Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor that can be targeted for inducing potent adjuvant effects. Mincle can recognize trehalose dimycolate and related glycolipids. Here, we present a protocol to identify the ligand binding mode of Mincle. We describe steps for preparing labeled Mincle ectodomain, data acquisition, and analysis of nuclear magnetic resonance experiments using non-detergent sulfobetaine-195. This protocol can be applied...
[NMR paper] Protocol to identify drug-binding sites in proteins using solution NMR spectroscopy
Protocol to identify drug-binding sites in proteins using solution NMR spectroscopy
Dusquetide is a next-generation IDR (innate defense regulator) targeting the major autophagy receptor protein SQSTM1/p62 and modulating the innate immune response. Here, we describe a protocol for determining dusquetide-binding sites of p62 by solution NMR spectroscopy. Step-by-step technique details were provided, including sample preparation, NMR experiment setup, data processing, and binding site analysis. This protocol could be applied to characterize other small molecules targeting the ZZ...
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01-04-2023 11:44 PM
[NMR paper] Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by (19)F NMR Spectroscopy
Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by (19)F NMR Spectroscopy
A mutant aminoacyl-tRNA synthetase identified by a library selection system affords site-specific incorporation of 7-fluoro-L-tryptophan in response to an amber stop codon. The enzyme allows the production of proteins with a single hydrogen atom replaced by a fluorine atom as a sensitive nuclear magnetic resonance (NMR) probe. The substitution of a single hydrogen atom by another element that is as closely similar in size and hydrophobicity as possible...
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01-11-2022 06:11 PM
[NMR paper] Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations.
Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary_FullTextOnline_120x27.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary_FullTextOnline_120x27.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc-MS.gif Related Articles Identification of the binding...
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10-27-2015 12:33 PM
[NMR paper] NMR study to identify a ligand-binding pocket in ras.
NMR study to identify a ligand-binding pocket in ras.
Related Articles NMR study to identify a ligand-binding pocket in ras.
Enzymes. 2013;33:15-39
Authors: Maurer T, Wang W
Abstract
Despite decades of intense drug discovery efforts, to date no small molecules have been described that directly bind to Ras protein and effectively antagonize its function. In order to identify and characterize small-molecule binders to KRas, we carried out a fragment-based lead discovery effort. A ligand-detected primary nuclear magnetic resonance...
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07-20-2014 03:27 PM
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Chem Biol Drug Des. 2011 Jan 14;
Authors: Chandra K, Mustafi SM, Muthukumar S, Chary KV
The study of protein-ligand interaction has been of a great interest in contemporary structural biology. The understanding of the nature...
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01-18-2011 10:22 PM
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
Biochemistry. 2011 Jan 12;
Authors: He Y, Estephan R, Yang X, Vela A, Wang H, Bernard C, Stark RE
Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to...
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01-14-2011 12:05 PM
[NMR paper] Docking multiple conformations of a flexible ligand into a protein binding site using
Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints.
Related Articles Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints.
Proteins. 2002 Feb 15;46(3):295-307
Authors: Zabell AP, Post CB
A method is described for docking a large, flexible ligand using intra-ligand conformational restraints from exchange-transferred NOE (etNOE) data. Numerous conformations of the ligand are generated in isolation, and a subset of representative conformations is...
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11-24-2010 08:49 PM
[NMR paper] An investigation of the ligand-binding site of the glutamine-binding protein of Esche
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR.
Related Articles An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR.
Biochemistry. 1994 Jul 26;33(29):8651-61
Authors: Hing AW, Tjandra N, Cottam PF, Schaefer J, Ho C
Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance...
Protocol to identify the ligand binding site of Mincle using NMR spectroscopy
Linear Mode
