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1.
The source of the regioselectivity in the intramolecular nucleophilic addition of nitrile-stabilized carbanions to arene chromium tricarbonyl complexes was investigated for seven different substitution patterns on the arenes. All of the arenes are 1,4-dioxygenated and the substitution varies in the oxygen substituent and in the substituents of the arene carbons (hydrogen and alkyl). The regioselectivity is correlated with the preferred conformations of the chromium tricarbonyl group which in turn was determined by solution and solid-state 13C NMR spectroscopy, 1H NMR spectroscopy in solution as well as X-ray diffraction. In the four complexes analyzed by X-ray diffraction and the three complexes analyzed by solid-state 13C NMR spectroscopy, there was only one complex where it was found that the preferred conformation of the -Cr(CO)3 is different in solution than it is in the solid-state.  相似文献   

2.
DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein–DNA and protein–ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein–DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy. Interactions are established by DNP-enhanced 31P–13C polarization-transfer experiments followed by the recording of a 2D 13C–13C correlation experiment. The NMR spectra were obtained in less than 2 days and allowed the identification of residues of the motor protein involved in nucleotide binding.  相似文献   

3.
Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.  相似文献   

4.
The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional 13C–13C chemical shift correlation spectra is presented. With the analyses of 13C–13C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly 13C labeled protein that are consistent with the high resolution structure of the M2 (22–62) protein (Sharma et al., Science 330(6003):509–512, 2010).  相似文献   

5.
13C spin diluted protein samples can be produced using [1-13C] and [2-13C]-glucose (Glc) carbon sources in the bacterial growth medium. The 13C spin dilution results in favorable 13C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-13C]- and [2-13C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-13C]-glycerol (13C labeled Cα sites on a 12C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17–26, 2011 ). Inspired by this approach and our own recent results using [2-13C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of 13C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.  相似文献   

6.
Multivariate curve resolution (MCR) was applied to 13C cross-polarisation (CP) magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of non-depolymerised alginate powders obtained from brown seaweed plus a pure mannuronate sample isolated from Pseudomonas fluorescens for estimation of the mannuronic acid/guluronic acid ratio (M/G ratio). An excellent MCR model with a correlation coefficient of r2 = 0.99 was established between the estimated M/G ratios and the M/G ratios obtained from the traditional 1H solution state NMR method. The new method allows for successful determination of the M/G ratio independent of the calcium content (at least up to 2.4%, which was the upper limit in this study) with a root mean square error of prediction of 0.05. It is thus concluded that 13C CP-MAS NMR in combination with multivariate curve resolution is a reliable, convenient (no sample preparation is required) and relatively rapid method for M/G ratio determinations of alginates and it may serve as a good alternative to the chemical techniques traditionally used.  相似文献   

7.
Ethanol organosolv pretreatment was performed on Loblolly pine to enhance the efficiency of enzymatic hydrolysis of cellulose to glucose. Solid-state 13C NMR spectroscopy coupled with line shape analysis was used to determine the structure and crystallinity of cellulose isolated from pretreated and enzyme-hydrolyzed Loblolly pine. The results indicate reduced crystallinity of the cellulose following the organosolv pretreatment, which renders the substrate easily hydrolyzable by cellulase. The degree of crystallinity increases and the relative proportion of para-crystalline and amorphous cellulose decreases after enzymatic hydrolysis, indicating preferential hydrolysis of these regions by cellulase. The structural and compositional changes in this material resulting from the organosolv pretreatment and cellulase enzyme hydrolysis of the pretreated wood were studied with solid-state CP/MAS 13C NMR spectroscopy. NMR spectra of the solid material before and after the treatments show that hemicelluloses and lignin are degraded during the organosolv pretreatment.  相似文献   

8.
The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail’s biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13C or 1H detection, have very narrow line widths (0.40–0.60 ppm for 13C, 0.11–0.15 ppm for 1H, and 0.46–0.64 ppm for 15N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1H-detected solid-state NMR 1H/15N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1H/15N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.  相似文献   

9.
采用高分辨魔角旋转核磁共振(HRMAS ^1H NMR)技术结合主成分分析(PCA)方法研究了39例人体脑肿瘤组织的代谢组特征.39例肿瘤样本分别来自39个脑肿瘤患者,包括15例低级星形细胞瘤,13例纤维型脑膜瘤和11例过渡型脑膜瘤.核磁共振波谱分析结果表明,脑肿瘤组织的代谢组中丰要含有脂肪酸、乳酸、胆碱代谢物(如胆碱、磷酸胆碱和甘油磷酸胆碱)、氯基酸(如丙氨酸、谷氨酸、谷氮酰胺、牛磺酸)、N-乙酰天门冬氨酸(NAA)和谷胱甘肽等代谢物.通过对核磁共振谱进行主成分分析(PCA),发现低级星形细胞瘤和脑膜瘤的代谢组之间具有明显的差异,而在过渡型和纤维型两个亚类脑膜瘤之间该差别相对较小.与脑膜瘤相比,低级星形细胞瘤中甘油磷酸胆碱、磷酸胆碱、肌醇与肌酸的含量较高,而丙氨酸、谷氨酸、谷氨酰胺、谷胱甘肽和牛磺酸的含量较低.NAA的含量在低级星形细胞瘤中尽管较低但能观察到,而脑膜瘤中却未发现NAA的信号.结果衷明,HRMAS ^1H NMR和多变量统计分析相结合的组织代谢组学方法,不仅能有效区分不同类型的脑肿瘤,而且还可以为脑肿瘤提供丰富的代谢组信息,这些信息对研究肿瘤发生发展的机制具有潜在的意义.  相似文献   

10.
By applying [1-13C]- and [2-13C]-glucose labeling schemes to the folded globular protein ubiquitin, a strong reduction of spectral crowding and increase in resolution in solid-state NMR (ssNMR) spectra could be achieved. This allowed spectral resonance assignment in a straightforward manner and the collection of a wealth of long-range distance information. A high precision solid-state NMR structure of microcrystalline ubiquitin was calculated with a backbone rmsd of 1.57 to the X-ray structure and 1.32 Å to the solution NMR structure. Interestingly, we can resolve structural heterogeneity as the presence of three slightly different conformations. Structural heterogeneity is most significant for the loop region β1-β2 but also for β-strands β1, β2, β3, and β5 as well as for the loop connecting α1 and β3. This structural polymorphism observed in the solid-state NMR spectra coincides with regions that showed dynamics in solution NMR experiments on different timescales.  相似文献   

11.
It is important to understand the structural characteristics of triacylglycerol (TAG), polysaccharides and trace elements in coffee beans, so that residues can be reutilized in applications including biodiesel oils. Here, we performed 1H and 13C solid-state NMR measurements on Indonesian green beans, roasted beans, and spent coffee grounds (SCGs). In the NMR spectra, there were liquid-like TAG containing linoleic acids based on observed signals of -CH=CH-CH2-CH=CH- group in an acyl chain, which play a role in decreasing TAG’s melting point. We found TAG was still abundant in the SCGs from NMR spectra. After lipids were removed from SCGs, the intensity of the TAG signal decreased considerably, with approximately 64% of the TAG was successfully extracted. We described the chemical structure of TAG in coffee beans and demonstrated that it is possible quantify the amount of extracted TAG using solid-state NMR.  相似文献   

12.
MAX8, a designer peptide known to undergo self-assembly following changes in temperature, pH, and ionic strength, has demonstrated usefulness for tissue engineering and drug delivery. It is hypothesized that the self-assembled MAX8 nanofiber structure consists of closed β-hairpins aligned into antiparallel β-sheets. Here, we report evidence from solid-state NMR spectroscopy that supports the presence of the hypothesized β-hairpin conformation within the nanofiber structure. Specifically, our 13C-13C two-dimensional exchange data indicate spatial proximity between V3 and K17, and 13C-13C dipolar coupling measurements reveal proximity between the V3 and V18 backbone carbonyls. Moreover, isotopic dilution of labeled MAX8 nanofibers did not result in a loss of the 13C-13C dipolar couplings, showing that these couplings are primarily intramolecular. NMR spectra also indicate the existence of a minor conformation, which is discussed in terms of previously hypothesized nanofiber physical cross-linking and possible nanofiber polymorphism.  相似文献   

13.
The polypeptide corresponding to the signal sequence of the M13 coat protein and the five N-terminal residues of the mature protein was prepared by solid-phase peptide synthesis with a 15N isotopic label at the alanine-12 position. Multidimensional solution NMR spectroscopy and molecular modeling calculations indicate that this polypeptide assumes helical conformations between residues 5 and 20, in the presence of sodium dodecylsulfate micelles. This is in good agreement with circular dichroism spectroscopic measurement, which shows an α-helix content of approximately 42%. The α-helix comprises an uninterrupted hydrophobic stretch of ≤12 amino acids, which is generally believed to be too short for a stable transmembrane alignment in a biological bilayer. The monoexponential proton-deuterium exchange kinetics of this hydrophobic helical region is characterized by half-lives of 15–75 minutes (pH 4.2, 323 K). When the polypeptide is reconstituted into phospholipid bilayers, the broad anisotropy of the proton-decoupled 15N solid-state NMR spectroscopy indicates that the hydrophobic helix is immobilized close to the lipid bilayer surface at the time scale of 15N solid-state NMR spectroscopy (10−4 seconds). By contrast, short correlation times, immediate hydrogen-deuterium exchange as well as nuclear Overhauser effect crosspeak analysis suggest that the N and C termini of this polypeptide exhibit a mobile random coil structure. The implications of these structural findings for possible mechanisms of membrane insertion and translocation as well as for membrane protein structure prediction algorithms are discussed. © 1997 Wiley-Liss Inc.  相似文献   

14.
Soil microorganisms are the primary mediators of organic matter decomposition and humification processes in soil, which represent a critical C flux in the global C cycle. Little is known about how soil microbes regulate carbon cycling including the contribution of their own biomass to stable soil organic matter. A comprehensive understanding of microbial composition is a first step to unraveling microbial regulation of soil humification processes. For this purpose, we isolated 23 microbial strains representing four major groups (Gram (+) bacteria, Gram (−) bacteria, Actinobacteria, and Fungi) from a temperate and a tropical forest soil. The microbial isolates were cultured with uniformly 13C-labeled glucose as the C source such that all biochemical components synthesized from glucose were 13C labeled. This approach enabled field mesocosm experiments on tracking microbial decomposition, while facilitating solution- and solid-state NMR analysis of microbial composition. Polar and lipid extracts of labeled biomass of the four microbial groups from the two forest sites were profiled by 2D NMR methods, including high-resolution heteronuclear single quantum coherence spectroscopy and HCCH-total correlation spectroscopy. This 13C labeling approach also enabled the analysis of intact biomass by 2D solid-state 13C–13C correlation spectroscopy. Distinction between microbial groups and sites was observed in the polar and lipophilic metabolite profiles. Dominant differences could also be related to the capacity for lipid β-oxidation or adaptation to desiccation. Solid-state NMR further revealed differential synthetic capacity for glycolipids among groups. This technology coupled with 13C metabolite profiling should facilitate future functional annotation of indigenous microbial genomes.  相似文献   

15.
Shih PC  Li GC  Yang KJ  Chen W  Tzou DL 《Steroids》2011,76(6):558-563
Solid-state 1H/13C cross-polarization/magic angle spinning (CP/MAS) NMR spectroscopy has been applied to two steroid compounds: dehydroepiandrosterone (DHEA) and spironolactone (SPI), to analyze their conformations at the atomic level. In the absence of lipid, the high-resolution 13C CP/MAS NMR signals of DHEA and SPI in a powder form reveal multiple patterns, with splittings of 30-160 Hz, indicating the existence of multiple conformations. In the mimic lipid environment formed by mixing 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) in a molar ratio 3:1, the resulting DHEA and SPI spectra revealed mostly singlet patterns, suggesting that these steroids undergo a conformational change leading to a specific conformation in the lipid environment. Evidence from chemical shift isotropy and anisotropy analysis indicates that DHEA might adopt conformations subtly different from that seen in solution and in the powder form. In conclusion, we demonstrate by solid-state NMR that the structures of DHEA and SPI may adopt slightly different conformations in different chemical environments.  相似文献   

16.
Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers.  相似文献   

17.
Solid-state NMR spectroscopic techniques were used to investigate the secondary structure of the transmembrane peptide phospholamban (TM-PLB), a sarcoplasmic Ca2+ regulator. 13C cross-polarization magic angle spinning spectra of 13C carbonyl-labeled Leu39 of TM-PLB exhibited two peaks in a pure 1-palmitoyl-2-oleoyl-phosphocholine (POPC) bilayer, each due to a different structural conformation of phospholamban as characterized by the corresponding 13C chemical shift. The addition of a negatively charged phospholipid (1-palmitoyl-2-oleoylphosphatidylglycerol (POPG)) to the POPC bilayer stabilized TM-PLB to an α-helical conformation as monitored by an enhancement of the α-helical carbonyl 13C resonance in the corresponding NMR spectrum. 13C-15N REDOR solid-state NMR spectroscopic experiments revealed the distance between the 13C carbonyl carbon of Leu39 and the 15N amide nitrogen of Leu42 to be 4.2 ± 0.2Å indicating an α-helical conformation of TM-PLB with a slight deviation from an ideal 3.6 amino acid per turn helix. Finally, the quadrupolar splittings of three 2H labeled leucines (Leu28, Leu39, and Leu51) incorporated in mechanically aligned DOPE/DOPC bilayers yielded an 11° ± 5° tilt of TM-PLB with respect to the bilayer normal. In addition to elucidating valuable TM-PLB secondary structure information, the solid-state NMR spectroscopic data indicates that the type of phospholipids and the water content play a crucial role in the secondary structure and folding of TM-PLB in a phospholipid bilayer.  相似文献   

18.
Xiao  Hang  Zhang  Zhengfeng  Zhao  Yongxiang  Yang  Jun 《Journal of biomolecular NMR》2021,75(4-5):193-202

Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit 13C-13C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077–8083]. The signals of alanine, serine, or threonine residues are selected out by selective 13Cα-13Cβ double-quantum filtering (DQF). The 13Cα-13Cβ correlations of alanine residues are selectively established with efficiency up to?~?1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly 13C, 15N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.

  相似文献   

19.
Summary NMR (nuclear magnetic resonance) spectroscopy was used to identify metabolic solutes in one normal and two habituated sugarbeet cell lines (Beta vulgaris L.altissima) obtained from the same mother strain. This technique was applied to investigate the intracellular naturally occurring13C isotopes (1.1% of total natural carbon) in living sugarbeet suspension cells and perchloric cell extracts. A combination of1H,13C, double-quantum filter correlation spectroscopy, heteronuclear multiple-bond correlation, and heteronuclear multiple-quantum coherence spectra from perchloric cell extracts enabled us to identify the main compounds in the different extract solutions. This was verified by spiking the solutions with small amounts of reference compounds to exclude the influence exerted by pH on the chemical shifts of the different compounds in the1H and13C spectra. The comparison of the three sugarbeet cell lines' NMR spectra showed the presence of sucrose, glucose, and fructose in the three strains. On the other hand, it revealed a strong discrepancy between metabolic solutes. Spectra from the habituated lines showed the presence of glutamine. Some amino acids such as alanine or valine, and unidentified signals corresponding to aromatic rings were only characterized in the habituated nonorganogenic cells. On the basis of these13C NMR data we assumed that the discrepancy between the different sugarbeet cell lines could be due to an increase in the metabolic activity of the habituated cell lines in relation to their autonomous growth.Abbreviations DQF-COSY double-quantum filter correlation spectroscopy - HO habituated organogenous - HNO habituated nonorganogenous - HMBC heteronuclear multiple-bond correlation - HMQC heteronuclear multiple-quantum coherence - N normal - NMR nuclear magnetic resonance - TSP sodium tetradeutero-3-(trimethylsilyl)-propionate  相似文献   

20.
To elucidate the native-state crystal structure of beeswax from the Japanese bee, Apis cerana japonica, we determined the relationship between temperature and the 13C solid-state nuclear magnetic resonance (NMR) chemical shift of methylene carbon of beeswax, with comparison to n-alkanes and polyethylene in the orthorhombic, monoclinic, or triclinic crystal form. Variable-temperature 13C solid-state NMR observations of n-alkanes and polyethylene revealed that the chemical shifts of methylene carbon in the orthorhombic crystal form increased linearly with increasing temperature, that of the triclinic form decreased, and that of the monoclinic form was unaltered. These relations were compared with results of variable-temperature 13C solid-state NMR observation of beeswax. Results clarified that the two crystal forms comprising the beeswax in the native state are orthorhombic and monoclinic. The variable-temperature 13C solid-state NMR observations were also applied to interpret the differential scanning calorimetry (DSC) curve of beeswax. They were used to clarify the structural changes of beeswax for widely various temperatures. For beeswax secreted by the Japanese bee, the transition from the orthorhombic form to the rotator phase occurred at 36 °C, that is from the crystalline to the intermediate state at 45 °C. Moreover, the variable-temperature 13C solid-state NMR spectrum of honeybee silk in the native state was observed. Results demonstrated that the secondary structures of honeybee silk proteins in the native state comprised coexisting α-helix and β-sheet conformations and that the amount of α-helices was greater. The α-helix content of honeybee silk was compared with that of hornet silk produced by Vespa larvae.  相似文献   

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