Siqueira Andrei Santos, Lima Alex Ranieri Jerônimo, Dall'Agnol Leonardo Teixeira, de Azevedo Juliana Simão Nina, da Silva Gonçalves Vianez João Lídio, Gonçalves Evonnildo Costa
Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
Universidade Federal Rural da Amazônia, Capanema, PA, Brazil.
J Mol Model. 2016 Mar;22(3):68. doi: 10.1007/s00894-016-2943-y. Epub 2016 Mar 2.
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.
核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco）催化碳固定途径中的第一步反应，将大气中的二氧化碳/氧气与1,5-二磷酸核酮糖结合；因此，它被认为是生物圈中最重要的酶之一。通过基因改造提高Rubisco的羧化酶活性是农学和生物技术领域非常感兴趣的课题，因为这可以提高植物、藻类和蓝细菌中生物质的生产力，并在作物和生物燃料生产中获得更高的产量。因此，本研究的目的是在计算机上对蓝细菌CACIAM14的Rubisco大亚基（rbcL基因）的催化结构域进行表征，并确定提高酶对1,5-二磷酸核酮糖亲和力的靶点。使用MODELLER 9.14构建三维模型，通过AMBER12进行分子动力学模拟生成100 ns的轨迹，并使用MM-PBSA、MM-GBSA和SIE方法结合丙氨酸扫描计算结合自由能。所得模型显示出I型Rubisco的特征，有15个β折叠和19个α螺旋，并保留了包含Lys175、Lys177、Lys201、Asp203和Glu204残基的高度保守催化位点。使用SIE方法时，蓝细菌CACIAM14的酶-底物复合物的结合自由能显示在-10 kcal mol(-1)左右。与1,5-二磷酸核酮糖相互作用最重要的残基是Arg295，其次是Lys334。生成的模型成功得到验证，在整个模拟过程中保持稳定，并显示出具有高羧化酶活性的酶的特征。结合分析揭示了用于定向诱变位点的候选物，以提高Rubisco的亲和力。
