Related ArticlesCatalytic 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, Katahira M
Abstract
APOBEC3G (A3G) is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC) hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC hotspots scattered through minus DNA strands, reverse-transcribed from genomic RNA. Previously, we developed a real-time NMR method and elucidated the origin of the 3'->5' polarity of deamination of DNA by the C-terminal domain of A3G (CD2), which is a phenomenon by which a hotspot located closer to the 5'-end is deaminated more effectively than one less close to the 5'-end, through quantitative analysis involving nonspecific binding to and sliding along DNA. In the present study we applied the real-time NMR method to analyze the catalytic activity of CD2 toward DNA oligonucleotides containing a nucleotide analog at a single or multiple positions. Analyses revealed the importance of the sugar and base moieties throughout the consecutive 5 nucleotides, the CCC hotspot being positioned at the center. It was also shown that the sugar or base moieties of the nucleotides outside this 5 nucleotide recognition sequence are also relevant as to CD2's activity. Analyses involving DNA oligonucleotides having two CCC hotspots linked by a long sequence of either deoxyribonucleotides, ribonucleotides or abasic deoxyribonucleotides suggested that the phosphate backbone is required for CD2 to slide along the DNA strand and to exert the 3'->5' polarity. Examination of the effects of different salt concentrations on the 3'->5' polarity indicated that the higher the salt concentration, the less prominent the 3'->5' polarity. This is most likely the result of alleviation of sliding due to a decrease in the affinity of CD2 with the phosphate backbone at high salt concentrations. We also investigated the reactivity of substrates containing 5-methylcytidine (5mC) or 5-hydroxymethylcytidine, and found that A3G exhibited low activity toward 5mC.
PhD scholarship in Development of DNP-NMR Methods for the Real-Time Investigation of Catalytic Reaction Mechanisms
From The DNP-NMR Blog:
PhD scholarship in Development of DNP-NMR Methods for the Real-Time Investigation of Catalytic Reaction Mechanisms
A 3-year PhD scholarship is available from the 1 September 2015 or as soon as possible thereafter at Department of Chemistry at Technical University of Denmark and DTU Electro.
The project is funded as a part of the Danish National Research Foundation Center of Excellence Center for Hyperpolarized Magnetic Resonance:http://www.dnp.dtu.dk/
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07-14-2015 02:59 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
...
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
Proteins. 2011 Oct;79(10):2988-91
Authors: Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT
Abstract
Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri,...
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09-10-2011 06:51 PM
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy
Abstract It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all detectable species. The analysis was carried out using experimental data obtained during aggregation of the 10.4 kDa Crh protein, which has been shown to involve a partially unfolded intermediate...
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01-27-2011 04:31 AM
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy.
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy.
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy.
J Biomol NMR. 2011 Jan 21;
Authors: Etzkorn M, Böckmann A, Baldus M
It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all...