Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins. 1990

Four new and complementary three-dimensional triple-resonance experiments are described for obtaining complete backbone ¹H, ¹³C, and ¹⁵N resonance assignments of proteins uniformly enriched with ¹³C and ¹⁵N. The new methods all rely on ¹H detection and use multiple magnetization transfers through well-resolved one-bond J couplings. Therefore, the 3D experiments are sensitive and permit relatively rapid recording of 3D spectra (l–2 days) for protein concentrations on the order of 1 mM. One experiment (HNCO) correlates the amide ¹H and ¹⁵N shifts with the ¹³C shift of the carbonyl resonance of the preceding amino acid. A second experiment (HNCA) correlates the intraresidue amide ¹H and ¹⁵N shifts with the Cα chemical shift. This experiment often also provides a weak correlation between the amide NH and ¹⁵N resonances of one amino acid and the Ca resonance of the preceding amino acid. A third experiment (HCACO) correlates the Hα and Cα shifts with the intraresidue carbonyl shift. Finally, a 3D relay experiment, HCA(CO)N, correlates Ha and Cal resonances of one residue with the ¹⁵N frequency of the succeeding residue. The principles of these experiments are described in terms of the operator formalism. To optimize spectral resolution, special attention is paid to removal of undesired J splittings in the 3D spectra. Technical details regarding the implementation of these triple-resonance experiments on a commercial spectrometer are also provided. The experiments are demonstrated for the protein calmodulin (16.7 kDa).     

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.     

Asymmetric MRI magnet design using a hybrid numerical method

Two-dimensional 1H/13C polarization inversion spin exchange at the magic angle experiments were applied to single crystal samples of amino acids to demonstrate their potential utility on oriented samples of peptides and proteins. High resolution is achieved and structural information obtained on backbone and side chain sites from these spectra. A triple-resonance experiment that correlates the 1H-13Calpha dipolar coupling frequency with the chemical shift frequencies of the alpha-carbon, as well as the directly bonded amide 15N site, is also demonstrated. In this experiment the large 1H-13Calpha heteronuclear dipolar interaction provides an independent frequency dimension that significantly improves the resolution among overlapping 13C resonances of oriented polypeptides, while simultaneously providing measurements of the 13Calpha chemical shift, 1H-13C dipolar coupling, and 15N chemical shift frequencies and angular restraints for backbone structure determination.     

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.     

Novel 2D triple-resonance NMR experiments for sequential resonance assignments of proteins

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the alpha- and beta-carbon and alpha-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H(N), N, C(alpha), C(beta), and H(alpha) nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D (15)N-(1)H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.     

1H,13C and15N resonance assignment for barnase

The nearly complete assignment of¹H,¹³C and¹⁵N resonances for bacterial ribonuclease barnase produced byBacillus amyloliquefaciens was obtained by standard methods of heteronuclear triple-resonance nuclear magnetic resonance spectroscopy. Analysis of the secondary chemical shifts of the backbone¹H^α,¹³C^α and¹³CO nuclei reveal their strong correlation with the protein secondary structure.     

The DQ-HN[CACB] and DQ-HN(CO)[CACB] sequences with evolution of double quantum Calpha-Cbeta coherences

The new variant of known HNCACB and HN(CO)CACB techniques is proposed that employs excitation and evolution of double quantum Calpha-Cbeta coherences. The most important features of the new method are: increased signal dispersion, lack of splittings due to 1J(Calpha-Cbeta) spin-spin couplings, and absence of accidental cancellations of positive and negative signals. The acquisition of both DQ-HN[CACB] and DQ-HN(CO)[CACB] techniques enables sequential assignment of protein backbone, using only Calpha-Cbeta DQ-frequencies. The determination of all Calpha and Cbeta chemical shifts requires, however, a comparison with HN(CO)CA or HNCA spectra. Examples of applications of the DQ-HN[CACB] and DQ-HN(CO)[CACB] experiments are presented, employing the 2D Reduced Dimensionality approach for 13C, 15N-labeled ubiquitin, and the 3D acquisition for 13C, 15N-double labeled Ca2+ -binding bovine S100A1 protein in the apo state (21 kDa) with overall correlation time of 8.1 ns.     

Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction

Non-uniform sampling is shown to provide significant time savings in the acquisition of a suite of three-dimensional NMR experiments utilized for obtaining backbone assignments of H, N, C', CA, and CB nuclei in proteins : HNCO, HN(CA)CO, HNCA, HN(CO)CA, HNCACB, and HN(CO)CACB. Non-uniform sampling means that data were collected for only a subset of all incremented evolution periods, according to a user-specified sampling schedule. When the suite of six 3D experiments was acquired in a uniform fashion for an 11 kDa cytoplasmic domain of a membrane protein at 1.5 mM concentration, a total of 146 h was consumed. With non-uniform sampling, the same experiments were acquired in 32 h and, through subsequent maximum entropy reconstruction, yielded spectra of similar quality to those obtained by conventional Fourier transform of the uniformly acquired data. The experimental time saved with this methodology can significantly accelerate protein structure determination by NMR, particularly when combined with the use of automated assignment software, and enable the study of samples with poor stability at room temperature. Since it is also possible to use the time savings to acquire a greater numbers of scans to increase sensitivity while maintaining high resolution, this methodology will help extend the size limit of proteins accessible to NMR studies, and open the way to studies of samples that suffer from solubility problems.     

Incorporating H chemical shift determination into C-direct detected spectroscopy of intrinsically disordered proteins in solution

Exclusively heteronuclear ¹³C-detected NMR spectroscopy of proteins in solution has seen resurgence in the past several years. For disordered or unfolded proteins, which tend to have poor ¹H-amide chemical shift dispersion, these experiments offer enhanced resolution and the possibility of complete heteronuclear resonance assignment at the cost of leaving the ¹H resonances unassigned. Here we report two novel ¹³C-detected NMR experiments which incorporate a ¹H chemical shift evolution period followed by ¹³C-TOCSY mixing for aliphatic ¹H resonance assignment without reliance on ¹H detection.     

Three-dimensional 13C shift/1H-15N coupling/15N shift solid-state NMR correlation spectroscopy.

Triple-resonance experiments capable of correlating directly bonded and proximate carbon and nitrogen backbone sites of uniformly 13C- and 15N-labeled peptides in stationary oriented samples are described. The pulse sequences integrate cross-polarization from 1H to 13C and from 13C to 15N with flip-flop (phase and frequency switched) Lee-Goldburg irradiation for both 13C homonuclear decoupling and 1H-15N spin exchange at the magic angle. Because heteronuclear decoupling is applied throughout, the three-dimensional pulse sequence yields 13C shift/1H-15N coupling/15N shift correlation spectra with single-line resonances in all three frequency dimensions. Not only do the three-dimensional spectra correlate 13C and 15N resonances, they are well resolved due to the three independent frequency dimensions, and they can provide up to four orientationally dependent frequencies as input for structure determination. These experiments have the potential to make sequential backbone resonance assignments in uniformly 13C- and 15N-labeled proteins.     

Triple resonance solid state NMR experiments with reduced dimensionality evolution periods

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CO N CA experiment establishes the correlation of (13)C(i-1) to (13)C alpha(i) and (15)N(i) by simultaneously encoding the (13)CO(i-1) and (15)N(i) chemical shifts. The CA N COCA experiment establishes the correlation (13)Ca(i) and (15)CO(i) to (13)C alpha(i-1) and (15)N(i-1) within a single experiment by simultaneous encoding of the (13)C alpha(i) and (15)N(i) chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.     

Improved Resolution from Double Constant-Time Evolution of 3D and 4D Triple-Resonance Experiments

Triple-resonance NMR experiments are nearly essential for performing backbone assignments of proteins larger than 15 kDa. Our work extends the double constant-time (2CT) evolution scheme to triple-resonance 3D and 4D experiments. The modifications needed to accomplish 2CT evolution in triple resonance experiments are straight forward, are completely general, and consequently, will yield increased resolution for all out-and-back experiments. We expect that the increased resolution of experiments presented here will be useful in the study of larger proteins (>30 kDa) and in the study of highly helical proteins where¹HN,¹⁵N, and¹³C dimensions are poorly dispersed.     

Sensitivity-enhanced MQ-HCN-CCH-TOCSY and MQ-HCN-CCH-COSY pulse schemes for (13)C/(15)N labeled RNA oligonucleotides

Sensitivity enhanced multiple-quantum 3D HCN-CCH-TOCSY and HCN-CCH-COSY experiments are presented for the ribose resonance assignment of (13)C/(15)N-labeled RNA sample. The experiments make use of the chemical shift dispersion of N1/N9 of pyrimidine/purine to distinguish the ribose spin systems. They provide a complementary approach for the assignment of ribose resonance to the currently used HCCH-COSY and HCCH-TOCSY type experiments in which either (13)C or (1)H is utilized to separate the different ribose spin systems. The pulse schemes have been demonstrated on a 23-mer (13)C/(15)N-labeled RNA aptamer complexed with neomycin and tested on a 32-mer RNA complexed with a 23-residue peptide.     

A set of 4D NMR experiments of enhanced resolution for easy resonance assignment in proteins

This paper presents examples of techniques based on the principle of random sampling that allows acquisition of NMR spectra featuring extraordinary resolution. This is due to increased dimensionality and maximum evolution time reached. The acquired spectra of CsPin protein and maltose binding protein were analyzed statistically with the aim to evaluate each technique. The results presented include exemplary spectral cross-sections. The spectral data provided by the proposed techniques allow easy assignment of backbone and side-chain resonances.     

Evaluation and optimization of coherence transfer in high molecular weight systems

For very large proteins in the highest magnetic fields, the large chemical shift anisotropy (CSA) of carbonyl carbon deteriorates coherence transfer efficiency in experiments designed for unambiguous sequential backbone assignment. In this communication, coherence throughput of several TROSY experiments is evaluated. Two new experiments, MP-HNCA and HN(CO)CANH, are also introduced as attractive alternatives for sequential assignment purposes of large proteins with correlation time over 50 ns. Their theoretical coherence transfer efficiencies for the interresidual (13)C(alpha) correlations are significantly better than in recently introduced MP-CT-HNCA and sequential HNCA experiments. The improvement with the new experiments is observed already on 60.8 kDa homodimer of protein Cel6A at 800 (1)H MHz.     

Two- and Three-Dimensional H/C PISEMA Experiments and Their Application to Backbone and Side Chain Sites of Amino Acids and Peptides

Two-dimensional ¹H/¹³C polarization inversion spin exchange at the magic angle experiments were applied to single crystal samples of amino acids to demonstrate their potential utility on oriented samples of peptides and proteins. High resolution is achieved and structural information obtained on backbone and side chain sites from these spectra. A triple-resonance experiment that correlates the ¹H–¹³C_α dipolar coupling frequency with the chemical shift frequencies of the α-carbon, as well as the directly bonded amide ¹⁵N site, is also demonstrated. In this experiment the large ¹H–¹³C_α heteronuclear dipolar interaction provides an independent frequency dimension that significantly improves the resolution among overlapping ¹³C resonances of oriented polypeptides, while simultaneously providing measurements of the ¹³C_α chemical shift, ¹H–¹³C dipolar coupling, and ¹⁵N chemical shift frequencies and angular restraints for backbone structure determination.     

Resonance assignment of<Superscript>13</Superscript>C−<Superscript>15</Superscript>N-labeled snake neurotoxin II from<Emphasis Type="Italic">Naja oxiana</Emphasis>

Neurotoxin II fromNaja oxiana venom is a short-chain snake curaremimetic neurotoxin containing four disulfide bonds. We obtained¹³C-¹⁵N-labeled neurotoxin II to study its internal dynamics and surface properties with atomic resolution. The recombinant protein has the native spatial structure and is biologically active. The nearly complete assignment of¹H,¹³C and¹⁵N resonances for neurotoxin II was obtained by heteronuclear triple-resonance nuclear magnetic resonance spectroscopy. Analysis of the secondary chemical shifts of the¹H^α,¹³C^α,¹³C^β and¹³CO nuclei reveal their strong correlation with the protein secondary structure.     

DEPT spectral editing in HCCONH-type experiments. Application to fast protein backbone and side chain assignment

2D DEPT-H(alpha,beta)C(alpha,beta)(CO)NH and 2D CT-DEPT-HC(CO)NH-TOCSY experiments are presented which allow fast resonance assignment of aliphatic protein side chains. In these 2D reduced-dimensionality experiments, two or three nuclei are frequency labeled in the indirect dimension. DEPT spectral editing reduces the number of correlation peaks detected in each 2D spectrum, and helps in amino-acid-type determination during sequential backbone resonance assignment. Applications are shown for a small 68-residue, and a highly deuterated 167-residue protein. The new experiments complement the set of 2D HNX correlation experiments, previously proposed for fast protein resonance assignment [J. Biomol. NMR, 27 (2003) 57].     

Assignment strategy for proteins with known structure

In protein NMR the assignment of nuclear spin resonances is a prerequisite for all subsequent applications, such as studies of ligand binding, protein-DNA interactions, and dynamics. Resonance assignment is a time consuming step even when the 3D x-ray structure of the protein is available. A new strategy is presented to solve the "inverse" assignment problem, which is the determination of the NMR resonance assignment from a known 3D protein structure. The protocol employs NMR data in the form of residual dipolar couplings and chemical shifts, while it does not require any sequential NMR connectivity information. The assignment problem is mathematically formulated in terms of a weighted matching problem that can be computationally efficiently solved by a combinatorial optimization algorithm. The protocol is applied to ubiquitin using two or three residual dipolar couplings per amino acid measured in Pfl phage medium together with chemical shift information. The algorithm yields for more than 90% of the protein backbone resonances the correct assignment.