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.
[NMR paper] Structural model of the human BTG2-PABPC1 complex by combining mutagenesis, NMR chemical shift perturbation data and molecular docking
Structural model of the human BTG2-PABPC1 complex by combining mutagenesis, NMR chemical shift perturbation data and molecular docking
Degradation of cytoplasmic mRNA in eukaryotes involves the shortening and removal of the mRNA poly(A) tail by poly(A)-selective ribonuclease (deadenylase) enzymes. In human cells, BTG2 can stimulate deadenylation of poly(A) bound by cytoplasmic poly(A)-binding protein PABPC1. This involves the concurrent binding by BTG2 of PABPC1 and the Caf1/CNOT7 nuclease subunit of the Ccr4-Not deadenylase complex. To understand in molecular detail how PABPC1 and BTG2...
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06-01-2022 11:03 AM
[NMR paper] Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification
Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification
Publication date: Available online 19 September 2017
Source:Journal of Magnetic Resonance</br>
Author(s): Yuwei Ge, Ivan Hung, Xiaoli Liu, Maili Liu, Zhehong Gan, Conggang Li</br>
Measuring 1H chemical shift anisotropy (CSA) is useful for probing proton environments and dynamics but remains a challenge due to strong homonuclear interaction and relatively small shift anisotropy, especially in proteins with multiple proton sites. Here the extended...
Using Chemical Shift Perturbation to Characterise Ligand Binding
Using Chemical Shift Perturbation to Characterise Ligand Binding
Available online 21 March 2013
Publication year: 2013
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
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Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during...
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03-21-2013 02:58 PM
[NMR paper] NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding
NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol.
Related Articles NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol.
Chembiochem. 2003 Sep 5;4(9):870-7
Authors: Dehner A, Furrer J, Richter K, Schuster I, Buchner J, Kessler H
Hsp90 is one of the most abundant chaperone proteins in the cytosol. In an ATP-dependent manner it plays an essential role in the folding and activation of a...
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11-24-2010 09:16 PM
[NMRwiki tweet] nmrwiki: How to "calculate" #nmr chemical shift perturbation using 13C and proton shi
nmrwiki: How to "calculate" #nmr chemical shift perturbation using 13C and proton shifts?http://qa.nmrwiki.org/question/181/
nmrwiki: How to "calculate" #nmr chemical shift perturbation using 13C and proton shifts?http://qa.nmrwiki.org/question/181/
Source: NMRWiki tweets
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10-05-2010 02:04 AM
[NMR paper] NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from t
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
Protein Sci. 1997 Sep;6(9):1835-48
...
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08-22-2010 05:08 PM
Measurement of signs of chemical shift differences between ground and excited protein
Abstract Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond exchange processes between a major, populated ground state and one or more minor, low populated and often invisible â??excitedâ?? conformers. Analysis of CPMG data-sets also provides the magnitudes of the chemical shift difference(s) between exchanging states (|Î?Ď?|), that inform on the structural properties of the excited state(s). The sign of Î?Ď? is, however, not available from CPMG data. Here we present...
The measurement of binding affinities by NMR chemical shift perturbation
Linear Mode
