title: Structural Studies of Trypanosoma brucei RNA Editing Ligases and Their Binding Partner Proteins.
abstract: To study the mechanism of ligating nicked RNA strands, we conducted molecular dynamics simulations of Trypanosoma brucei RNA editing ligases L1 and L2 complexed with double-stranded RNA (dsRNA) fragments. In each resulting model, a Mg(2+) ion coordinates the 5'-PO4 of the nicked nucleotide and the 3'-OH of the terminal nucleotide for a nucleophilic reaction consistent with the postulated step 3 chemistry of the ligation mechanism. Moreover, coordination of the 3'-OH to the Mg(2+) ion may lower its pKa, thereby rendering it a more effective nucleophile as an oxyanion. Thus, Mg(2+) may play a twofold role: bringing the reactants into the proximity of each other and activating the nucleophile. We also conducted solvated interaction energy calculations to explore whether ligation specificities can be correlated to ligase-dsRNA binding affinity changes. The calculated dsRNA binding affinities are stronger for both L1 and L2 when the terminal nucleotide is changed from cytosine to guanine, in line with their experimentally measured ligation specificities. Because the ligation mechanism is also influenced by interactions of the ligase with partner proteins from the editosome subcomplex, we also modeled the structure of the RNA-bound L2 in complex with the oligonucleotide binding (OB) domain of largest editosome interacting protein A1. The resulting L2-dsRNA-A1 model, which is consistent with mutagenesis and binding data recorded to date, provides the first atomic-level glimpse of plausible interactions around the RNA ligation site in the presence of an OB domain presented in-trans to a nucleic acid ligase.
authors.affiliation: Institute of Parasitology, McGill University , 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9 Quebec, Canada.|McGill Centre for Bioinformatics, McGill University , Bellini Building, 3649 Promenade Sir William Osler, Montreal, H3G 0B1 Quebec, Canada.
authors.forename: Alireza
authors.initials: A
authors.lastname: Shaneh
authors.affiliation: Human Health Therapeutics, National Research Council Canada , 6100 Royalmount Avenue, Montreal, H4P 2R2 Quebec, Canada.|Department of Biochemistry, McGill University , McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, H3G 1Y6 Quebec, Canada.|McGill Centre for Bioinformatics, McGill University , Bellini Building, 3649 Promenade Sir William Osler, Montreal, H3G 0B1 Quebec, Canada.
authors.forename: Enrico O
authors.initials: EO
authors.lastname: Purisima
authors.affiliation: Institute of Parasitology, McGill University , 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9 Quebec, Canada.|Department of Biochemistry, McGill University , McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, H3G 1Y6 Quebec, Canada.|McGill Centre for Bioinformatics, McGill University , Bellini Building, 3649 Promenade Sir William Osler, Montreal, H3G 0B1 Quebec, Canada.
authors.forename: Reza
authors.initials: R
authors.lastname: Salavati
authors.affiliation: Institute of Parasitology, McGill University , 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, H9X 3V9 Quebec, Canada.|Human Health Therapeutics, National Research Council Canada , 6100 Royalmount Avenue, Montreal, H4P 2R2 Quebec, Canada.
authors.forename: Traian
authors.initials: T
authors.lastname: Sulea
mesh_terms: D006801:Humans; D008025:Ligases / Q000737:chemistry / Q000378:metabolism*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D060066:Protein Interaction Maps; D015800:Protozoan Proteins / Q000737:chemistry / Q000378:metabolism*; D017393:RNA Editing; D016053:RNA, Protozoan / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics; D014346:Trypanosoma brucei brucei / Q000737:chemistry / Q000378:metabolism*; D014353:Trypanosomiasis, African / Q000469:parasitology
chemical_list: D015800:Protozoan Proteins; D016053:RNA, Protozoan; D008025:Ligases