Hydrogen-deuterium exchange (HDX) measured by nuclear magnetic resonance (NMR) provides structural information for proteins relating to solvent accessibility and flexibility. While this structural information is beneficial, the data cannot be used exclusively to elucidate structures. However, the structural information provided by the HDX-NMR data can be supplemented by computational methods. In previous work, we developed an algorithm in Rosetta to predict structures using qualitative HDX-NMR...
[NMR paper] Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data
Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data
Amide hydrogen-deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse for full structural characterization. Experiments that measure HDX rates, such as HDX-NMR, have far higher throughput compared to structure determination via X-ray crystallography, cryo-EM, or a full suite of NMR experiments. Data from HDX-NMR experiments encode information on the protein structure, making HDX a prime candidate to be...
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03-30-2021 08:29 AM
[NMR paper] Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR.
Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR.
Related Articles Residual 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...
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11-04-2020 05:04 PM
Quantifying Protection in Disordered Proteins UsingMillisecond Hydrogen Exchange-Mass Spectrometry and Peptic ReferencePeptides
Quantifying Protection in Disordered Proteins UsingMillisecond Hydrogen Exchange-Mass Spectrometry and Peptic ReferencePeptides
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b01312/20170726/images/medium/bi-2016-013127_0005.gif
Biochemistry
DOI: 10.1021/acs.biochem.6b01312
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07-28-2017 08:34 AM
[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] [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] Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR.
Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR.
PLoS One. 2013;8(2):e56467
Authors: Alexandrescu AT
Abstract
Amylin is an endocrine hormone that...
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08-29-2013 01:53 PM
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
Abstract 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 backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15Nâ??T 1 timescales). We observed chemical exchange for 6...
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10-27-2010 08:51 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...
Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR
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