Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. (February 2017)
- Record Type:
- Journal Article
- Title:
- Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. (February 2017)
- Main Title:
- Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA
- Authors:
- Mickiewicz, Agnieszka
Sarzyńska, Joanna
Miłostan, Maciej
Kurzyńska-Kokorniak, Anna
Rybarczyk, Agnieszka
Łukasiak, Piotr
Kuliński, Tadeusz
Figlerowicz, Marek
Błażewicz, Jacek - Abstract:
- Graphical abstract: Highlights: Plant Dicer-like proteins have Platform domain similar to Giardia and human Dicers. Assembling of the AtDCL-dsRNA complex was performed using NMA and template-based approaches. The arrangement of the Platform and PAZ domains, rather than the length of the Connector, are responsible for the size of Dicer products. Abstract: Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA. In this work, we present models of the catalytic core of AtDCL4 and AtDCL4-dsRNA complex constructed by computational methods. We built a homology model of the catalytic core of AtDCL4 comprising Platform, PAZ, Connector helix and two RNase III domains. To assemble the AtDCL4-dsRNA complex two modeling approaches were used. In the first method, to establish conformations that allow building a consistent model of the complex, we used Normal Mode Analysis for both dsRNA and AtDCL4. The second strategy involved template-based approach for positioning of the PAZ domain andGraphical abstract: Highlights: Plant Dicer-like proteins have Platform domain similar to Giardia and human Dicers. Assembling of the AtDCL-dsRNA complex was performed using NMA and template-based approaches. The arrangement of the Platform and PAZ domains, rather than the length of the Connector, are responsible for the size of Dicer products. Abstract: Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA. In this work, we present models of the catalytic core of AtDCL4 and AtDCL4-dsRNA complex constructed by computational methods. We built a homology model of the catalytic core of AtDCL4 comprising Platform, PAZ, Connector helix and two RNase III domains. To assemble the AtDCL4-dsRNA complex two modeling approaches were used. In the first method, to establish conformations that allow building a consistent model of the complex, we used Normal Mode Analysis for both dsRNA and AtDCL4. The second strategy involved template-based approach for positioning of the PAZ domain and manual arrangement of the Connector helix. Our results suggest that the spatial orientation of the Connector helix, Platform and PAZ relative to the RNase III domains is crucial for measuring dsRNA of defined length. The modeled complexes provide information about interactions that may contribute to the relative orientations of these domains and to dsRNA binding. All these information can be helpful for understanding the mechanism of AtDCL4-mediated dsRNA recognition and binding, to produce small RNA of specific size. … (more)
- Is Part Of:
- Computational biology and chemistry. Volume 66(2017)
- Journal:
- Computational biology and chemistry
- Issue:
- Volume 66(2017)
- Issue Display:
- Volume 66, Issue 2017 (2017)
- Year:
- 2017
- Volume:
- 66
- Issue:
- 2017
- Issue Sort Value:
- 2017-0066-2017-0000
- Page Start:
- 44
- Page End:
- 56
- Publication Date:
- 2017-02
- Subjects:
- RNAi -- siRNA -- siRNA biogenesis -- Dicer-like proteins -- Homology modeling -- PAZ -- RNase III
Chemistry -- Data processing -- Periodicals
Biology -- Data processing -- Periodicals
Biochemistry -- Data processing
Biology -- Data processing
Molecular biology -- Data processing
Periodicals
Electronic journals
542.85 - Journal URLs:
- http://www.sciencedirect.com/science/journal/14769271 ↗
http://www.elsevier.com/journals ↗ - DOI:
- 10.1016/j.compbiolchem.2016.11.003 ↗
- Languages:
- English
- ISSNs:
- 1476-9271
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 3390.576700
British Library DSC - BLDSS-3PM
British Library STI - ELD Digital store - Ingest File:
- 309.xml