The Experts below are selected from a list of 4260 Experts worldwide ranked by ideXlab platform
Paolo Carloni - One of the best experts on this subject based on the ideXlab platform.
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A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α-synuclein·dopamine adducts.
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
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a molecular dynamics simulation based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α synuclein dopamine adducts
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
Domenica Dibenedetto - One of the best experts on this subject based on the ideXlab platform.
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A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α-synuclein·dopamine adducts.
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
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a molecular dynamics simulation based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α synuclein dopamine adducts
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
Rocco Caliandro - One of the best experts on this subject based on the ideXlab platform.
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A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α-synuclein·dopamine adducts.
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
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a molecular dynamics simulation based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α synuclein dopamine adducts
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
Giulia Rossetti - One of the best experts on this subject based on the ideXlab platform.
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A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α-synuclein·dopamine adducts.
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
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a molecular dynamics simulation based interpretation of nuclear magnetic resonance multidimensional Heteronuclear Spectra of α synuclein dopamine adducts
Biochemistry, 2013Co-Authors: Domenica Dibenedetto, Giulia Rossetti, Rocco Caliandro, Paolo CarloniAbstract:Multidimensional Heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements o...
François Bontems - One of the best experts on this subject based on the ideXlab platform.
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first structural investigation of the restriction ribonuclease regb nmr spectroscopic conditions 13c 15n double isotopic labelling and two dimensional Heteronuclear Spectra
Protein Expression and Purification, 2004Co-Authors: Fakhri Saïda, Benoit Odaert, Marc Uzan, François BontemsAbstract:The bacteriophage T4 genome-encoded ribonuclease RegB is the unique well-defined restriction endoribonuclease. This protein cleaves with an almost absolute specificity its RNA substrate in the middle of the GGAG tetranucleotide mainly found in the Shine-Dalgarno sequence (required for the prokaryotic initiation of the translation). This protein has no significant homology to any known ribonuclease and its structure has never been investigated. The extreme toxicity of this ribonuclease prevents the expression of large quantities for structural studies. Here, we show that the toxicity of RegB can be bypassed by using the RegB H48A point mutant and explain why resolving the structure of this mutant is relevant. For nuclear magnetic resonance (NMR) purposes, we report the preparation of highly pure (13)C/(15)N double-labelled 1.2mM samples of RegB H48A using a high yield expression procedure in minimal medium (30 mg/L). We also present a set of solution conditions that maintain the concentrated samples of this protein stable for long periods at the NMR-required temperature. Finally, we present the first (1)H/(15)N and (1)H/(13)C two-dimensional NMR Spectra of RegB H48A. These Spectra show that the protein is folded and that the full structural analysis of RegB by NMR is feasible.
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First structural investigation of the restriction ribonuclease RegB: NMR spectroscopic conditions, 13C/15N double-isotopic labelling and two-dimensional Heteronuclear Spectra
Protein expression and purification, 2004Co-Authors: Fakhri Saïda, Benoit Odaert, Marc Uzan, François BontemsAbstract:The bacteriophage T4 genome-encoded ribonuclease RegB is the unique well-defined restriction endoribonuclease. This protein cleaves with an almost absolute specificity its RNA substrate in the middle of the GGAG tetranucleotide mainly found in the Shine-Dalgarno sequence (required for the prokaryotic initiation of the translation). This protein has no significant homology to any known ribonuclease and its structure has never been investigated. The extreme toxicity of this ribonuclease prevents the expression of large quantities for structural studies. Here, we show that the toxicity of RegB can be bypassed by using the RegB H48A point mutant and explain why resolving the structure of this mutant is relevant. For nuclear magnetic resonance (NMR) purposes, we report the preparation of highly pure (13)C/(15)N double-labelled 1.2mM samples of RegB H48A using a high yield expression procedure in minimal medium (30 mg/L). We also present a set of solution conditions that maintain the concentrated samples of this protein stable for long periods at the NMR-required temperature. Finally, we present the first (1)H/(15)N and (1)H/(13)C two-dimensional NMR Spectra of RegB H48A. These Spectra show that the protein is folded and that the full structural analysis of RegB by NMR is feasible.