title: dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.
abstract: Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex.
authors.affiliation: Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Ocampo y Esmeralda, Predio CCT, 2000 Rosario, Argentina; Área Física, Departamento de Químico-Física, Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Santa Fe, Argentina.
authors.forename: Salvador I
authors.initials: SI
authors.lastname: Drusin
authors.affiliation: Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Ocampo y Esmeralda, Predio CCT, 2000 Rosario, Argentina.
authors.forename: Irina P
authors.initials: IP
authors.lastname: Suarez
authors.affiliation: Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Ocampo y Esmeralda, Predio CCT, 2000 Rosario, Argentina.
authors.forename: Diego F
authors.initials: DF
authors.lastname: Gauto
authors.affiliation: Instituto de Biología Molecular y Celular de Rosario (CONICET-UNR), Ocampo y Esmeralda, Predio CCT, 2000 Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Santa Fe, Argentina.
authors.forename: Rodolfo M
authors.initials: RM
authors.lastname: Rasia
authors.affiliation: Instituto de Química de Rosario (CONICET-UNR), Suipacha 570, S2002LRK Rosario, Santa Fe, Argentina; Área Inorgánica, Departamento de Químico-Física, Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Santa Fe, Argentina. Electronic address: moreno@iquir-conicet.gov.ar.
authors.forename: Diego M
authors.initials: DM
authors.lastname: Moreno
mesh_terms: D017360:Arabidopsis / Q000201:enzymology*; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000737:chemistry* / Q000378:metabolism; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D043244:Ribonuclease III / Q000737:chemistry* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D018797:Cell Cycle Proteins; D035683:MicroRNAs; D012330:RNA, Double-Stranded; D018749:RNA, Plant; C402383:DCL1 protein, Arabidopsis; D043244:Ribonuclease III
keywords: Binding free energy; Mismatch base pair; Molecular dynamics; dsRBD; dsRNA recognition; miRNA processing