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The measurement of binding affinities by NMR chemical shift perturbation
Aug 04, 2022 - 1:03 AM - by nmrlearner
nmrlearner's Avatar The measurement of binding affinities by NMR chemical shift perturbation

Abstract

We have carried out chemical shift perturbation titrations on three contrasting proteins. The resulting chemical shifts have been analysed to determine the best way to fit the data, and it is concluded that a simultaneous fitting of all raw shift data to a single dissociation constant is both the most accurate and the most precise method. It is shown that the optimal weighting of 15N chemical shifts to 1H chemical shifts is protein dependent, but is around the consensus value of 0.14. We show that chemical shift changes of individual residues can be fit to give residue-specific affinities. Residues with affinities significantly stronger than average are found in close contact with the ligand and are suggested to form a rigid contact surface, but only when the binding involves little conformational change. This observation may be of value in analysing binding and conformational change.



Source: Journal of Biomolecular NMR
0 Replies | 27 Views
[ASAP] Unraveling the Capacitive Charge Storage Mechanism of Nitrogen-Doped Porous Carbons by EQCM and ssNMR
Aug 04, 2022 - 1:03 AM - by nmrlearner
nmrlearner's Avatar [ASAP] Unraveling the Capacitive Charge Storage Mechanism of Nitrogen-Doped Porous Carbons by EQCM and ssNMR

En Zhang, Yih-Chyng Wu, Hui Shao, Vytautas Klimavicius, Hanyue Zhang, Pierre-Louis Taberna, Julia Grothe, Gerd Buntkowsky, Fei Xu, Patrice Simon, and Stefan Kaskel



Journal of the American Chemical Society
DOI: 10.1021/jacs.2c04841



Source: Journal of the American Chemical Society
0 Replies | 24 Views
Mechanism of bacterial toxins in deadly attacks: Cryo-EM and protein NMR 3D snapshots reveal sophisticated mechanism of action of a bacterial Tc toxin - Science Daily
Aug 04, 2022 - 1:03 AM - by nmrlearner
nmrlearner's Avatar Mechanism of bacterial toxins in deadly attacks: Cryo-EM and protein NMR 3D snapshots reveal sophisticated mechanism of action of a bacterial Tc toxin - Science Daily

Mechanism of bacterial toxins in deadly attacks: Cryo-EM and protein NMR 3D snapshots reveal sophisticated mechanism of action of a bacterial Tc toxin Science Daily Read here
0 Replies | 9 Views
Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy | Proceedings of the National Academy of Sciences - pnas.org
Aug 04, 2022 - 1:03 AM - by nmrlearner
nmrlearner's Avatar Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy | Proceedings of the National Academy of Sciences - pnas.org

Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy | Proceedings of the National Academy of Sciences pnas.org Read here
0 Replies | 11 Views
DeepMind Uncovers Structure of 200 Million Proteins in Scientific Leap Forward - Slashdot
Jul 30, 2022 - 7:25 AM - by nmrlearner
nmrlearner's Avatar DeepMind Uncovers Structure of 200 Million Proteins in Scientific Leap Forward - Slashdot

DeepMind Uncovers Structure of 200 Million Proteins in Scientific Leap Forward Slashdot Read here
0 Replies | 17 Views
[NMR paper] Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus FoF1-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure
Jul 30, 2022 - 7:25 AM - by nmrlearner
nmrlearner's Avatar Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus FoF1-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure

Proton translocation through the membrane-embedded F(o) component of F-type ATP synthase (F(o)F(1)) is facilitated by the rotation of the F(o) c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) structures of F(o)F(1) suggest a unique proton translocation mechanism. To elucidate it based on the chemical conformation of the essential acidic residues of the c-ring in F(o)F(1), we determined the structure of the isolated thermophilic...

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0 Replies | 24 Views
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