title: Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA.
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.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Mickiewicz
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland. Electronic address: joanna.sarzynska@ibch.poznan.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Sarzyńska
authors.affiliation: Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Maciej
authors.initials: M
authors.lastname: Miłostan
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Kurzyńska-Kokorniak
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Rybarczyk
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Łukasiak
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
authors.forename: Tadeusz
authors.initials: T
authors.lastname: Kuliński
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Figlerowicz
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznań, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Błażewicz
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism*; D020134:Catalytic Domain; D008958:Models, Molecular; D011487:Protein Conformation; D012330:RNA, Double-Stranded / Q000378:metabolism*; D018749:RNA, Plant / Q000378:metabolism*; D043244:Ribonuclease III / Q000737:chemistry / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid
chemical_list: D012330:RNA, Double-Stranded; D018749:RNA, Plant; C504982:DCL4 protein, Arabidopsis; D043244:Ribonuclease III
keywords: Dicer-like proteins; Homology modeling; PAZ; RNAi; RNase III; siRNA; siRNA biogenesis