title: Comparative modeling and molecular dynamics suggest high carboxylase activity of the Cyanobium sp. CACIAM14 RbcL protein.
abstract: Rubisco catalyzes the first step reaction in the carbon fixation pathway, bonding atmospheric CO2/O2 to ribulose 1,5-bisphosphate; it is therefore considered one of the most important enzymes in the biosphere. Genetic modifications to increase the carboxylase activity of rubisco are a subject of great interest to agronomy and biotechnology, since this could increase the productivity of biomass in plants, algae and cyanobacteria and give better yields in crops and biofuel production. Thus, the aim of this study was to characterize in silico the catalytic domain of the rubisco large subunit (rbcL gene) of Cyanobium sp. CACIAM14, and identify target sites to improve enzyme affinity for ribulose 1,5-bisphosphate. A three-dimensional model was built using MODELLER 9.14, molecular dynamics was used to generate a 100 ns trajectory by AMBER12, and the binding free energy was calculated using MM-PBSA, MM-GBSA and SIE methods with alanine scanning. The model obtained showed characteristics of form-I rubisco, with 15 beta sheets and 19 alpha helices, and maintained the highly conserved catalytic site encompassing residues Lys175, Lys177, Lys201, Asp203, and Glu204. The binding free energy of the enzyme-substrate complexation of Cyanobium sp. CACIAM14 showed values around -10 kcal mol(-1) using the SIE method. The most important residues for the interaction with ribulose 1,5-bisphosphate were Arg295 followed by Lys334. The generated model was successfully validated, remaining stable during the whole simulation, and demonstrated characteristics of enzymes with high carboxylase activity. The binding analysis revealed candidates for directed mutagenesis sites to improve rubisco's affinity.
authors.affiliation: Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. andrei.siqueira@icb.ufpa.br.
authors.forename: Andrei Santos
authors.initials: AS
authors.lastname: Siqueira
authors.affiliation: Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Alex Ranieri Jerônimo
authors.initials: AR
authors.lastname: Lima
authors.affiliation: Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Leonardo Teixeira
authors.initials: LT
authors.lastname: Dall'Agnol
authors.affiliation: Universidade Federal Rural da Amazônia, Capanema, PA, Brazil.
authors.forename: Juliana Simão Nina
authors.initials: JS
authors.lastname: de Azevedo
authors.affiliation: Centro de Inovações Tecnológicas, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
authors.forename: João Lídio
authors.initials: JL
authors.lastname: da Silva Gonçalves Vianez
authors.affiliation: Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ecostag@ufpa.br.
authors.forename: Evonnildo Costa
authors.initials: EC
authors.lastname: Gonçalves
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D020134:Catalytic Domain; D000458:Cyanobacteria / Q000201:enzymology*; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D012273:Ribulose-Bisphosphate Carboxylase
keywords: Comparative modeling; Cyanobacteria; Molecular dynamics; Rubisco; rbcL