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In silico characterization of a cyanobacterial plant-type isoaspartyl aminopeptidase/asparaginase

  • Ronaldo Correia da Silva
  • Andrei Santos Siqueira
  • Alex Ranieri Jerônimo Lima
  • Adonis de Melo Lima
  • Alberdan Silva Santos
  • Délia Cristina Figueira Aguiar
  • Evonnildo Costa Gonçalves
Original Paper
  • 167 Downloads

Abstract

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.

Keywords

Comparative modeling Molecular dynamics Cyanobacteria Limnothrix Asparaginase 

Notes

Acknowledgements

We acknowledge the financial support provided by the Fundação Amazônia de Amparo a Estudos e Pesquisas do Pará (FAPESPA): ICAAF 099/2014. The Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) also supported one of the authors (ECG) through grant 311686/2015-0.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Ronaldo Correia da Silva
    • 1
  • Andrei Santos Siqueira
    • 1
  • Alex Ranieri Jerônimo Lima
    • 1
  • Adonis de Melo Lima
    • 1
  • Alberdan Silva Santos
    • 2
  • Délia Cristina Figueira Aguiar
    • 1
  • Evonnildo Costa Gonçalves
    • 1
  1. 1.Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas (ICB)Universidade Federal do Pará (UFPA)BelémBrasil
  2. 2.Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular, Instituto de Ciências Exatas e Naturais (ICEN)Universidade Federal do Pará (UFPA)BelémBrasil

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