da Silva Ronaldo Correia, Siqueira Andrei Santos, Lima Alex Ranieri Jerônimo, de Melo Lima Adonis, Santos Alberdan Silva, Aguiar Délia Cristina Figueira, Gonçalves Evonnildo Costa
Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Rua Augusto Correa, 01, CEP 66075-110, Guamá, Belém, Pará, Brasil.
Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular, Instituto de Ciências Exatas e Naturais (ICEN), Universidade Federal do Pará (UFPA), Belém, Pará, Brasil.
J Mol Model. 2018 Apr 4;24(5):108. doi: 10.1007/s00894-018-3635-6.
Asparaginases are found in a range of organisms, although those found in cyanobacteria have been little studied, in spite of their great potential for biotechnological application. This study therefore sought to characterize the molecular structure of an L-asparaginase from the cyanobacterium Limnothrix sp. CACIAM 69d, which was isolated from a freshwater Amazonian environment. After homology modeling, model validation was performed using a Ramachandran plot, VERIFY3D, and the RMSD. We also performed molecular docking and dynamics simulations based on binding free-energy analysis. Structural alignment revealed homology with the isoaspartyl peptidase/asparaginase (EcAIII) from Escherichia coli. When compared to the template, our model showed full conservation of the catalytic site. In silico simulations confirmed the interaction of cyanobacterial isoaspartyl peptidase/asparaginase with its substrate, β-Asp-Leu dipeptide. We also observed that the residues Thr154, Thr187, Gly207, Asp218, and Gly237 were fundamental to protein-ligand complexation. Overall, our results suggest that L-asparaginase from Limnothrix sp. CACIAM 669d has similar properties to E. coli EcAIII asparaginase. Our study opens up new perspectives for the biotechnological exploitation of cyanobacterial asparaginases.
天冬酰胺酶存在于多种生物体中，尽管蓝细菌中的天冬酰胺酶尽管具有巨大的生物技术应用潜力，但对其研究甚少。因此，本研究旨在表征从淡水亚马逊环境中分离出的蓝细菌Limnothrix sp. CACIAM 69d的L-天冬酰胺酶的分子结构。在进行同源建模后，使用拉氏图、VERIFY3D和均方根偏差（RMSD）进行模型验证。我们还基于结合自由能分析进行了分子对接和动力学模拟。结构比对显示与大肠杆菌的异天冬氨酰肽酶/天冬酰胺酶（EcAIII）具有同源性。与模板相比，我们的模型显示催化位点完全保守。计算机模拟证实了蓝细菌异天冬氨酰肽酶/天冬酰胺酶与其底物β-天冬氨酰-亮氨酸二肽的相互作用。我们还观察到，苏氨酸154、苏氨酸187、甘氨酸207、天冬氨酸218和甘氨酸237残基对蛋白质-配体络合至关重要。总体而言，我们的结果表明Limnothrix sp. CACIAM 669d的L-天冬酰胺酶具有与大肠杆菌EcAIII天冬酰胺酶相似的特性。我们的研究为蓝细菌天冬酰胺酶的生物技术开发开辟了新的前景。
