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Information


Unique identifier OMICS_03305
Name CleanEx
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Viviane Praz

Publication for CleanEx

CleanEx citations

 (15)
library_books

Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism

2017
Sci Rep
PMCID: 5537299
PMID: 28761155
DOI: 10.1038/s41598-017-07250-4

[…] and δb are chemical shifts of the nucleus in the protonated and the deprotonated states, respectively, and n is the Hill’s coefficient. To study the water accessibility of amide protons, we used the CLEANEX experiment with 20 ms mixing. Ratio of peak intensities in the CLEANEX spectrum and reference HSQC spectrum was considered as a measure of the exchange rate. To quantify the chemical shifts ch […]

library_books

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists

2017
Comput Struct Biotechnol J
PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] rogen bonds can be used as distance restraints . The rate of chemical exchange between the amide proton in the protein and protons in the solvent water can be estimated by performing H/D exchange or CLEANEX-PM experiments. It is possible that amide protons showing a significantly slow exchange rate may be involved in the formation of hydrogen bonds. At a stage of the structure calculation proces […]

library_books

Structured and disordered regions cooperatively mediate DNA binding autoinhibition of ETS factors ETV1, ETV4 and ETV5

2017
Nucleic Acids Res
PMCID: 5389675
PMID: 28161714
DOI: 10.1093/nar/gkx068

[…] lation experiments, including 15N-HSQC, HNCO, HN(CA)CO, CBCA(CO)NH and HNCACB (). Amide 1H/2H hydrogen exchange (HX), after transfer into ∼99% D2O NMR sample buffer via a Sephadex G25 spin column and CLEANEX-PM 1H/1H HX measurements were recorded using 850 MHz NMR spectrometer and analyzed as described previously (,). The two approaches detect slow (minutes-days) and fast (seconds) timescale excha […]

library_books

D19S Mutation of the Cationic, Cysteine Rich Protein PAF: Novel Insights into Its Structural Dynamics, Thermal Unfolding and Antifungal Function

2017
PLoS One
PMCID: 5224997
PMID: 28072824
DOI: 10.1371/journal.pone.0169920

[…] ts, the same instrumentation was used in the same temperature range (265-343K). Modelling of two-state thermal unfolding was carried out using in-house written MATLAB® scripts as described before []. CLEANEX NMR data were fitted against the theoretical function using an in-house written MATLAB® script to yield NH-H2O exchange rates as described []. […]

library_books

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

2016
Sci Rep
PMCID: 4919784
PMID: 27340016
DOI: 10.1038/srep28486

[…] igned manually and converted into distance restraints using CCPNmr Analysis. The program DANGLE was used to obtain ϕ and ψ dihedral angles on the basis of backbone and 13Cβ chemical shift values. The CLEANEX-PM pulse-sequence has been used to identify fast and slow exchanging backbone amides. H-Bond restraints have been used only for residues showing slow exchanging amides (not observed on the CLE […]

library_books

Structural and Biochemical Analysis of the Hordeum vulgare L. HvGR RBP1 Protein, a Glycine Rich RNA Binding Protein Involved in the Regulation of Barley Plant Development and Stress Response

2014
Biochemistry
PMCID: 4278681
PMID: 25495582
DOI: 10.1021/bi5007223

[…] le, followed by resuspension of the lyophilized protein in the same volume of 100% D2O, and acquisition of a series of 2D 1H–15N-HSQC correlation spectra at subsequent time points. Additionally, a 2D-CLEANEX-PM NMR experiment was performed to detect amide protons participating in fast chemical exchange with solvent. […]

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CleanEx institution(s)
ISREC, Swiss Institute of Bioinformatics, Epalinges, VD, Switzerland

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