Related ArticlesCombined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
Bioorg Med Chem Lett. 2015 Mar 15;25(6):1284-7
Authors: Shi Y, Ardá A, Pinto BM
Abstract
UDP-galactopyranose mutase (UGM) is an enzyme involved in the biosynthesis of the Mycobacterium tuberculosis cell wall, and is essential for the growth and survival of the organism. A micromolar inhibitor developed by tetrafluorination of the UGM substrate has been previously studied by saturation transfer difference (STD) NMR spectroscopy. To elucidate the bioactive conformation of the inhibitor bound to UGM, we employ molecular dynamics (MD) simulations to construct a structural model. The MD model is subsequently validated by a good fit between experimental and theoretical STD effects, the latter calculated by a complete relaxation and conformational exchange matrix (CORCEMA) analysis. This structural model is used to explain the relative binding affinities of the inhibitor and the parent substrate.
[NMR paper] Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
Related Articles Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.
J Chem Theory Comput. 2014 Apr 8;10(4):1781-7
Authors: Li DW, Brüschweiler R
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...
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[NMR paper] A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study.
A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study.
Related Articles A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: Enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study.
Eur J Med Chem. 2014 Jun 11;83C:92-101
Authors: Sim?i? M, Pureber K, Kristan K, Urleb U, Kocjan D, Grdadolnik SG
Abstract
N-(5-(5-nitro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)4-oxo-2-thioxo-1,3-thiazolidin-3-yl)nicotinamide,...
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A Novel 2-oxoindolinylidene Inhibitor of Bacterial MurD Ligase: Enzyme Kinetics, Protein-Inhibitor Binding by NMR and a Molecular Dynamics Study
A Novel 2-oxoindolinylidene Inhibitor of Bacterial MurD Ligase: Enzyme Kinetics, Protein-Inhibitor Binding by NMR and a Molecular Dynamics Study
Publication date: Available online 11 June 2014
Source:European Journal of Medicinal Chemistry</br>
Author(s): Mihael Sim?i? , Kaja Pureber , Katja Kristan , Uroš Urleb , Darko Kocjan , Simona Goli? Grdadolnik</br>
N-(5-(5-nitro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)4-oxo-2-thioxo-1,3-thiazolidin-3-yl)nicotinamide, an 2-oxoindolinylidene derivative with novel structure scaffold, was evaluated for inhibition potency...
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06-12-2014 10:52 PM
[NMR paper] Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Related Articles Combined (1) H-NMR and Molecular Dynamics Studies on Conformational Behaviour of a Model Heptapeptide, GRGDSPC.
Chem Biol Drug Des. 2014 Apr 25;
Authors: Kulkarni AK, Ojha RP
Abstract
Among various strategies, the de novo design and in silico approaches are being used to develop the short peptides, models of modified peptides and mimetics as clinically useful drugs with improved stability and...
A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility
A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility
Abstract An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract,...
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[NMR paper] A combined STD-NMR/molecular modeling protocol for predicting the binding modes of th
A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II.
Related Articles A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II.
Biochemistry. 2005 May 10;44(18):6729-37
Authors: Wen X, Yuan Y, Kuntz DA, Rose DR, Pinto BM
A combined STD-NMR/molecular modeling protocol to probe the binding modes of the glycosidase inhibitors...
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[NMR paper] Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis,
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
Related Articles Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
Structure. 2004 Apr;12(4):633-44
Authors: Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R
The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4...
Combined molecular dynamics, STD-NMR, and CORCEMA protocol yields structural model for a UDP-galactopyranose mutase-inhibitor complex.
Linear Mode
