional multiplet components. However, all of the variants published so far are prone to relaxation-induced artifacts at the positions of two of the other multiplet components. This article introduces modifications to the two spin-state-selective coherence transfer building blocks of the TROSY mixing sequence resulting in a clean TROSY spectrum with the artifacts largely suppressed. It works by having the new mixing sequence generate peaks of opposite phase at the positions of the relaxation artifacts. The clean TROSY pulse sequence is marginally shorter than the original one and contains the same pulses. Experimental demonstration is presented for the (15)N-labeled proteins RAP 17-97 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein) and EQT, equinatoxin II, from the Mediterranean anemone Actinia equina.     

Development of a method for the measurement of long-range 13C-1H coupling constants from HMBC spectra

This paper describes a number of improvements to a method, developed in this laboratory and described in J. Magn. Reson. 85 (1989) 111-113, which makes it possible to determine values of long-range 13C-1H coupling constants from heteronuclear multiple bond correlation (HMBC) spectra. First, it is shown how pulsed-field gradients can be introduced into the HMBC experiment without perturbing the form of the cross-peak multiplets; a one-dimensional version of the experiment is also described which permits the rapid measurement of a small number of couplings. Second, the experiment is modified so that one-bond and long-range cross-peaks can be separated, and so that the one-bond cross-peaks have more reliable intensities. Finally, it is shown how these one-bond cross-peaks can be used to advantage in the fitting procedure.     

J-modulated ADEQUATE (JM-ADEQUATE) experiment for accurate measurement of carbon-carbon coupling constants

A new method for the accurate determination of carbon-carbon coupling constants is described. The method is based on a modified ADEQUATE experiment, where a J-modulated spin-echo sequence precedes the ADEQUATE pulse scheme. The J-modulation and scaling of carbon-carbon couplings is based on simultaneous incrementation of 13C chemical shift and coupling evolution periods. The time increment for the homonuclear carbon-carbon coupling evolution can be suitably scaled with respect to the corresponding increment for the chemical shift evolution. Typically a scaling factor of 2 to 3 is employed for the measurement of one-bond coupling constants, while multiplication by a factor of 10 to 15 is applied when small long-range couplings are determined. The same pulse scheme with coupling evolution period optimized for one-bond or long-range couplings allows the determination of the corresponding carbon-carbon coupling constants. The splittings of the ADEQUATE crosspeaks in the F1 dimension yield the appropriately multiplied coupling constants.     

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C'-13Calpha and 13Calpha-1Halpha residual dipolar couplings in proteins

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.     

Simultaneous measurement of protein one-bond residual dipolar couplings without increased resonance overlap

A NMR strategy designed to measure simultaneously and without increased resonance overlap scalar and dipolar couplings (RDCs) in (13)C-, (15)N-labeled proteins is presented. Contrary to common schemes for simultaneous measurement of RDCs, a single reference experiment is used for the extraction of more than one type of coupling, thereby reducing the required measurement time. This is accomplished by a common reference spectrum followed by a series of interleaved experiments, in which a particular coupling dependent parameter is varied according to the quantitative J-correlation method or using accordion spectroscopy. To illustrate this idea, we have modified the 3D TROSY-HNCO and the 3D CBCA(CO)NH experiment allowing efficient measurement of one-bond (1)D(NH), (1)D(C'N), (1)D(CalphaHalpha), (1)D(CbetaHbeta), and (1)D(CalphaC') couplings in small to medium sized proteins. In addition, the experiments are expected to be useful for largely unfolded proteins, which show strong resonance overlap but have very favorable relaxation properties. Measurement of RDCs is demonstrated on uniformly (15)N-(13)C-labeled ubiquitin and on the sensory domain of the membraneous two-component fumarate sensor DcuS of Escherichia coli (17 kDa). DcuS was found to be unstable and to precipitate in one to two weeks. RDCs obtained from these experiments are in good agreement with the 1.8A X-ray structure of ubiquitin.     

New techniques for the measurement of C'N and C'H(N) J coupling constants across hydrogen bonds in proteins

Two new two- or three-dimensional NMR methods for measuring (3h)J(C'N) and (2h)J(C'H) coupling constants across hydrogen bonds in proteins are presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D or 3D spectra into two separate subspectra corresponding to the two possible spin states of the (1)H(N) spin during evolution of (13)CO coherences. This allows (2h)J(C'H) to be measured in an E.COSY-type way while (3h)J(C'N) can be measured in the so-called quantitative way provided a reference spectrum is also recorded. A demonstration of the new methods is shown for the (15)N,(13)C-labeled protein chymotrypsin inhibitor 2.     

Sensitivity-enhanced IPAP experiments for measuring one-bond C–C and C–H residual dipolar couplings in proteins

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.     

Measurement of homonuclear proton couplings based on cross-peak nulling in CT-COSY

A method in which 1H-1H scalar and dipolar couplings are obtained from the cross-peak nulling condition in a series of constant-time (CT) COSY spectra, as a function of the duration of the CT period, is described. The method is best suited for measurement of 1H-1H couplings in the range 5-20 Hz. It is shown, however, that results can be sensitive to cross-correlated relaxation effects. Also, artifactual resonances, resulting from strong coupling, can be quite pronounced in CT-COSY spectra, even when /J(AB)/(deltaA-deltaB)/<0.1. The experiments are demonstrated for the DNA dodecamer d(CGCGAATTCGCG)2, both in isotropic solution and in a liquid crystalline phase.     

Visualisation of enantiomers via insertion of a BIRD module in X-H correlation experiments in chiral liquid crystal solvent

Several 13C-1H NMR techniques are derived simplifying the visualisation of enantiomers in chiral ordering solvents. They proceed through various heteronuclear 2D experiments where a bilinear rotation decoupling sequence (BIRD) is inserted in the middle of the t1 evolution period. In this way, the small couplings are refocused while the large couplings are preserved. The methods allow extracting precise values of one-bond carbon-proton residual dipolar couplings for each enantiomer out of unresolved proton-coupled 13C or carbon-coupled 1H spectra. Illustrative examples are analysed and discussed using various pulse sequences.     

Determination of internucleotide (h)J(HN) couplings by the modified 2D J(NN)-correlated [(15)N, (1)H] TROSY

Recent developments in the direct observation of J couplings across hydrogen bonds in proteins and nucleic acids provide additional information for structure and function studies of these molecules by NMR spectroscopy. A J(NN)-correlated [(15)N, (1)H] TROSY experiment proposed by Pervushin et al. (Proc. Natl. Acad. Sci. USA 95, 14147-14151, 1998) can be applied to measure (h)J(HN) in smaller nucleic acids in an E.COSY manner. However, it cannot be effectively applied to large nucleic acids, such as tRNA(Trp), since one of the peaks corresponding to a fast relaxing component will be too weak to be observed in the spectra of large molecules. In this Communication, we proposed a modified J(NN)-correlated [(15)N, (1)H] TROSY experiment which enables direct measurement of (h)J(HN) in large nucleic acids.