The Experts below are selected from a list of 244299 Experts worldwide ranked by ideXlab platform
John Christodoulou - One of the best experts on this subject based on the ideXlab platform.
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Two-Dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments
Journal of Biomolecular NMR, 2020Co-Authors: Christopher A. Waudby, Margaux Ouvry, Ben Davis, John ChristodoulouAbstract:NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to the rate of exchange, and in the case of one-dimensional experiments chemical exchange regimes are well established and well known. However, Two-Dimensional experiments present additional complexity, as at least one additional frequency difference must be considered. Here we provide a systematic classification of chemical exchange regimes in Two-Dimensional NMR spectra. We highlight important differences between exchange in HSQC and HMQC experiments, that on a practical level result in more severe exchange broadening in HMQC spectra, but show that complementary alternatives to the HMQC are available in the form of HZQC and HDQC experiments. We present the longitudinal relaxation optimised SOFAST-H(Z/D)QC experiment for the simultaneous acquisition of sensitivity-enhanced HZQC and HDQC spectra, and the longitudinal and transverse relaxation optimised BEST-ZQ-TROSY for analysis of large molecular weight systems. We describe the application of these experiments to the characterisation of the interaction between the Hsp90 N-terminal domain and a small molecule ligand, and show that the independent analysis of HSQC, HMQC, HZQC and HDQC experiments provides improved confidence in the fitted dissociation constant and dissociation rate. Joint analysis of such data may provide improved sensitivity to detect and analyse more complex multi-state interaction mechanisms such as induced fit or conformational selection.
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two dimensional NMR lineshape analysis
bioRxiv, 2016Co-Authors: Christopher A. Waudby, Andres Ramos, Lisa D Cabrita, John ChristodoulouAbstract:NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of Two-Dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire Two-Dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.
Michae Zasloff - One of the best experts on this subject based on the ideXlab platform.
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structure of the novel steroidal antibiotic squalamine determined by two dimensional NMR spectroscopy
Steroids, 1993Co-Authors: Suzanne L. Wehrli, Karen S Moore, Stewart Durell, Michae Zasloff, Heinrich RoderAbstract:Abstract Squalamine is a novel aminosterol recently isolated from the dogfish shark, Squalus acanthias . This water-soluble steroid exhibits potent antibacterial activity against both gram-negative and gram-positive bacteria. In addition, squalamine is fungicidal and induces osmotic lysis of protozoa. We report here the structural determination of squalamine, 3β-N-1-[N(3-[4-aminobutyl])-1,3 diaminopropanel]-7α,24ζ-dihydroxy-5α-cholestane 24-sulfate, which was nuclear magnetic resonance (NMR) specta. Squalamine is a cationic steroid characterized by a condensation of an anionic bile salt intermediate with the polyamine, spermidine. This molecule is a potential host-defese agent in the shark, and provides insight into a new class of vertebrate antimicrobial molecules. (Steroids 58: 370–378, 1993 )
Christopher A. Waudby - One of the best experts on this subject based on the ideXlab platform.
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Two-Dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments
Journal of Biomolecular NMR, 2020Co-Authors: Christopher A. Waudby, Margaux Ouvry, Ben Davis, John ChristodoulouAbstract:NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to the rate of exchange, and in the case of one-dimensional experiments chemical exchange regimes are well established and well known. However, Two-Dimensional experiments present additional complexity, as at least one additional frequency difference must be considered. Here we provide a systematic classification of chemical exchange regimes in Two-Dimensional NMR spectra. We highlight important differences between exchange in HSQC and HMQC experiments, that on a practical level result in more severe exchange broadening in HMQC spectra, but show that complementary alternatives to the HMQC are available in the form of HZQC and HDQC experiments. We present the longitudinal relaxation optimised SOFAST-H(Z/D)QC experiment for the simultaneous acquisition of sensitivity-enhanced HZQC and HDQC spectra, and the longitudinal and transverse relaxation optimised BEST-ZQ-TROSY for analysis of large molecular weight systems. We describe the application of these experiments to the characterisation of the interaction between the Hsp90 N-terminal domain and a small molecule ligand, and show that the independent analysis of HSQC, HMQC, HZQC and HDQC experiments provides improved confidence in the fitted dissociation constant and dissociation rate. Joint analysis of such data may provide improved sensitivity to detect and analyse more complex multi-state interaction mechanisms such as induced fit or conformational selection.
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two dimensional NMR lineshape analysis
bioRxiv, 2016Co-Authors: Christopher A. Waudby, Andres Ramos, Lisa D Cabrita, John ChristodoulouAbstract:NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of Two-Dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire Two-Dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.
Bernhard Brutscher - One of the best experts on this subject based on the ideXlab platform.
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hadamard amino acid type edited NMR experiment for fast protein resonance assignment
Journal of the American Chemical Society, 2008Co-Authors: Ewen Lescop, Rodolfo M Rasia, Bernhard BrutscherAbstract:An original Hadamard-encoding scheme allows discrimination among seven amino acid types in a single Two-Dimensional NMR experiment. Combined with hyperdimensional NMR techniques, this presents a promising new method for fast, automated backbone resonance assignment of proteins in only a few hours time.
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protein folding and unfolding studied at atomic resolution by fast two dimensional NMR spectroscopy
Proceedings of the National Academy of Sciences of the United States of America, 2007Co-Authors: Paul Schanda, Vincent Forge, Bernhard BrutscherAbstract:Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.
Dominique Massiot - One of the best experts on this subject based on the ideXlab platform.
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high resolution two dimensional NMR spectra of half integer spin quadrupolar nuclei from one dimensional projections
Chemical Physics Letters, 2007Co-Authors: Thomas Vosegaard, Dominique MassiotAbstract:Abstract We present a technique providing high-resolution spectra of quadrupolar nuclei with half-integer nuclear spin displaying significant second-order linebroadening. The technique, dubbed chemical shift – quadrupolar projection-reconstruction of one-dimensional spectra (CQ-PRODI) exploits the different magnetic field dependence of the chemical shift and second-order quadrupolar effect. One-dimensional spectra recorded at different magnetic field strengths are represented as projections along different directions in the Two-Dimensional spectrum that correlates the chemical shift and the second-order quadrupolar lineshape. We present CQ-PRODI spectra for 27 Al in 9Al 2 O 3 · 2B 2 O 3 and for 71 Ga in β-Ga 2 O 3 which display resolution of all sites in the chemical shift dimension.
