Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak proteinâ??ligand interactions is a key element. 1H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed 15N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A 15N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.
Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data
Determination of ligand binding modes in weak proteinâ??ligand complexes using sparse NMR data
Abstract
We describe a general approach to determine the binding pose of small molecules in weakly bound proteinâ??ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of...
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11-19-2016 08:35 PM
Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR
From The DNP-NMR Blog:
Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR
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Joseph, B., et al., Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR. Angew Chem Int Ed Engl, 2016. 55(38): p. 11538-42.
https://www.ncbi.nlm.nih.gov/pubmed/27511025
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11-19-2016 08:35 PM
Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations
Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations
Abstract
The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) â??5Â*mM). The determination of the proteinâ??fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for...
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09-26-2014 01:03 PM
Accuracy and precision of proteinâ??ligand interaction kinetics determined from chemical shift titrations
Accuracy and precision of proteinâ??ligand interaction kinetics determined from chemical shift titrations
Abstract NMR-monitored chemical shift titrations for the study of weak proteinâ??ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods...
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10-24-2012 10:28 PM
Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations
Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations
Abstract NMR is ideally suited for the analysis of proteinâ??protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K D ) of 1:1 proteinâ??protein or proteinâ??ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K D , and nonlinear least squares...
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05-01-2012 07:06 AM
Clean STD-NMR spectrum for improved detection of ligand-protein interactions at low c
Clean STD-NMR spectrum for improved detection of ligand-protein interactions at low concentration of protein.
Related Articles Clean STD-NMR spectrum for improved detection of ligand-protein interactions at low concentration of protein.
Magn Reson Chem. 2010 Oct 18;
Authors: Xia Y, Zhu Q, Jun KY, Wang J, Gao X
Saturation transfer difference (STD)-NMR has been widely used to screen ligand compound libraries for their binding activities to proteins and to determine the binding epitopes of the ligands. We report herein, a Clean STD-NMR method...
[NMR paper] 1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residu
1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles 1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase.
Biochemistry. 1999 Feb 16;38(7):2127-34
Authors: Morgan WD, Birdsall B, Nieto PM, Gargaro AR, Feeney J
...
Target-specific NMR detection of proteinâ??ligand interactions with antibody-relayed 15 N-group selective STD
Linear Mode
