PMID- 27907832 OWN - NLM STAT- MEDLINE DCOM- 20171109 LR - 20171109 IS - 1476-928X (Electronic) IS - 1476-9271 (Linking) VI - 66 DP - 2017 Feb TI - Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. PG - 44-56 LID - S1476-9271(16)30337-1 [pii] LID - 10.1016/j.compbiolchem.2016.11.003 [doi] AB - 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. CI - Copyright (c) 2016 Elsevier Ltd. All rights reserved. FAU - Mickiewicz, Agnieszka AU - Mickiewicz A AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. FAU - Sarzynska, Joanna AU - Sarzynska J AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. Electronic address: joanna.sarzynska@ibch.poznan.pl. FAU - Milostan, Maciej AU - Milostan M AD - Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. FAU - Kurzynska-Kokorniak, Anna AU - Kurzynska-Kokorniak A AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland. FAU - Rybarczyk, Agnieszka AU - Rybarczyk A AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. FAU - Lukasiak, Piotr AU - Lukasiak P AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. FAU - Kulinski, Tadeusz AU - Kulinski T AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland. FAU - Figlerowicz, Marek AU - Figlerowicz M AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. FAU - Blazewicz, Jacek AU - Blazewicz J AD - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland. LA - eng PT - Journal Article DEP - 20161117 PL - England TA - Comput Biol Chem JT - Computational biology and chemistry JID - 101157394 RN - 0 (RNA, Double-Stranded) RN - 0 (RNA, Plant) RN - EC 3.1.- (DCL4 protein, Arabidopsis) RN - EC 3.1.26.3 (Ribonuclease III) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/*metabolism MH - Catalytic Domain MH - Models, Molecular MH - Protein Conformation MH - RNA, Double-Stranded/*metabolism MH - RNA, Plant/*metabolism MH - Ribonuclease III/chemistry/*metabolism MH - Sequence Homology, Amino Acid OTO - NOTNLM OT - Dicer-like proteins OT - Homology modeling OT - PAZ OT - RNAi OT - RNase III OT - siRNA OT - siRNA biogenesis EDAT- 2016/12/03 06:00 MHDA- 2017/11/10 06:00 CRDT- 2016/12/02 06:00 PHST- 2016/07/08 00:00 [received] PHST- 2016/10/11 00:00 [revised] PHST- 2016/11/16 00:00 [accepted] PHST- 2016/12/03 06:00 [pubmed] PHST- 2017/11/10 06:00 [medline] PHST- 2016/12/02 06:00 [entrez] AID - S1476-9271(16)30337-1 [pii] AID - 10.1016/j.compbiolchem.2016.11.003 [doi] PST - ppublish SO - Comput Biol Chem. 2017 Feb;66:44-56. doi: 10.1016/j.compbiolchem.2016.11.003. Epub 2016 Nov 17.