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Comparative modeling and molecular dynamics suggest high carboxylase activity of the Cyanobium sp. CACIAM14 RbcL protein

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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.

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Acknowledgments

We would like to thank the Universidade Federal do Pará (Federal University of Para) for providing the computer systems, including the software licences needed to carry out this investigation; the Center for Technological Innovation for technical support and development of scripts; and the Fundação Amazônia de Amparo a Estudos e Pesquisas do Pará (FAPESPA) for financially supporting the project (process ICAAF 099/2014).

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Authors and Affiliations

  1. Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil

    Andrei Santos Siqueira, Alex Ranieri Jerônimo Lima, Leonardo Teixeira Dall’Agnol & Evonnildo Costa Gonçalves

  2. Universidade Federal Rural da Amazônia, Capanema, PA, Brazil

    Juliana Simão Nina de Azevedo

  3. Centro de Inovações Tecnológicas, Instituto Evandro Chagas, Ananindeua, PA, Brazil

    João Lídio da Silva Gonçalves Vianez Jr

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  1. Andrei Santos Siqueira
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  2. Alex Ranieri Jerônimo Lima
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  3. Leonardo Teixeira Dall’Agnol
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  4. Juliana Simão Nina de Azevedo
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  5. João Lídio da Silva Gonçalves Vianez Jr
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  6. Evonnildo Costa Gonçalves
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Correspondence to Andrei Santos Siqueira or Evonnildo Costa Gonçalves.

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Siqueira, A.S., Lima, A.R.J., Dall’Agnol, L.T. et al. Comparative modeling and molecular dynamics suggest high carboxylase activity of the Cyanobium sp. CACIAM14 RbcL protein. J Mol Model 22, 68 (2016). https://doi.org/10.1007/s00894-016-2943-y

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  • DOI: https://doi.org/10.1007/s00894-016-2943-y

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