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.     

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.     

Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins

Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H(α), C(α), C(β) and CO) for establishing sequential backbone assignment. Because most conventional 4-D triple-resonance experiments share an overlapping C(α) evolution period, combining existing 4-D experiments does not offer an optimal solution for non-redundant collection of a complete set of backbone resonances. Using alternative chemical shift evolution schemes, we propose a new pair of 4-D triple-resonance experiments--HA(CA)CO(CA)NH/HA(CA)CONH--that complement the 4-D HNCACB/HN(CO)CACB experiments to provide complete backbone resonance information. Collection of high-resolution 4-D spectra with sparse sampling and FFT-CLEAN processing enables efficient acquisition and assignment of complete backbone resonances of IDPs. Importantly, because the CLEAN procedure iteratively identifies resonance signals and removes their associating aliasing artifacts, it greatly reduces the dependence of the reconstruction quality on sampling schemes and produces high-quality spectra even with less-than-optimal sampling schemes.     

Towards an inhalative 13C breath test method

Customary 13CO2 breath tests--and also 15N urine tests--always start with an oral administration of a test substrate. The test person swallows a stable isotope labelled diagnostic agent. This technique has been used to study several pathophysiological changes in gastrointestinal organs. However, to study pathophysiological changes of the bronchial and lung epithelium, the inhalative administration of a stable isotope labelled agent appeared more suitable to us. [1-13C]Hexadecanol and [1-13C]glucose were chosen. Inhaled [1-13C]hexadecanol did not yield 13CO2 in the exhaled air, but [1-13C]glucose did. To study the practicability of the [1-13C]glucose method and the reproducibility of the results, 18 inhalation tests were performed with healthy subjects. In 6 self-tests, the optimum inhalative dose of [13C]glucose was determined to be 205 mg. Using the APS aerosol provocation system with the nebulizer 'Medic Aid' (Erich Jaeger Würzburg), a 25% aqueous solution was inhaled. Then, breath samples were collected at 15 min. intervals and analysed for 13CO2. 75-120 min after the end of inhalation a well-reproducible maximum delta13C value of 6%o over baseline (DOB) was detected for 12 healthy probands. Speculating that the pulmonary resorption of the [13C]glucose is the rate-limiting step of elimination, decompensations in the epithelium ought to be reflected in changed [1-13C]glucose resorption rates and changed 13CO2 output. Therefore, we speculate that the inhalation of suitable 13C-labelled substrates will pave the way for a new group of 13CO2 breath tests aiding investigations of specific pathophysiological changes in the pulmonary tract, such as inflammations of certain sections and decompensations of cell functions.     

A 'just-in-time' HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity

Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13Calpha-13Cbeta coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13Calpha-13Cbeta coupling while collecting 13CO shifts in real time. Sensitivity comparisons of the 3-D JIT HN(CA)CO, a CT-HMQC-based control, and a HSQC-based control with selective 13Calpha inversion pulses were performed using a 2H/13C/15N labeled sample of the 29 kDa HCA II protein at 15 degrees C. The JIT experiment shows a 42% signal enhancement over the CT-HMQC-based experiment. Compared to the HSQC-based experiment, the JIT experiment is 16% less sensitive for residues experiencing proper 13Calpha refocusing and13Calpha-13Cbeta decoupling. However, for the remaining residues, the JIT spectrum shows a 106% average sensitivity gain over the HSQC-based experiment. The high-sensitivity JIT HNCACO experiment should be particularly beneficial for studies of large proteins to provide 13CO resonance information regardless of residue type.     

Multi-band frequency encoding method for metabolic imaging with hyperpolarized [1-(13)C]pyruvate

A new method was developed for simultaneous spatial localization and spectral separation of multiple compounds based on a single echo, by designing the acquisition to place individual compounds in separate frequency encoding bands. This method was specially designed for rapid and robust metabolic imaging of hyperpolarized (13)C substrates and their metabolic products, and was investigated in phantom studies and studies in normal mice and transgenic models of prostate cancer to provide rapid metabolic imaging of hyperpolarized [1-(13)C]pyruvate and its metabolic products [1-(13)C]lactate and [1-(13)C]alanine at spatial resolutions up to 3mm in-plane. Elevated pyruvate and lactate signals in the vicinity of prostatic tissues were observed in transgenic tumor mice. The multi-band frequency encoding technique enabled rapid metabolic imaging of hyperpolarized (13)C compounds with important advantages over prior approaches, including less complicated acquisition and reconstruction methods.     

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.     

一种螺[4.5]癸烷衍生物的NMR数据分析

应用核磁共振技术（¹H NMR,¹³C NMR,DEPT, ¹H-¹H COSY, HSQC, HMBC）,确定了3,4-双(-4-甲基苯基)-1-羟基-7, 4′-二氧代-1′, 2′, 3′, 4′-四氢苯并[h]双环[3. 4]壬烷-2-螺-2′-萘-1′-酮的结构,准确归属了它的¹H, ¹³C信号,为其结构鉴定提供了重要依据.     

The set of triple-resonance sequences with a multiple quantum coherence evolution period

The new pulse sequence building block that relies on evolution of heteronuclear multiple quantum coherences is proposed. The particular chemical shifts are obtained in multiple quadrature, using linear combinations of frequencies taken from spectra measured at different quantum levels. The pulse sequences designed in this way consist of small number of RF-pulses, are as short as possible, and could be applied for determination of coupling constants. The examples presented involve 2D correlations HNCO, HNCA, HN(CO)CA, and H(N)COCA via heteronuclear zero and double coherences, as well as 2D HNCOCA technique with simultaneous evolution of triple and three distinct single quantum coherences. Applications of the new sequences are presented for 13C,15N-labeled ubiquitin.     

金属羰基化合物（CpFe（CO）2）2与金属氧化物表面作用的傅里叶变…

用漫反射红外光谱和光声红外光谱研究了金属羰基化合物（ＣｐＦｅ（ＣＯ）２）２Ｃｐ＝η＾５－Ｃ５Ｈ５与酸性，中性和碱性Ａｌ２Ｏ３及ＴｉＯ２的相互作用，结果表明，在Ａｌ２Ｏ３表面生成的洗生物种类及浓度与Ａｌ２Ｏ３的酸碱度明显相关，在酸性Ａｌ２Ｏ３表面，主要存在衍生物（ＣｐＦｅ（ＣＯ）２Ｆｅ－Ｈ－Ｆｅ（ＣＯ２Ｃｐ）＾＋及少量的ＣｐＦｅ（ＣＯ）２（－Ｏ－）；在中性Ａｌ２Ｏ３表面存在的ＣｐＦｅ（ＣＯ）２（－Ｏ     

2-(2-苯并噁唑啉酮-3-甲基)-6-芳基-咪唑[2,1-b][1,3,4]噻二唑的NMR谱研究

许多文献已报道,含有咪唑[2,1-b][1,3,4]噻唑环的衍生物具有抗癌、抗结核、抗菌、抗真菌、抗惊厥、止痛等活性. 该文合成了一个新的在医药方面具有潜在应用价值的咪唑[2,1-b][1,3,4]噻二唑衍生物,即2-(2-苯噁唑啉酮-3-甲基)-6-苯基-咪唑[2,1-b][1,3,4]噻二唑,并利用2D NMR技术对其¹H NMR 和¹³C NMR谱进行了全归属.      

The 2D [31P] spin-echo-difference constant-time [13C, 1H]-HMQC experiment for simultaneous determination of 3J(H3'P) and 3J(C4'P) in 13C-labeled nucleic acids and their protein complexes.

A two-dimensional [31P] spin-echo-difference constant-time [13C, 1H]-HMQC experiment (2D [31P]-sedct-[13C, 1H]-HMQC) is introduced for measurements of 3J(C4'P) and 3J(H3'P) scalar couplings in large 13C-labeled nucleic acids and in DNA-protein complexes. This experiment makes use of the fact that 1H-13C multiple-quantum coherences in macromolecules relax more slowly than the corresponding 13C single-quantum coherences. 3J(C4'P) and 3J(H3'P) are related via Karplus-type functions with the phosphodiester torsion angles beta and epsilon, respectively, and their experimental assessment therefore contributes to further improved quality of NMR solution structures. Data are presented for a uniformly 13C, 15N-labeled 14-base-pair DNA duplex, both free in solution and in a 17-kDa protein-DNA complex.     

4-[(E)-2-(3, 4-二甲氧基苯基)乙烯基]苯氧基乙酸乙酯的合成及其NMR研究

以对硝基甲苯、3, 4-二甲氧基苯甲醛为起始原料,经过缩合,还原,重氮化水解,亲核取代反应,最终合成了新的化合物4-[(E)-2-(3, 4-二甲氧基苯基)乙烯基]苯氧基乙酸乙酯,用¹H 和¹³C NMR及多种二维核磁共振谱确定了该化合物的结构,完成了¹H 和¹³C NMR的归属,给出了分子中各氢,碳原子的准确化学位移.     

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.     

Development of high resolution 3D hyperpolarized carbon-13 MR molecular imaging techniques

The goal of this project was to develop and apply techniques for T₂ mapping and 3D high resolution (1.5 mm isotropic; 0.003 cm³) ¹³C imaging of hyperpolarized (HP) probes [1-¹³C]lactate, [1-¹³C]pyruvate, [2-¹³C]pyruvate, and [¹³C,¹⁵N₂]urea in vivo. A specialized 2D bSSFP sequence was implemented on a clinical 3T scanner and used to obtain the first high resolution T₂ maps of these different hyperpolarized compounds in both rats and tumor-bearing mice. These maps were first used to optimize timings for highest SNR for single time-point 3D bSSFP acquisitions with a 1.5 mm isotropic spatial resolution of normal rats. This 3D acquisition approach was extended to serial dynamic imaging with 2-fold compressed sensing acceleration without changing spatial resolution. The T₂ mapping experiments yielded measurements of T₂ values of > 1 s for all compounds within rat kidneys/vasculature and TRAMP tumors, except for [2-¹³C]pyruvate which was ~ 730 ms and ~ 320 ms, respectively. The high resolution 3D imaging enabled visualization the biodistribution of [1-¹³C]lactate, [1-¹³C]pyruvate, and [2-¹³C]pyruvate within different kidney compartments as well as in the vasculature. While the mouse anatomy is smaller, the resolution was also sufficient to image the distribution of all compounds within kidney, vasculature, and tumor. The development of the specialized 3D sequence with compressed sensing provided improved structural and functional assessments at a high (0.003 cm³) spatial and 2 s temporal resolution in vivo utilizing HP ¹³C substrates by exploiting their long T₂ values. This 1.5 mm isotropic resolution is comparable to ¹H imaging and application of this approach could be extended to future studies of uptake, metabolism, and perfusion in cancer and other disease models and may ultimately be of value for clinical imaging.     

Comparison between the oral and intravenous L-[1-13C]phenylalanine breath test for the assessment of liver function

To simplify the L-[1-13C]phenylalanine breath test which is used to assess liver function the tracer is usually given orally, and CO2 production rate is estimated. In 12 healthy volunteers and 10 liver cirrhotics we compared the oral approach with i.v. tracer administration combined with measurement of individual CO2 production rate. The 13CO2/12CO2 enrichment was assessed by isotope-ratio mass spectrometry. After i.v. [1-13C]phenylalanine application exhaled 13C recovery per minute peaked within 10 minutes (controls: 0.17 +/- 0.06%; cirrhotics: 0.05 +/- 0.02%, p < 0.01). The oral approach yielded comparable separation between 30-60 minutes, with average peak values being 0.18 +/- 0.03% and 0.06 +/- 0.03% (p < 0.01), respectively. Variable gastrointestinal resorption kinetics after oral application probably causes this difference.     

Sensitivity-enhanced double-TROSY experiment for simultaneous measurement of one-bond 15N-1H, 15N-13C' and two-bond 1H-13C' couplings

A recently published experiment for the measurement of 1JHN, 1JNC', and 2JHC' coupling constants [J. Am. Chem. Soc. 125 (2003) 11504] was modified to yield a double-TROSY experiment which selects 1 of the 16 multiplet components from a 15N-HSQC spectrum recorded of a uniformly 15N/13C-labelled protein. Subspectra containing any 1 of the 16 multiplet components can be generated allowing accurate coupling constant measurements. The experiment is sensitivity enhanced, turning all magnetization components precessing during the evolution time into observable magnetization during the detection time. The experiment is discussed with regard to the previously published alpha/beta-filtered HN(alpha/beta-NC'-J) experiment [J. Magn. Reson. 140 (1999), 32] which measures the same coupling constants.     

1H and 13C NMR Spectra of Alditolyl Derivatives of 3-Hydrazino-5-Methyl[1,2,4]triazino[5,6-b]indole and Their Cyclized Products.

The ¹H and ¹³C NMR spectra of sugar (5-methyl [1, 2, 4]-triazino [5, 6-b] indol-3-yl) hydrazones (1), per-0-acetyl aldehydo sugar 1-acetyl-1-(5-methyl [1, 2, 4] triazino [5, 6-b]-indol-3-yl) hydrazones (2), l- (penta-0-acetyl-pentitol-1-yl)-10-methyl [l, 2, 4] triazolo [3′, 4′:3, 4] [l, 2, 4] triazino [5, 6-b]-indoles (3) have been investigated. The 2 D NMR (H, C COSY) spectrum of 2a has been studied.     

Compartmental approach for evaluation of plasma kinetics and (13)co(2)-exhalation after oral loading with L-[1-(13)c]leucine

Abstract A seven compartment model was applied for evaluation of oral L-[1-(13)C]leucine loading tests (38 μmol/kg body wt.) in healthy volunteers. The model comprises transport and absorption in stomach and gut into a central L-leucine-compartment which is connected to a protein compartment and to the compartment of the corresponding 2-oxo acid. CO(2) release from the latter occurs in a fast and a slow compartment into the central CO(2) compartment for exhalation. Using the fmins routine of MATLAB for parameter estimation, a good agreement was obtained between calculated and actually measured kinetics of (13)C-labelled metabolites and a mean in vivo L-leucine oxidation of 0.365 ± 0.071 μmol/kg per min (n = 5) was computed. Plausibility of the model was checked by predicting in vivo leucine oxidation rates from primed continuous infusion tests (priming: L-[1-(13)C]leucine, 5 μmol/kg; NaH(13)CO(2), 1.2 μmol/kg; infusion: L-[1-(13)C]leucine, 5 μmol/kg per h). In 5 tested volunteers, the experimental L-leucine oxidation rate amounted to 0.358 ± 0.105 μmol/kg per min versus predicted 0.324±0.099 μmol/kg per min. Possible causes for some observed intraindividual variations are discussed.     

Determination of backbone angle psi in proteins using a TROSY-based alpha/beta-HN(CO)CA-J experiment

Transverse relaxation-optimized NMR experiment (TROSY) for the measurement of three-bond scalar coupling constant between (1)H(alpha)(i-1) and (15)N(i) defining the dihedral angle psi is described. The triple-spin-state-selective experiment allows measurement of (3)J(H(alpha)N) from (13)C(alpha), (15)N, and (1)H(N) correlation spectra H(2)O with minimum resonance overlap. Transverse relaxation of (13)C(alpha) spin is minimized by using spin-state-selective filtering and by acquiring a signal longer in (15)N-dimension in a manner of semi-constant-time TROSY evolution. The (3)J(H(alpha))(N) values obtained with the proposed alpha/beta-HN(CO)CA-J TROSY scheme are in good agreement with the values measured earlier from ubiquitin in D(2)O using the HCACO[N] experiment.