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Abstract: Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions. [Copyright &y& Elsevier]

Methods for measuring longitudinal relaxation times of protons in heavily overlapped [sup 1]H NMR spectra are introduced and exemplified using a solution of cholesteryl acetate. The methods are based on 1-dimensional and 2-dimensional maximum quantum NMR spectroscopy (MAXY), which makes possible the selective detection of CH, CH[sub 2] and CH[sub 3] [sup 1]H NMR resonances. A modification of the BIRD pulse sequence to achieve selective inversion of protons bonded to either [sup 12]C or [sup 13]C is given. The approach should find application in studies of molecular dynamics where isotopic enrichment is not possible and the level of available sample dictates the use of [sup 1]H NMR spectroscopy. [ABSTRACT FROM AUTHOR]

NMR spectroscopy can be used to measure molecular self-diffusion coefficients using a modified spin-echo pulse sequence known as the longitudinal eddy current delay (LED) method which incorporates pulsed magnetic field gradients. The effect of such gradients on multiple quantum coherences is investigated and shown to be of benefit for the measurement of diffusion coefficients using modest gradient strengths. The multiple quantum coherences involved in the spin operator 8Ix Iy Iy Sy of a weakly coupled SI spin system (13CH at natural abundance, in alanine in this case) were studied. The multiple quantum coherences included the quadruple-quantum (QQ) order of (3 I + S ), double-quantum (DQ) order of (3 I - S ) and (3 I + S ), and zero-quantum (ZQ) order of ( I - S ) with effective magnetogyric ratios of (3gammaH + gammaC), (3gammaH-gammaC), (gammaH + gammaC) and (gammaH-gammaC) respectively. The results show that the use of higher level quantum coherences for diffusion coefficient measurement can have the practical effect of significantly enhancing the gradient strength and this is important for slowly diffusing species. [ABSTRACT FROM AUTHOR]

Demonstrate the use of two-dimensional diffusion-edited total-correlation nuclear magnetic resonance spectroscopy in measuring diffusion coefficients of molecules in biofluids. Diffusion coefficients for the small endogenous species; Interpretation of the derived diffusion coefficients; Measurement of diffusion coefficient of various lipoprotein resonances.

Discusses an approach to the characterization of biomolecules in whole biological fluids based on simplification of 1H nuclear magnetic resonance (NMR) spectra. Differences in molecular diffusion coefficients alone and combinations of relaxation and diffusion parameters; Incorporation of both spectral editing features and solvent water resonance elimination.

Metabolism is a fundamental process that underlies human health and diseases. Nuclear magnetic resonance (NMR) techniques offer a powerful approach to identify metabolic processes and track the flux of metabolites at the molecular level in living systems. An in vitro study through in-cell NMR tracks metabolites in real time and investigates protein structures and dynamics in a state close to their most natural environment. This technique characterizes metabolites and proteins involved in metabolic pathways in prokaryotic and eukaryotic cells. In vivo magnetic resonance spectroscopy (MRS) enables whole-organism metabolic monitoring by visualizing the spatial distribution of metabolites and targeted proteins. One limitation of these NMR techniques is the sensitivity, for which a possible improved approach is through isotopic enrichment or hyperpolarization methods, including dynamic nuclear polarization (DNP) and parahydrogen-induced polarization (PHIP). DNP involves the transfer of high polarization from electronic spins of radicals to surrounding nuclear spins for signal enhancements, allowing the detection of low-abundance metabolites and real-time monitoring of metabolic activities. PHIP enables the transfer of nuclear spin polarization from parahydrogen to other nuclei for signal enhancements, particularly in proton NMR, and has been applied in studies of enzymatic reactions and cell signaling. This review provides an overview of in-cell NMR, in vivo MRS, and hyperpolarization techniques, highlighting their applications in metabolic studies and discussing challenges and future perspectives. [ABSTRACT FROM AUTHOR]

ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single‐domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP‐dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply. [ABSTRACT FROM AUTHOR]

ATP (adenosine triphosphate) is a vital energy source for living organisms, and its biosynthesis and precise concentration regulation often depend on macromolecular machinery composed of protein complexes or complicated multidomain proteins. We have identified a single‐domain protein HK853CA derived from bacterial histidine kinases (HK) that can catalyze ATP synthesis efficiently. Here, we explored the reaction mechanism and multiple factors that influence this catalysis through a combination of experimental techniques and molecular simulations. Moreover, we optimized its enzymatic activity and applied it as an ATP replenishment machinery to other ATP‐dependent systems. Our results broaden the understanding of ATP biosynthesis and show that the single CA domain can be applied as a new biomolecular catalyst used for ATP supply. [ABSTRACT FROM AUTHOR]

The aggregation of amyloidogenic proteins is often related to the occurrence of neurodegenerative diseases, including fused in sarcoma protein (FUS) in frontotemporal lobar degeneration and amyotrophic lateral sclerosis diseases. Recently, the SERF protein family has been reported to have a significant regulatory effect on amyloid formation, but it is still unclear about the detailed mechanisms of SERF acting on different amyloidogenic proteins. Herein, nuclear magnetic resonance (NMR) spectroscopy and fluorescence spectroscopy were used to explore interactions of ScSERF with three amyloidogenic proteins FUS‐LC, FUS‐Core, and α‐Synuclein. NMR chemical shift perturbations reveal them sharing similar interaction sites on the N‐terminal region of ScSERF. However, the amyloid formation of α‐Synuclein protein is accelerated by ScSERF, while ScSERF inhibits fibrosis of FUS‐Core and FUS‐LC proteins. Both the primary nucleation and the total amount of fibrils produced are detained. Our results suggest a diverse role of ScSERF in regulating the fibril growth of amyloidogenic proteins. [ABSTRACT FROM AUTHOR]

In‐cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high‐sensitivity tag (wPSP‐6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6–40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 μM, which would not have been achievable with 15N or 3‐fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive 19F NMR tag may significantly expand the scope of protein NMR in human cells. [ABSTRACT FROM AUTHOR]

In‐cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high‐sensitivity tag (wPSP‐6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6–40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 μM, which would not have been achievable with 15N or 3‐fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive 19F NMR tag may significantly expand the scope of protein NMR in human cells. [ABSTRACT FROM AUTHOR]

The Arabidopsis WRKY11 (AtWRKY11) protein is an important transcription factor involved in plant response to biotic and abiotic stresses. Its DNA-binding domain specifically binds to gene promoter regions harboring the W-box consensus motif. Herein we report the high-resolution structure of the AtWRKY11 DNA-binding domain (DBD) determined by solution NMR spectroscopy. The results show that AtWRKY11-DBD adopts an all-β fold comprising five β-strands packed in an antiparallel topology, stabilized by a zinc-finger motif. Structural comparison reveals that the long β 1 -β 2 loop shows the highest structural variation from other available WRKY domain structures. Moreover, this loop was further found to contribute to the binding between AtWRKY11-DBD and W-box DNA. Our current study provides atomic-level structural basis for further understanding the structure-function relationship of plant WRKY proteins. • This is the first structure reported for the IId subgroup of the WRKY superfamily. • The β1-β2 loop region of AtWRKY11-DBD shows high variation among other WRKY proteins. • The DNA-binding site on AtWRKY11 involves not only the consensus WRKY motif, but also the aforementioned β1-β2 loop region. • Our model of the AtWRKY11-DNA complex suggests the possible roles of the β1-β2 loop in binding DNA. [ABSTRACT FROM AUTHOR]

Nuclear magnetic resonance (NMR) has been used in a variety of fields due to its powerful analytical capability. To facilitate biochemical NMR (bioNMR) analysis for samples with a limited mass, a number of integrated systems have been developed by coupling microfluidics and NMR. However, there are few review papers that summarize the recent advances in the development of microfluidics-based NMR (μNMR) systems. Herein, we review the advancements in μNMR systems built on high-field commercial instruments and low-field compact platforms. Specifically, μNMR platforms with three types of typical microcoils settled in the high-field NMR instruments will be discussed, followed by summarizing compact NMR systems and their applications in biomedical point-of-care testing. Finally, a conclusion and future prospects in the field of μNMR were given. [ABSTRACT FROM AUTHOR]

SHIP2 is a multi-domain inositol 5-phosphatase binding to a variety of phosphotyrosine (pY)-containing proteins through its SH2 domain, so as to regulate various cell signaling pathways by modulating the phosphatidylinositol level in the plasma membrane. Unfavorably, Helicobacter pylori can hijack SHIP2 through the CagA protein to induce gastric cell carcinogenesis. To date, the interaction between SHIP2 and CagA was not analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Tyr-phosphorylated peptides from four EPIYA motifs (A/B/C/D) in CagA was studied using NMR spectroscopy. The results showed that EPIYA-C and -D bind to a similar interface of SHIP2-SH2, including a pY-binding pocket and a hydrophobic pocket, to achieve high affinity, while EPIYA-A and -B bind to a smaller interface of SHIP2-SH2 with weak affinity. By summarizing the interface and affinity of SHIP2-SH2 for CagA EPIYA-A/B/C/D, c-MET and FcgR2B ITIM, it was proposed that, potentially, SHIP2-SH2 has a selective preference for L > I > V for the aliphatic residues at the pY+3 position in its ligand. This study reveals the rule of the ligand sequence bound by SHIP2-SH2 and the mechanism by which CagA protein hijacks SHIP2, which will help design a peptide inhibitor against SHIP2-SH2. [ABSTRACT FROM AUTHOR]

α-Synuclein (α-syn) is the main protein component of Lewy bodies, the major pathological hallmarks of Parkinson's disease (PD). C-terminally truncated α-syn is found in the brain of PD patients, reduces cell viability and tends to form fibrils. Nevertheless, little is known about the mechanisms underlying the role of C-terminal truncation on the cytotoxicity and aggregation of α-syn. Here, we use nuclear magnetic resonance spectroscopy to show that the truncation alters α-syn conformation, resulting in an attractive interaction of the N-terminus with membranes and molecular chaperone, protein disulfide isomerase (PDI). The truncated protein is more toxic to mitochondria than full-length protein and diminishes the effect of PDI on α-syn fibrillation. Our findings reveal a modulatory role for the C-terminus in the cytotoxicity and aggregation of α-syn by interfering with the N-terminus binding to membranes and chaperone, and provide a molecular basis for the pathological role of C-terminal truncation in PD pathogenesis. C-terminal truncation of a-syn results in a more extended and exposed conformation, providing further insight into the pathological role of this truncation event in the progression of Parkinson's disease. [ABSTRACT FROM AUTHOR]

SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) plays an essential role in regulating phosphatidylinositol level in human cell, and is recruited to many phosphotyrosine (pY)-dependent signal transduction pathways by the SH2 domain. In immunity signaling, immunoreceptor FcγRIIB binds to SHIP2-SH2 via its Y292-phosphorylated immunoreceptor tyrosine-based inhibitory motif (ITIM) and transmits inhibitory signal, which regulates B cell and neuronal cell activity and is associated with immune diseases and Alzheimer's disease. To date, the interaction between SHIP2 and FcγRIIB has not been analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Y292-phosphorylated FcγRIIB-ITIM was analyzed using NMR spectroscopy. The results demonstrated that SHIP2-SH2 mainly utilizes two regions including a pY-binding pocket and a specificity pocket formed by βD, βE, and EF-loop, to bind with FcγRIIB-ITIM in high affinity. In addition to the two regions, the BG-loop of SHIP2-SH2 functions as an auxiliary interface enhancing affinity. By comparing the binding of SHIP2-SH2 with ligands from FcγRIIB and c-MET, a hepatocyte growth factor receptor associated with tumorigenesis, significant differences in interface and affinity were found, suggesting that SHIP2-SH2 applies diverse patterns for binding to different ligand proteins. Moreover, S49, S51, and R70 of SHIP2 were identified to mediate the binding of both FcγRIIB and c-MET, while R28 and Q107 were found to only participate in the binding of c-MET and FcγRIIB respectively. Taken together, this study reveals the diverse mechanisms of SHIP2-SH2 for recognizing different ligands, and provides important clues for selectively manipulating various signaling pathways and specific drug design. [ABSTRACT FROM AUTHOR]

The Ca2+-mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by 19F NMR spectroscopy of the transition of the Ca2+-free and -bound forms in Xenopus laevis oocytes at different Ca2+ levels. We find that the Ca2+-bound CaM population increased greatly upon binding the target protein myosin light-chain kinase (MLCK) at the same Ca2+ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long-range structural constraints in cells. Our study shows that 19F NMR spectroscopy can be used to obtain long-range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants. [ABSTRACT FROM AUTHOR]

To eliminate the effects of complex background signals and to enhance the accuracy of the diffusion coefficient measurement, derivative NMR spectroscopy with negligible loss of the spectral quality is introduced based on the customized Savitzky-Golay method and used to construct diffusion-ordered NMR spectroscopy (DOSY). The criterion of the method was established by simulations. The application of this method on mouse urine and serum showed that the accuracy and precision of diffusion coefficient measurements in a complex background were improved to enhance the identification of molecules. [ABSTRACT FROM AUTHOR]

A protein gel electrophoresis procedure using 0.05% w/v sarkosyl, is reported. The method called 05SAR-PAGE can be used to identify the native masses, dimeric states and modification states of proteins, and also be suitable for pursuing native electroblotting and immunodetection. It has been demonstrated by NMR spectroscopy that 0.05% w/v SAR is much milder than SDS, so it has subtle effects on the native structure of proteins. Therefore, the non-covalent dimerization of PhoB N and PhoR cp can be identified by 05SAR-PAGE which cannot be observed by SDS-PAGE. It has also been demonstrated that 05SAR-PAGE can be used to identify the phosphorylated or methylated proteins. Besides, 05SAR-PAGE shows the advantages of simple operation and low cost, and can be easily adapted to diverse applications. Image 1 • Determination of the dimerization states of PhoB N and PhoR cp by 05SAR-PAGE. • Mild effect of SAR on protein structure. • Western-blot of monomer and dimer states in vivo by 05SAR-PAGE. • Identification of different modification states of proteins by 05SAR-PAGE. [ABSTRACT FROM AUTHOR]

2D diffusion-ordered NMR spectroscopy (DOSY) has been widely recognized as a powerful tool for analyzing mixtures and probing inter-molecular interactions in situ. But it is difficult to differentiate molecules with similar diffusion coefficients in presence of overlapped spectra. Its performance is susceptible to the number of chemical components, and usually gets worse when the number of components increases. Here, to alleviate the problem, numerical simultaneous inversion of Laplace transform (SILT) of many related variables is proposed for reconstructing DOSY spectrum (SILT-DOSY). The advantage of the proposed method in comparison to other methods is that it is capable of estimating the number of analytes more accurately and deriving corresponding component spectra, which in turn leads to the more reliable identification of the components. [ABSTRACT FROM AUTHOR]

A holistic and comparative quality assessment of vinegars from different countries is needed with international trade of vinegar become frequent. In this study, compounds characterization and comparison of commercial-grade Chinese cereal and European grape vinegars were performed using 1H NMR spectroscopy coupled with principal component analysis (PCA) and orthogonal projection to latent structures discriminate analysis (OPLS-DA). The results showed that Balsamic vinegars of Modena were clearly discriminated by higher amount of fructose and glucose, while Chinese aromatic vinegar and aged vinegars were characterized by higher amount of amino acids, volatile compounds, succinate and betaine. On the other hand, flavoring compounds in Chinese rice vinegar and European wine vinegars are less than the others. These characteristic components are associated with the special raw materials and producing process of each types of vinegar and endow them special flavor. The results obtained in this study provide a global insight into vinegar through a 1H NMR based compounds analysis that allows a holistic quality assessment and comparison of vinegars from different manufacture origins. [ABSTRACT FROM AUTHOR]

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. [ABSTRACT FROM AUTHOR]

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. [ABSTRACT FROM AUTHOR]

We used Xenopus laevis oocytes, a paradigm for a variety of biological studies, as a eukaryotic model system for in-cell protein NMR spectroscopy. The small globular protein GB1 was one of the first studied in Xenopus oocytes, but there have been few reports since then of high-resolution spectra in oocytes. The scarcity of data is at least partly due to the lack of good labeling strategies and the paucity of information on resonance broadening mechanisms. Here, we systematically evaluate isotope enrichment and labeling methods in oocytes injected with five different proteins with molecular masses of 6 to 54 kDa. 19F labeling is more promising than 15N, 13C, and 2H enrichment. We also used 19F NMR spectroscopy to quantify the contribution of viscosity, weak interactions, and sample inhomogeneity to resonance broadening in cells. We found that the viscosity in oocytes is only about 1.2 times that of water, and that inhomogeneous broadening is a major factor in determining line width in these cells. [ABSTRACT FROM AUTHOR]

Abstract: Although Zn2+ ions are involved in large numbers of physiopathological processes, non-invasive detection of Zn2+ ions in opaque biological samples remains a huge challenge. Here, we developed a novel zinc-responsive hyperpolarized (HP) 129Xe-based NMR molecular sensor. This HP 129Xe-based NMR molecular sensor was synthesized by attaching 2-(diphenylphosphino) benzenamine as ligand for zinc ions to the xenon-binding supramolecular cage, cryptophane. The 129Xe NMR spectroscopy of such molecular sensor was shifted up to 6.4ppm in the presence of Zn2+ ions, which was nearly four times larger than that of the reported similar sensor. The application of the sensor would benefit low concentration detection by using indirect NMR/MRI method. The response exhibited high sensitivity and selectivity as discriminated from other six potentially competing metal ions. The application of this sensor in the analysis of zinc ions in the rat serum samples was also evaluated. The strategy is generally applicable in developing sensitive and selective sensors for quantitative determination of zinc ions. [Copyright &y& Elsevier]

Nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography are the two main methods for protein three-dimensional structure determination at atomic resolution. According to the protein structures deposited in the Protein Data Bank, X-ray crystallography has become the dominant method for structure determination, particularly for large proteins and complexes. However, with the developments of isotope labeling, increase of magnetic field strength, common use of a cryogenic probe, and ingenious pulse sequence design, the applications of NMR spectroscopy have expanded in biological research, especially in characterizing protein dynamics, sparsely populated transient structures, weak protein interactions, and proteins in living cells at atomic resolution, which is difficult if not impossible by other biophysical methods. Although great advances have been made in protein NMR spectroscopy, its applications in protein therapeutics, which represents the fastest growing segment of the pharmaceutical industry, are still limited. Here we review the recent advances in the use of NMR spectroscopy in studies of large proteins or complexes, posttranslation modifications, weak interactions, and aggregation, and in-cell NMR spectroscopy. The potential applications of NMR spectroscopy in protein therapeutic assays are discussed. [ABSTRACT FROM AUTHOR]

Abstract: α-Synuclein is involved in Parkinson's disease and its interaction with cell membrane is crucial to its pathological and physiological functions. Membrane properties, such as curvature and lipid composition, have been shown to affect the interactions by various techniques, but ion effects on α-synuclein membrane interactions remain elusive. Ca2+ dynamic fluctuation in neurons plays important roles in the onset of Parkinson's disease and its influx is considered as one of the reasons to cause cell death. Using solution Nuclear Magnetic Resonance (NMR) spectroscopy, here we show that Ca2+ can modulate α-synuclein membrane interactions through competitive binding to anionic lipids, resulting in dissociation of α-synuclein from membranes. These results suggest a negative modulatory effect of Ca2+ on membrane mediated normal function of α-synuclein, which may provide a clue, to their dysfunction in neurodegenerative disease. [Copyright &y& Elsevier]

Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein-protein interactions affect mobility, but examining viscosity and weak interaction effects is challenging. Herein, we demonstrate the use of 19F NMR spectroscopy to measure cytoplasmic viscosity and to characterize nonspecific protein-protein interactions in living Escherichia coli cells. The origins of resonance broadening in Escherichia coli cells were also investigated. We found that sample inhomogeneity has a negligible effect on resonance broadening, the cytoplasmic viscosity is only about 2-3 times that of water, and ubiquitous transient weak protein-protein interactions in the cytosol play a significant role in governing the detection of proteins by using in-cell NMR spectroscopy. [ABSTRACT FROM AUTHOR]

Abstract: Detection and quantification of total choline-containing metabolites (CCMs) in tissues by magnetic resonance spectroscopy (MRS) has received considerable attention as a biomarker of cancer. Tissue CCMs are mainly choline (Cho), phosphocholine (PCho), and glycerophosphocholine (GPCho). Because the methyl 1H resonances of tissue CCMs exhibit small chemical shift differences and overlap significantly in 1D 1H MRS, quantification of individual components is precluded. Development of a MRS method capably of resolving individual components of tissue CCMs would be a significant advance. Herein, a modification of the 2D 1H–14N HSQC technique is targeted on the two methylene 1H in the CH2O group (3 J 1H14N =2.7Hz) and applied to ex vivo mouse and human liver samples at physiological temperature (37°C). Specifically, the 1H–14N HSQC technique is modified into a 2D 1H–14N three-bond correlation (HN3BC) experiment, which selectively detects the 1H of CH2O coupled to 14N in CCMs. Separate signals from Cho, PCho, and GPCho components are resolved with high detection sensitivity. A 2D HN3BC spectrum can be recorded from mouse liver in only 1.5min and from human carcinoma liver tissue in less than 3min with effective sample volume of 0.2ml at 14.1T. [Copyright &y& Elsevier]

Abstract: As an effective method for solvent suppression, WATERGATE is widely used in high resolution NMR spectroscopy. It is usually composed of a number of pulses separated by constant intervals. However, theoretical and experimental analyses indicate that narrower bandwidth and lower intensities around the secondary suppression points occur in the excitation profile of the composite WATERGATE. The excitation profile distortion is caused by the chemical shift evolution during the RF pulses. The higher the ratio of pulse duration to the inter-pulse delay is, the severer the profile distorts. Therefore, in high magnetic fields, the effect will be serious when WATERGATE is applied to some biological samples whose resonances distribute over a wide range. As can be seen obviously by applying WATERGATE to detect a RNA–protein mixture sample in an 800MHz spectrometer, the resonances of the imino protons were partially suppressed by showing decreased intensities, though the intended secondary suppression points were set far away from them. In this article, we proposed an optimized WATERGATE that could effectively compensate the chemical shift evolution during the RF pulses, and relieve the excitation profile distortion. The optimized experiment will be a good way to retain the imino signal intensities when WATERGATE is applied to detect the RNA samples in high magnetic field. [ABSTRACT FROM AUTHOR]

Abstract: Choline nitrogen (14N) has a long relaxation time (seconds) which is due to the highly symmetric chemical environments. 14N in choline also has coupling constants with protons (0.6Hz to methyl protons, 2.7Hz to CH2O protons and 0.2Hz to NCH2 protons). Based on these properties, we introduce a two-dimensional NMR method to detect choline and its derivatives in solutions. This method is the 1H–14N hetero-nuclear single-quantum correlation (HSQC) experiment which has been developed in solid-state NMR in recent years. Experiments have demonstrated that the 1H–14N HSQC technique is a sensitive method for detection of choline-containing compounds in solutions. From 1mM choline solution in 16min on a 500MHz NMR spectrometer, a 1H–14N HSQC spectrum has been recorded with a signal-to-noise ratio of 1700. Free choline, phosphocholine and glycerophosphocholine in milk can be well separated in 1H–14N HSQC spectra. This technique would become a promising analytical approach to mixture analyses where choline-containing compounds are of interest, such as tissue extracts, body fluids and food solutions. [ABSTRACT FROM AUTHOR]

Abstract: The metabolic changes in hippocampus, temporal cortex and prefrontal cortex in SD rats along with aging were explored using a metabonomic approach, which based on high resolution “magic angle spinning”1H NMR spectroscopy. The metabolite profiles were analyzed by partial least squares-discriminant analysis, and the results showed that the metabolites of the above three brain regions in old rats were dramatically different from that in the adult and young rats. The old rats showed increased myo-inositol and lactate in all of the three brain regions, and decreased N-acetylaspartate in temporal and frontal cortex, Glutamate–GABA level became imbalance in temporal cortex of old rats. In addition, compared with the adult female rats, male rats had higher levels of N-acetylaspartate, taurine, and creatine in temporal or frontal cortex. The age-related metabolic changes may indicate the early functional alterations of neural cells in these brain regions, especially the temporal cortex. The gender-related metabolic changes suggest the significance of the hormonal regulation in brain metabolism. Our work highlights the potential of metabolic profiling to enhance our understanding of biological mechanisms of brain aging. [Copyright &y& Elsevier]

Conformational change of cytochrome c (cyt c) caused by interaction with cardiolipin (CL) is an important step during apoptosis, but the underlying mechanism is controversial. To comprehensively clarify the structural transformations of cyt c upon interaction with CL and avoid the unpredictable alias that might come from protein labeling or mutations, the conformation of purified yeast iso–1 cyt c with natural isotopic abundance in different contents of CL was measured by using NMR spectroscopy, in which the trimethylated group of the protein was used as a natural probe. The data demonstrate that cyt c has two partially unfolded conformations when interacted with CL: one with Fe–His33 coordination and the other with a penta–coordination heme. The Fe–His33 coordination conformation can be converted into a penta–coordination heme conformation in high content of CL. The structure of cyt c becomes partially unfolded with more exposed heme upon interaction with CL, suggesting that cyt c prefers a high peroxidase activity state in the mitochondria, which, in turn, makes CL easy to be oxidized, and causes the release of cyt c into the cytoplasm as a trigger in apoptosis. [ABSTRACT FROM AUTHOR]

Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs. [ABSTRACT FROM AUTHOR]

The Ca2+-mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by 19F NMR spectroscopy of the transition of the Ca2+-free and -bound forms in Xenopus laevis oocytes at different Ca2+ levels. We find that the Ca2+-bound CaM population increased greatly upon binding the target protein myosin light-chain kinase (MLCK) at the same Ca2+ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long-range structural constraints in cells. Our study shows that 19F NMR spectroscopy can be used to obtain long-range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants. [ABSTRACT FROM AUTHOR]

A non-destructive and comprehensive 13C isotopic evaluation approach based on 1H NMR spectroscopy was developed. The carbon isotope distribution (CID) of most of the components (S/N ≥ 1000) in food matrices were evaluated using frequency distribution of peak area ratios (PAR) of decoupling to non-13C-decoupling spectra at natural abundance. The approach was applied successfully to vinegar and it was found that the PAR of fermented vinegars is obviously narrower than that of the blended one and the one produced via chemically defined culture medium. Besides, the extra additives can also be evaluated by their characteristic PAR values. It was found that the sugars are the most commonly added components into the blended vinegars. The results obtained from the developed approach show good validity (baseline effect, RSD < 0.1%) and internal reproducibility (RSD < 0.1%). Practicability of the method is confirmed by gas chromatography-isotope ratio mass spectrometry (GC-IRMS) detection method. The results imply that the proposed approach could be used not only for the discrimination but also for the primary authentication of the blended components in the fermented food matrices. Image 1 • A non-destructive and comprehensive 13C isotopic evaluation approach based on 1H NMR spectroscopy was developed. • The carbon isotope distribution (CID) of most components (S/N ≥ 1000) in food matrices was evaluated. • CID was determined by using frequency distribution of peak area ratios (PAR) of decoupling to non-13C-decoupling spectrum at natural abundance. • The approach was applied successfully to authenticate the quality of vinegar. • Practicability of the method was confirmed by gas chromatography-isotope ratio mass spectrometry (GC-IRMS). [ABSTRACT FROM AUTHOR]

We present a method to identify and sort the oils in oil-water mixtures based on the Overhauser dynamic nuclear polarization (ODNP) enhancement at low field. Through combining two types of radicals, e.g. ODNP enhancer TEMPO and relaxation reagent Mn2+, we can selectively enhance the 1H NMR signal of oil in oil-water mixture infiltrated in porous media. More importantly, we have found that the enhancements of light oils in porous materials are inversely dependent of their viscosities but independent of pore size approximately above 10 μm. This allows us to roughly sort oils according to their ODNP enhancement values. The verification experiments in sandstones saturated with several oil and water mixtures show that the method is useful for oils identification and classification in porous media, especially for reservoir assessment or development. [ABSTRACT FROM AUTHOR]

NMR Spectroscopy In their Communication on page 8686 ff., C. Li et al., demonstrate that 19F labeling is a good first choice for studying globular and disordered proteins in Xenopus oocytes, especially compared with conventional 15N ‐ or 13C ‐ methyl enrichment. By using 19F labeling, they found that, unlike E. coli cells, the viscosity in oocytes is only about 1.2 times that of water and that inhomogeneous broadening contributes 60 – 70 % to the line width. The labeling strategies and resonance broadening mechanisms in Xenopus oocytes were explored with the goal of expanding the application of this cell type. [ABSTRACT FROM AUTHOR]