Related ArticlesObservation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B.
ACS Chem Biol. 2017 Nov 17;12(11):2704-2708
Authors: Wan L, Nagata T, Morishita R, Takaori-Kondo A, Katahira M
Abstract
Human APOBEC3B (A3B) deaminates a cytosine into a uracil in single-stranded (ss) DNA, resulting in human cancers. A3B's deamination activity is conferred by its C-terminal domain (CTD). However, little is known about the mechanism by which target sequences are searched and deaminated. Here, we applied a real-time NMR method to elucidate the deamination properties. We found that A3B CTD shows higher activity toward its target sequence in short ssDNA and efficiently deaminates a target sequence located near the center of ssDNA. These properties are quite different from those of well-studied APOBEC3G, which shows higher activity toward its target sequence in long ssDNA and one located close to the 5'-end. The unique properties of the A3B CTD can be rationally interpreted by considering that after nonspecific binding to ssDNA, A3B slides only for a relatively short distance and tends to dissociate from the ssDNA before reaching the target sequence.
[NMR paper] Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR.
Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR.
Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR.
Int J Mol Sci. 2017 Oct 28;18(11):
Authors: Iwakawa N, Morimoto D, Walinda E, Kawata Y, Shirakawa M, Sugase K
Abstract
Amyloid fibril formation is associated with numerous neurodegenerative diseases. To elucidate the mechanism of fibril formation, the thioflavin T (ThT) fluorescence assay is...
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[NMR paper] NMR Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.
NMR Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.
Related Articles NMR Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity.
Biochemistry. 2016 May 10;
Authors: Byeon IL, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM
Abstract
Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous...
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05-11-2016 08:04 PM
[NMR paper] Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination.
Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination.
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.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination.
PLoS One. 2015;10(4):e0124142
Authors: Kamba K, Nagata T,...
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04-27-2016 01:51 PM
Real-time pure shift 15 N HSQC of proteins: a real improvement in resolution and sensitivity
Real-time pure shift 15 N HSQC of proteins: a real improvement in resolution and sensitivity
Abstract
Spectral resolution in proton NMR spectroscopy is reduced by the splitting of resonances into multiplets due to the effect of homonuclear scalar couplings. Although these effects are often hidden in protein NMR spectroscopy by low digital resolution and routine apodization, behind the scenes homonuclear scalar couplings increase spectral overcrowding. The possibilities for biomolecular NMR offered by new pure shift NMR methods are illustrated here....
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03-04-2015 08:56 AM
[NMR paper] Quantitative analysis of location- and sequence-dependent deamination by APOBEC3G using real-time NMR spectroscopy.
Quantitative analysis of location- and sequence-dependent deamination by APOBEC3G using real-time NMR spectroscopy.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles Quantitative analysis of location- and sequence-dependent deamination by APOBEC3G using real-time NMR spectroscopy.
Angew Chem Int Ed Engl. 2014 Feb 24;53(9):2349-52
Authors: Furukawa A, Sugase K, Morishita R, Nagata T, Kodaki T, Takaori-Kondo A, Ryo A, Katahira M
...
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10-24-2014 07:18 PM
[NMR paper] Real-Time Monitoring of New Delhi Metallo-?-Lactamase Activity in Living Bacterial Cells by (1) H NMR Spectroscopy.
Real-Time Monitoring of New Delhi Metallo-?-Lactamase Activity in Living Bacterial Cells by (1) H NMR Spectroscopy.
Related Articles Real-Time Monitoring of New Delhi Metallo-?-Lactamase Activity in Living Bacterial Cells by (1) H NMR Spectroscopy.
Angew Chem Int Ed Engl. 2014 Jan 23;
Authors: Ma J, McLeod S, Maccormack K, Sriram S, Gao N, Breeze AL, Hu J
Abstract
Disconnections between in vitro responses and those observed in whole cells confound many attempts to design drugs in areas of serious medical need. A method based on 1D (1) H...
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01-25-2014 02:07 PM
Defining a Stem Length-Dependent Binding Mechanism for the Cocaine-Binding Aptamer. A
Defining a Stem Length-Dependent Binding Mechanism for the Cocaine-Binding Aptamer. A Combined NMR and Calorimetry Study
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100952k/aop/images/medium/bi-2010-00952k_0010.gif
Biochemistry
DOI: 10.1021/bi100952k
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09-08-2010 07:29 AM
[NMR paper] pH-dependent redox activity and fluxionality of the copper site in amicyanin from Thi
pH-dependent redox activity and fluxionality of the copper site in amicyanin from Thiobacillus yersutus as studied by 300- and 600- MHz 1H NMR.
Related Articles pH-dependent redox activity and fluxionality of the copper site in amicyanin from Thiobacillus yersutus as studied by 300- and 600- MHz 1H NMR.
J Biol Chem. 1990 Feb 15;265(5):2768-74
Authors: Lommen A, Canters GW
The kinetics of the deuteronation of one of the copper ligand histidines of the reduced Type I blue-copper protein amicyanin from Thiobacillus versutus was studied as a...