9 years 4 months ago
Among human body fluids, serum plays a key role for diagnostic tests and, increasingly, for metabolomics analysis. However, the high protein content of serum poses significant challenges for nuclear magnetic resonance (NMR)-based metabolomics studies because it can strongly interfere with metabolite signal detection and quantitation. Although several methods for protein removal have been proposed, including ultrafiltration and organic-solvent-induced protein precipitation, there is currently no...
Bo Zhang
9 years 4 months ago
Among human body fluids, serum plays a key role for diagnostic tests and, increasingly, for metabolomics analysis. However, the high protein content of serum poses significant challenges for nuclear magnetic resonance (NMR)-based metabolomics studies because it can strongly interfere with metabolite signal detection and quantitation. Although several methods for protein removal have been proposed, including ultrafiltration and organic-solvent-induced protein precipitation, there is currently no...
Bo Zhang
9 years 5 months ago
Functional protein motions covering a wide range of time scales can be studied, among other techniques, by NMR and by molecular dynamics (MD) computer simulations. MD simulations of proteins now routinely extend into the hundreds of nanoseconds time scale range exceeding the overall tumbling correlation times of proteins in solution by several orders of magnitude. This provides a unique opportunity to rigorously validate these simulations by quantitative comparison with model-free order...
Yina Gu
9 years 5 months ago
J Chem Theory Comput. 2014 Apr 8;10(4):1781-7. doi: 10.1021/ct4010646.
ABSTRACT
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.
PMID:26580385 | DOI:10.1021/ct4010646
Da-Wei Li
Rafael Brüschweiler
9 years 5 months ago
The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast...
Yina Gu
9 years 5 months ago
Functional protein motions covering a wide range of time scales can be studied, among other techniques, by NMR and by molecular dynamics (MD) computer simulations. MD simulations of proteins now routinely extend into the hundreds of nanoseconds time scale range exceeding the overall tumbling correlation times of proteins in solution by several orders of magnitude. This provides a unique opportunity to rigorously validate these simulations by quantitative comparison with model-free order...
Yina Gu
9 years 5 months ago
The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast...
Yina Gu
9 years 5 months ago
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better...
Da-Wei Li
9 years 9 months ago
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain...
Dawei Li
9 years 9 months ago
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain...
Dawei Li
9 years 10 months ago
Metabolomics aims at a complete characterization of all metabolites in biological samples in terms of both their identities and concentrations. Because changes of metabolites and their concentrations are a direct reflection of cellular activity, it allows for a better understanding of cellular processes and function to be obtained. Although NMR spectroscopy is routinely applied to complex biological mixtures without purification, overlapping NMR peaks often pose a challenge for the comprehensive...
Bo Zhang
9 years 10 months ago
Metabolomics aims at a complete characterization of all metabolites in biological samples in terms of both their identities and concentrations. Because changes of metabolites and their concentrations are a direct reflection of cellular activity, it allows for a better understanding of cellular processes and function to be obtained. Although NMR spectroscopy is routinely applied to complex biological mixtures without purification, overlapping NMR peaks often pose a challenge for the comprehensive...
Bo Zhang
10 years ago
A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum...
Kerem Bingol
10 years ago
A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum...
Kerem Bingol
10 years ago
DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is...
Ran Furman
10 years ago
DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is...
Ran Furman
10 years 5 months ago
A new metabolomics database and query algorithm for the analysis of (13)C-(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C-(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index . Our new HSQC...
Kerem Bingol
10 years 5 months ago
A new metabolomics database and query algorithm for the analysis of (13)C-(1)H HSQC spectra is introduced, which unifies NMR spectroscopic information on 555 metabolites from both the Biological Magnetic Resonance Data Bank (BMRB) and Human Metabolome Database (HMDB). The new database, termed Complex Mixture Analysis by NMR (COLMAR) (13)C-(1)H HSQC database, can be queried via an interactive, easy to use web interface at http://spin.ccic.ohio-state.edu/index.php/hsqc/index . Our new HSQC...
Kerem Bingol
10 years 10 months ago
J Magn Reson Imaging. 2014 Sep;40(3):682-90. doi: 10.1002/jmri.24397. Epub 2013 Oct 31.
ABSTRACT
PURPOSE: To compare DW-MRI between 1.5 and 3 Tesla (T) in terms of image quality, apparent diffusion coefficient (ADC), reproducibility, lesion-to-background contrast and signal-to-noise ratio (SNR), using a test object.
MATERIALS AND METHODS: A spherical diffusion phantom was used for qualitatively assessing image quality and performing quantitative measurements between the two field strengths.
RESULTS: Distortions and signal losses degraded image quality at 3T even when the protocols were optimized for minimum TE. The ADC, in the majority of the phantom compartments, was significantly different between 1.5T and 3T (P < 0.009), while the average coefficient of variation, excluding the phantom compartments affected by artifacts, was <1.3% at both field strengths. The lesion-to-background contrast was improved at 1.5T for images acquired with b = 1000 s/mm(2) and comparable contrast was achieved at 3T with higher b-values. The SNR gain at 3T could, in theory, be balanced by the increased number of signal excitations one can accommodate at 1.5T to perform DW-MRI within the same acquisition time and possibly improved image quality, when 3T systems with no parallel transmission are used.
CONCLUSION: Further phantom and in vivo studies are required to investigate the utility of DW-MRI at 3T, if image quality and acquisition times comparable to the ones from 1.5T are assumed.
PMID:24925470 | DOI:10.1002/jmri.24397
Ioannis Lavdas
Marc E Miquel
Donald W McRobbie
Eric O Aboagye
14 years ago
Phytochemistry. 2011 Jun;72(9):875-81. doi: 10.1016/j.phytochem.2011.03.010. Epub 2011 Apr 7.
ABSTRACT
An integrated LC-MS and NMR metabolomic study was conducted to investigate metabolites whose formation was induced by lactofen (1), a soybean (Glycine max L.) disease resistance-inducing herbicide. First, LC-MS analyses of control and lactofen (1)-induced soybean extracts were performed. The LC-MS raw data were then processed by a custom designed bioinformatics program to detect the induced metabolites so formed. Finally, structures of unknown induced metabolites were determined on the basis of their 1D and 2D NMR spectroscopic data. Structure of two previously unreported compounds, 7,8-dihydroxy-4'-methoxy-3'-prenylisoflavone (2) and 7-hydroxy-4',8-dimethoxy-3'-prenylisoflavone (3) were elucidated together with four known prenylated compounds, 3'-prenyldaidzein (4), 8-prenyldaidzein (5), 3'-prenylgenistein (6), and 4-prenylcoumestrol (7). Compounds (2-6) are reported for the first time in soybean, as are the (13)C chemical shift assignments for compound (7). Formation of these six prenylated compounds was also induced by the primary defense glucan elicitor from the cell wall of the pathogen Phytophthora sojae (Kauf. and Gerde.), further suggesting a potential role in soybean defense. These results highlight the metabolic flexibility within soybean secondary product pathways and suggest that prenylation may be associated with defense responses. Moreover, this study demonstrates a promising future approach using metabolomics on elicitor-induced plants for discovery of unknown compounds even in relatively well studied plants.
PMID:21477824 | DOI:10.1016/j.phytochem.2011.03.010
Jiye Cheng
Chunhua Yuan
Terrence L Graham
