The characterization of protein-ligand interaction modes becomes recalcitrant in the NMR intermediate exchange regime as the interface resonances are broadened beyond detection. Here, we determined the 19F low-populated bound-state pseudocontact shifts (PCSs) of mono- and di-fluorinated inhibitors of the BRM bromodomain using a highly-skewed protein/ligand ratio. The bound-state 19F PCSs were retrieved from 19F chemical exchange saturation transfer (CEST) in the presence of the lanthanide-labeled protein, which was termed the 19F PCS-CEST approach. These PCSs enriched in spatial information enabled the identification of best-fitting poses, which agree well with the crystal structure of a more soluble analog in complex with the BRM bromodomain. This 19F PCS-CEST approach fills the gap of the NMR structural characterization of lead-like inhibitors with intermediate affinities, which are essential for structure-guided hit-to-lead evolution.
[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
[NMR paper] Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.
Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.
Related Articles Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.
Chemistry. 2016 Apr 26;
Authors: Dalvit C, Vulpetti A
Abstract
It is known that strong hydrogen-bonding interactions play an important role in many chemical and...
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04-27-2016 01:51 PM
[NMR paper] Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer.
Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer.
Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer.
Phys Chem Chem Phys. 2016 Mar 22;
Authors: Ma RS, Li QF, Wang AD, Zhang JH, Liu ZJ, Wu JH, Su XC, Ruan K
Abstract
Despite the critical roles of excited states in protein functions, they remain intractable for most structural studies because of their notably low populations. Chemical shifts for...
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03-24-2016 04:30 PM
Integral membrane protein structure determination using pseudocontact shifts
Integral membrane protein structure determination using pseudocontact shifts
Abstract
Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary...
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01-21-2015 08:39 PM
Proteinâ??protein HADDocking using exclusively pseudocontact shifts
Proteinâ??protein HADDocking using exclusively pseudocontact shifts
<div class="Abstract" lang="en">Abstract <div class="normal">In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal ε domain of the E. coli DNA polymerase III (ε186) in complex with the HOT domain. Docking from the bound form of the two...
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06-06-2011 12:53 AM
Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded
Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded Cobalt(II)-Binding Amino Acid.
Related Articles Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded Cobalt(II)-Binding Amino Acid.
Angew Chem Int Ed Engl. 2010 Nov 25;
Authors: Nguyen TH, Ozawa K, Stanton-Cook M, Barrow R, Huber T, Otting G
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11-27-2010 02:45 PM
[NMR paper] Analysis of protein-carbohydrate interaction at the lower size limit of the protein p
Analysis of protein-carbohydrate interaction at the lower size limit of the protein part (15-mer peptide) by NMR spectroscopy, electrospray ionization mass spectrometry, and molecular modeling.
Related Articles Analysis of protein-carbohydrate interaction at the lower size limit of the protein part (15-mer peptide) by NMR spectroscopy, electrospray ionization mass spectrometry, and molecular modeling.
Biochemistry. 2002 Jul 30;41(30):9707-17
Authors: Siebert HC, Lü SY, Frank M, Kramer J, Wechselberger R, Joosten J, André S, Rittenhouse-Olson K, Roy R, von...
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11-24-2010 08:58 PM
[NMR paper] Spin labels as a tool to identify and characterize protein-ligand interactions by NMR
Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy.
Related Articles Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy.
Chembiochem. 2002 Mar 1;3(2-3):167-73
Authors: Jahnke W
NMR spectroscopy based discovery and optimization of lead compounds for a given molecular target requires the development of methods with maximum sensitivity and robustness. It is shown here that organic nitroxide radicals ("spin labels") can be used to boost the sensitivity...
Use of Fluorine Pseudocontact Shifts to Characterize the Protein-Ligand Interaction Mode in the Limit of NMR Intermediate Exchange
Linear Mode
