Spin-state-selective excitation in selective 1D inverse NMR experiments

A general and very simple strategy for achieving clean spin-state-selective excitation with full sensitivity in carbon-selective gradient-enhanced 1D HMQC and HSQC pulse schemes is presented. The incorporation of an additional hard 90 degrees (13)C pulse applied along a specific orthogonal axis just prior to acquisition into the conventional sequences allows us to select a simultaneous coherence transfer pathway which usually is not detected. The superimposition of this resulting antiphase magnetization to the conventional in-phase magnetization gives the exclusive excitation of the directly attached proton showing only the alpha or beta spin state of the passive (13)C nucleus. The propagation of this particular spin state to other protons can be accomplished by adding any homonuclear mixing process just after this supplementary pulse. Such an approach affords a suite of powerful selective 1D (13)C-edited NMR experiments which are helpful for resonance assignment purposes in overcrowded proton spin systems and also for the accurate determination of the magnitude and sign of long-range proton-carbon coupling constants in CH spin sytems for samples at natural abundance. Such measurements are performed by measuring the relative displacement of relayed signals in the corresponding alpha and beta 1D subspectra.     

Side-chain H and C resonance assignment in protonated/partially deuterated proteins using an improved 3D(13)C-detected HCC-TOCSY

We propose the use of (13)C-detected 3D HCC-TOCSY experiments for assignment of (1)H and (13)C resonances in protonated and partially deuterated proteins. The experiments extend 2D C-13-start and C-13-observe TOCSY type experiments proposed earlier. Introduction of the third (1)H dimension to 2D TOCSY: (i) reduces the peak overlap and (ii) increases the sensitivity per unit time, even for highly deuterated (>85%) protein samples, which makes this improved method an attractive tool for the side-chain H and C assignment of average sized proteins with natural isotope abundance as well as large partially deuterated proteins. The experiments are demonstrated with a 16 kDa (15)N, (13)C-labeled non-deuterated apo-CcmE and a 48 kDa uniformly (15)N, (13)C-labeled and fractionally ( approximately 90%) deuterated dimeric sFkpA. It is predicted that this method should be suitable for the assignment of methyl (13)C and (1)H chemical shifts of methyl protonated, highly deuterated and (13)C-labeled proteins with even higher molecular weight.     

Correlation of backbone amide and side-chain (13)C resonances in perdeuterated proteins

Side-chain carbon resonance assignments are difficult to obtain for larger proteins. While standard methods require protons for excitation and detection of magnetization, their presence is often unacceptable and often leads to unacceptable relaxation losses at the directly bound carbon sites. In this paper, pulse sequences are presented which provide connectivities between aliphatic side-chain (13)C and amide (1)H and (15)N chemical shifts in fully deuterated, (13)C/(15)N-enriched proteins. Magnetization either starts off from carbons or from both nitrogens and protons and is passed along the side-chain via (13)C-(13)C isotropic mixing. Direct rather than (13)CO-relayed (15)N-->(13)C(alpha) or (13)C(alpha)-->(15)N transfer steps allow the detection of intraresidual as well as sequential correlations. To avoid ambiguities between these two types in the three-dimensional version of the experiments, a fourth dimension can be introduced to achieve their separation along a (13)C(alpha) frequency axis. The novel methods are demonstrated with the uniformly (2)H/(13)C/(15)N labeled 35-kDa protein diisopropylfluorophosphatase from Loligo vulgaris.     

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.     

MUSIC and aromatic residues: amino acid type-selective (1)H-(15)N correlations, III.

Amino acid type-selective experiments can help to remove ambiguities in automated assignment procedures for (15)N/(13)C-labeled proteins. Here we present five triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations for aromatic amino acids. Four of the novel experiments are based on the MUSIC coherence transfer scheme that replaces the initial INEPT transfer and is selective for CH(2). The MUSIC sequence is combined with selective excitation pulses to create experiments for Trp (W-HSQC) as well as Phe, Tyr, and His (FYH-HSQC). In addition, an experiment selective for Trp H(epsilon1)-N(epsilon1) is presented. The new experiments are recorded as two-dimensional experiments and their performance is demonstrated with the application to a protein domain of 115 amino acids.     

Initial conditions for carbon-13 MAS NMR 1D exchange involving chemically equivalent and inequivalent nuclei

A major problem in dynamic 1D ¹³C MAS NMR concerns the exchange between magnetically inequivalent, but chemically equivalent sites, whose signals are not resolved in the regular 1D spectrum. This difficulty may be overcome by properly preparing the initial nonequilibrium state of the spin system in the exchange experiments. In the present paper we discuss the advantages and limitations of several such experiments already in use and propose a new sequence, which we term SELDOM-ODESSA. Unlike the other 1D-exchange methods, this experiment yields pure absorption spectra that can more readily be analyzed quantitatively. The experiment is a hybrid comprising a SELDOM sequence, for selective excitation of one of the spinning sideband manifolds in the spectrum, followed by the ODESSA sequence, which induces alternate polarization in the excited sideband manifold. The evolution of the spectrum following this sequence provides information on both the exchange between congruent sites belonging to the same group of equivalent nuclei, and the exchange between inequivalent sites. Results are presented for a tropolone sample specifically enriched in carbon-13 at the carbonyl and hydroxyl sites. The dominant exchange mechanism in this sample involves spin diffusion. The various spin exchange processes in this sample, in the presence and absence of proton decoupling during the mixing time, are measured and discussed.     

Measurement of Relaxation Rates of N and H Backbone Protons in Proteins with Tailored Initial Conditions

Several methods are presented for the selective determination of spin–lattice and spin–spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in ¹⁵N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H^α relaxation rates can be achieved by combining this method with homonuclear Hartmann–Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in ¹⁵N-labeled human ubiquitin and to leucine L5 in ¹⁵N- and ¹³C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are ¹⁵N- and ¹³C-labeled.     

Geometry of multiple-spin systems as reflected in 13C-{1H} dipolar spectra measured at Lee-Goldburg cross-polarization

Theoretical calculation and analysis of (13)C-{(1)H} dipolar spectra of small-size spin clusters is presented. Dipolar spectra simulated using the time-independent average Hamiltonian are compared with the dipolar profiles obtained by 2D and 3D (1)H-(13)C correlation experiments employing Lee-Goldburg off-resonance cross-polarization (LG-CP). It is demonstrated that the structural parameters such as interatomic distances as well as mutual orientation of internuclear vectors can be derived from the dipolar profiles of simple spin clusters. Simplified analysis of the dipolar spectra based on isolated-like spin-pair approach can be used only if interacting spin cluster is reduced to the three-spin system in which the angle between both internuclear vectors ranges from 45 degrees to 135 degrees . For other local arrangements of spin systems the produced dipolar spectra must be analyzed with high caution. Contributions of all interacting spins to dipolar evolution of (13)C magnetization are mutually mixed and cannot be easily separated. However, simplification of the dipolar spectra is achieved by selective excitation. Enhanced selectivity of LG-CP transfer due to the initial (1)H chemical-shift-evolution period makes it possible to construct the dipolar spectra from (1)H-(13)C cross-peak intensities for every detected (1)H-(13)C spin-pair. Consequently, isolated-like spin pair evolution of the detected (1)H-(13)C coherence dominates to the resulting dipolar profile, while the influence of other interacting spins is suppressed. However, this suppression is not quite complete and analysis of the selective dipolar spectra based on isolated-like spin-pair approach cannot be used generally. Especially evolution of long-range (1)H-(13)C coherence is still significantly affected by spin states of other coupled hydrogen atoms.     

Determination of multiple ***φ***-torsion angles in proteins by selective and extensive (13)C labeling and two-dimensional solid-state NMR.

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive (13)C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective (13)C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-(13)C]glucose preferentially labels the ends of the side chains, while [2-(13)C]glycerol labels the C(alpha) of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles phi; simultaneously, using an isotropic-anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively (13)C labeled protein were performed using (15)N-(13)C 2D correlation spectroscopy. From the time dependence of the (15)N-(13)C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective (13)C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.     

Impact of selective excitation on carbon longitudinal relaxation: Towards fast solid-state NMR techniques

The effect of selective pulses on the apparent carbon longitudinal relaxation is investigated in three fully ¹³C-labeled systems, histidine as a model system and two proteins MerP and YajG. It is shown that the longitudinal relaxation of a selectively excited carbon spin is greatly enhanced, mainly because of fast spin-diffusion. This relaxation enhancement allows reducing the time necessary for polarization recovery between two experiments. This effect can be exploited either to improve the sensitivity of NMR experiments or to reduce the experimental time. Using selective carbon excitation combined with fast pulsing on fully ¹³C-labeled proteins, a sensitivity improvement of 20–45% over standard cross-polarization methods is predicted from the measured relaxation times.     

Use of the Carbonyl Chemical Shift to Relieve Degeneracies in Triple-Resonance Assignment Experiments

We illustrate an approach that uses the backbone carbonyl chemical shift to relieve resonance overlaps in triple-resonance assignment experiments conducted on protein samples. We apply this approach to two cases of simultaneous overlaps: those of ((1)H(N), (15)N) spin pairs and those of ((1)H(alpha), (13)C(alpha)) spin pairs in residues preceding prolines. For these cases we employed respectively CBCACO(N)H and H(CA)CON experiments, simple variants of the commonly used CBCA(CO)NH and HCA(CO)N experiments obtained by replacing one of the indirect dimensions with a carbonyl dimension. We present data collected on ribosomal protein S4 using these experiments, along with overlap statistics for four other polypeptides ranging in size from 76 to 263 residues. These data indicate that the CBCACO(N)H, in combination with the CBCA(CO)NH, can relieve >83% of the ((1)H(N), (15)N) and ((1)H(N), (13)C') overlaps for these proteins. The data also reveal how the H(CA)CON experiment successfully completed the assignment of triply and quadruply degenerate X-Pro spin systems in a mobile, proline-rich region of S4, even when X was a glycine. Finally, we discuss the relative sensitivities of these experiments compared to those of existing sequences, an analysis that reinforces the usefulness of these experiments in assigning extensively overlapped and/or proline-rich sequences in proteins.     

Improvement of resolution in solid state NMR spectra with J-decoupling: an analysis of lineshape contributions in uniformly C-enriched amino acids and proteins

In magic angle spinning (MAS) NMR spectra of highly and uniformly 13C,15N-enriched amino acids and proteins, homo-nuclear coupling interactions contribute significantly to the 13C linewidths, particularly for moderate applied magnetic field strengths and sample spinning frequencies. In this work, we attempted to dissect, analyze, and control the contributions of J-coupling and residual homo-nuclear dipolar coupling interactions to the linewidths of uniformly 13C,15N-enriched crystalline alanine; these studies were carried out at 9.4 T using a range of spinning frequencies from 5 to 15 kHz. The anisotropic second-order dipolar shifts and the J-splittings are comparable in their contribution to the linewidths, but behave very differently in terms of experimental protocols for line narrowing. In contrast to the J-coupling interactions, the second-order dipolar broadening cannot be refocused using selective pulses on the passively coupled spin. We carried out experiments to remove or refocus the 13C J-coupling interactions (omega1 J-decoupling) using a selective DANTE pulse in the center of the indirect evolution period. Inversion profiles and bandwidths of selective DANTE pulses acting on transverse magnetization, in the regime of moderate spinning frequencies, were characterized computationally and experimentally. A dramatic improvement in the resolution of the 2D spectrum was achieved when this decoupling protocol was employed.     

Improvement of resolution in solid state NMR spectra with J-decoupling: an analysis of lineshape contributions in uniformly 13C-enriched amino acids and proteins

In magic angle spinning (MAS) NMR spectra of highly and uniformly 13C,15N-enriched amino acids and proteins, homo-nuclear coupling interactions contribute significantly to the 13C linewidths, particularly for moderate applied magnetic field strengths and sample spinning frequencies. In this work, we attempted to dissect, analyze, and control the contributions of J-coupling and residual homo-nuclear dipolar coupling interactions to the linewidths of uniformly 13C,15N-enriched crystalline alanine; these studies were carried out at 9.4 T using a range of spinning frequencies from 5 to 15 kHz. The anisotropic second-order dipolar shifts and the J-splittings are comparable in their contribution to the linewidths, but behave very differently in terms of experimental protocols for line narrowing. In contrast to the J-coupling interactions, the second-order dipolar broadening cannot be refocused using selective pulses on the passively coupled spin. We carried out experiments to remove or refocus the 13C J-coupling interactions (omega1 J-decoupling) using a selective DANTE pulse in the center of the indirect evolution period. Inversion profiles and bandwidths of selective DANTE pulses acting on transverse magnetization, in the regime of moderate spinning frequencies, were characterized computationally and experimentally. A dramatic improvement in the resolution of the 2D spectrum was achieved when this decoupling protocol was employed.     

Determination of Multiple φ-Torsion Angles in Proteins by Selective and Extensive C Labeling and Two-Dimensional Solid-State NMR

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive ¹³C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective ¹³C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-¹³C]glucose preferentially labels the ends of the side chains, while [2-¹³C]glycerol labels the C^α of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles φ simultaneously, using an isotropic–anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively ¹³C labeled protein were performed using ¹⁵N–¹³C 2D correlation spectroscopy. From the time dependence of the ¹⁵N–¹³C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective ¹³C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.     

Measurement of relaxation rates of N(H) and H(alpha) backbone protons in proteins with tailored initial conditions.

Several methods are presented for the selective determination of spin-lattice and spin-spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in (15)N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H(alpha) relaxation rates can be achieved by combining this method with homonuclear Hartmann-Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in (15)N-labeled human ubiquitin and to leucine L5 in (15)N- and (13)C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are (15)N- and (13)C-labeled.     

Slow-down of 13C spin diffusion in organic solids by fast MAS: a CODEX NMR Study.

One- and two-dimensional 13C exchange nuclear magnetic resonance experiments under magic-angle spinning (MAS) can provide detailed information on slow segmental reorientations and chemical exchange in organic solids, including polymers and proteins. However, observations of dynamics on the time scale of seconds or longer are hampered by the competing process of dipolar 13C spin exchange (spin diffusion). In this Communication, we show that fast MAS can significantly slow down the dipolar spin exchange effect for unprotonated carbon sites. The exchange is measured quantitatively using the centerband-only detection of exchange technique, which enables the detection of exchange at any spinning speed, even in the absence of changes of isotropic chemical shifts. For chemically equivalent unprotonated 13C sites, the dipolar spin exchange rate is found to decrease slightly less than proportionally with the sample-rotation frequency, between 8 and 28 kHz. In the same range, the dipolar spin exchange rate for a glassy polymer with an inhomogeneously broadened MAS line decreases by a factor of 10. For methylene groups, no or only a minor slow-down of the exchange rate is found.     

A suite of 3D NMR methods for characterizing complex hydrocarbon structure fragments

A suite of triple resonance 3D NMR experiments is presented for the complete connectivity assignment of the hydrocarbon network in complex macromolecular and supramolecular organic structures. These new 3D NMR methods rely only on the presence of a unique set of (13)C resonances (from (13)C(X)) which are separated from the rest of the (13)C NMR spectrum. These experiments take the advantage of region selective excitation and selective inversion by composite pulses to provide correlations among H(A), (13)C(A); H(B), (13)C(B) and neighboring (13)C(X) resonances along three frequency dimensions. These methods include: gHC(A)C(X), gHC(A)C(X)-HH-TOCSY and gHC(A)C(X)-CC-TOCSY experiments. The utility of this approach is illustrated with spectra of selected structure fragments in poly(ethylene-co-n-butyl acrylate-co-carbon monoxide) (polyEBC) prepared from 1,2,3-(13)C(3)-n-butyl acrylate.     

ORSAT and modifications of SEFT and APT

Up to now, three subspectra are usually needed for the complete assignment of all signals in 13C spectrum: two DEPT spectra (phi = 90 degrees and phi = 135 degrees) and a proton decoupled spectrum. In this paper, we present a method in which a complete assignment becomes possible with merely two spectra. For this purpose, a new pulse sequence (ORSAT) has been elaborated by using off-resonance irradiation. The method described here is a further development of SEFT and APT. The second required spectrum is a DEPT (phi = 135 degrees). Signal assignment of cholesteryl acetate is demonstrated as an example. 13C routine spectroscopy can be significantly accelerated by applying this method.     

Alanine check points in HNN and HN(C)N spectra

Rapid resonance assignment is a key requirement in structural genomics research by NMR. In this context we present here two new pulse sequences, namely, HNN-A and HN(C)N-A that have been developed by simple modification of the previously described pulse sequences, HNN and HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for H(N) and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR, 20 (2001) 135-147]. These increase the number of start/check points in HNN and/or HN(C)N spectra and hence help in pacing up resonance assignment in proteins.     

用首尾减半法改善DANTE序列边瓣的抑制

用Dante脉冲序列作选择激励的缺点是它的激励边瓣太大.对于强峰存在的谱在选择激励其他峰时残留部分有时很大而引起对相干转移的误判.这里提出把Dante序列中首尾两个脉冲宽度减半的方法可以把抑制比降低至原来残留部分的1/50左右.