Related ArticlesResidual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR.
Biophys J. 2020 Oct 14;:
Authors: Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K
Abstract
The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded human ubiquitin in 6*M guanidinium chloride. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to perform a quick medium exchange from 6*M guanidinium chloride to a quenching DMSO solution. Based on the backbone resonance assignment of ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 60 identified peptide amide groups in the ubiquitin sequence. Although a majority of these amide groups were not protected, certain amide groups involved in a middle helix (residues 23-34) and an N-terminal ?-hairpin (residues 2-16) were significantly protected with a protection factor of 2.1-4.2, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were more than 52% hydrogen bonded in the residual structures. We show that the hydrogen-bonded residual structures in the ?-helix and the ?-hairpin are formed even in 6*M guanidinium chloride, suggesting that these residual structures may function as a folding initiation site to guide the subsequent folding reactions of ubiquitin.
PMID: 33142107 [PubMed - as supplied by publisher]
[NMR paper] Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph.
Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--journals.plos.org-plosone-resource-img-external-pone_120x30.png http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph.
PLoS One. 2017;12(3):e0172862
Authors: Wälti MA, Orts J, Riek R
Abstract
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08-25-2017 04:11 AM
[NMR paper] Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange.
Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange.
Related Articles Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange.
Molecules. 2017 Aug 16;22(8):
Authors: Chien CH, Ho MR, Lin CH, Hsu SD
Abstract
Galectins are ?-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their...
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08-17-2017 01:01 PM
[NMR paper] Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.
Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkout.jstage.jst.go.jp-logo.gif Related Articles Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.
Proc Jpn Acad Ser B Phys Biol Sci. 2017;93(1):10-27
Authors: Nishimura C
Abstract
The structures of apomyoglobin folding intermediates have...
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01-14-2017 06:24 AM
[NMR paper] Partially unfolded forms of the prion protein populated under misfolding-promoting conditions: characterization by hydrogen exchange mass spectrometry and NMR.
Partially unfolded forms of the prion protein populated under misfolding-promoting conditions: characterization by hydrogen exchange mass spectrometry and NMR.
Partially unfolded forms of the prion protein populated under misfolding-promoting conditions: characterization by hydrogen exchange mass spectrometry and NMR.
J Biol Chem. 2015 Aug 25;
Authors: Moulick R, Das R, Udgaonkar JB
Abstract
The susceptibility of the cellular prion protein (PrP(C)) to convert to an alternative misfolded conformation (PrP(Sc)), which is the key...
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08-26-2015 10:21 AM
[NMR paper] [Interactions between proteins and cation exchange adsorbents analyzed by NMR and hydrogen/deuterium exchange technique].
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Sheng Wu Gong Cheng Xue Bao. 2014 Sep;30(9):1454-63
Authors: Wang K, Hao D, Qi S, Ma G
Abstract
In silico acquirement of the accurate residue details of protein on chromatographic media is a bottleneck in protein chromatography separation and purification. Here we developed a novel approach by coupling with H/D exchange and nuclear magnetic resonance to observe hen egg white lysozyme (HEWL) unfolding behavior adsorbed on cation exchange media (SP Sepharose FF). Analysis of 1D 1H-NMR shows that protein unfolding accelerated...
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03-01-2015 12:18 PM
[NMR paper] NMR-Based Detection of Hydrogen/Deuterium Exchange in Liposome-Embedded Membrane Proteins.
NMR-Based Detection of Hydrogen/Deuterium Exchange in Liposome-Embedded Membrane Proteins.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png Related Articles NMR-Based Detection of Hydrogen/Deuterium Exchange in Liposome-Embedded Membrane Proteins.
PLoS One. 2014;9(11):e112374
Authors: Yao X, Dürr UH, Gattin Z, Laukat Y, Narayanan RL, Brückner AK, Meisinger C, Lange A, Becker S, Zweckstetter M
Abstract
Membrane proteins play key roles in biology. Determination of...
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11-08-2014 12:08 AM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
Related Articles Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
J Biomol NMR. 2010 Oct 20;
Authors: Del Amo JM, Fink U, Reif B
We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that...
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[NMR paper] Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR.
Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR.
J Mol Biol. 1995 Nov 3;253(4):576-89
Authors: Finucane MD, Jardetzky O
Amide proton exchange rates have been measured for fast-exchanging amides in trp aporepressor, and compared with the rates measured in the holorepressor. The results indicate that the presence...