Related ArticlesAn NMR Method to Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins.
Angew Chem Int Ed Engl. 2017 Sep 06;:
Authors: Hogeweg A, Sowislok A, Schrader T, Beuck C
Abstract
Targeting protein surfaces involved in protein-protein interactions using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand binding sites with single residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We employed Lys- and Arg-specific H2(C)N NMR experiments to directly observe the side chain atoms in close contact with the ligand, for which the most drastic changes in the NMR signals are expected. Binding of lysine- and arginine-specific supramolecular tweezers to the small hPin1 WW domain was studied as a model system. The H2(C)N spectra track the terminal CH2 groups of all two Lys and four Arg residues, revealing significant differences in their binding kinetics and allow to clearly pinpoint the order of tweezers binding.
PMID: 28877391 [PubMed - as supplied by publisher]
[NMR paper] Protein-Observed Fluorine NMR is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR.
Protein-Observed Fluorine NMR is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Protein-Observed Fluorine NMR is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR.
ACS Chem Biol. 2016 Sep 14;
Authors: Urick AK, Calle Jiménez LP, Espinosa JF, Hu H, Pomerantz WC
Abstract
To evaluate its potential as a ligand discovery tool, we compare a newly developed...
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09-22-2016 06:31 AM
A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation
A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation
Abstract
By nature of conducting ions, transporting substrates and transducing signals, membrane channels, transporters and receptors are expected to exhibit intrinsic conformational dynamics. It is therefore of great interest and importance to understand the various properties of conformational dynamics acquired by these proteins, for example, the relative population of states, exchange rate, conformations of multiple states, and how small molecule ligands modulate the conformational exchange....
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03-29-2016 04:59 PM
A Functional NMR for Membrane Proteins: Dynamics, Ligand Binding, and Allosteric Modulation
A Functional NMR for Membrane Proteins: Dynamics, Ligand Binding, and Allosteric Modulation
SUMMARY
By nature of conducting ions, transporting substrates and transducing signals, membrane channels, transporters and receptors are expected to exhibit intrinsic conformational dynamics. It is therefore of great interest and importance to understand the various properties of conformational dynamics acquired by these proteins, e.g., the relative population of states, exchange rate, conformations of multiple states, and how small molecule ligands modulate the conformational exchange. Because...
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03-01-2016 05:59 PM
[NMR paper] NMR Characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding.
NMR Characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding.
Related Articles NMR Characterization of the electrostatic interaction of the basic residues in HDGF and FGF2 during heparin binding.
Biochim Biophys Acta. 2014 Aug 9;
Authors: Chiu LY, Hung KW, Tjong SC, Chiang YW, Sue SC
Abstract
Electrostatic interaction is a major driving force in the binding of proteins to highly acidic glycosaminoglycan, such as heparin. Although NMR backbone chemical shifts have generally...
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08-15-2014 12:53 PM
The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method
The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method
Abstract Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of...
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09-24-2012 01:02 AM
Engineering [Ln(DPA)3]3â?? binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions
Engineering 3â?? binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions
Abstract Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and...
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07-26-2011 11:11 AM
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...
An NMR Method to Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins.
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