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

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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.

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References

  1. Shrivastava A, Khan AA, Khurshid M, Kalam MA, Jain SK, Singhal PK (2017) Recent developments in asparaginase discovery and its potential as anticancer agent. Critic Rev Oncol/Hematol 100:1–10

    Google Scholar 

  2. Ln R, Doble M, Rekha VPB, Pulicherla KK (2011) In silico engineering of L-asparaginase to have reduced glutaminase side activity for effective treatment of acute lymphoblastic leukemia. J Pediat Hematol/Oncol 33(8):617–621

  3. Mohan Kumar NS, Shimray CA, Indrani D, Manonmani HK (2014) Reduction of acrylamide formation in sweet bread with l-asparaginase treatment. Food Bioprocess Technol 7(3):741–748

  4. Borek D, Jaskólski M (2001) Sequence analysis of enzymes with asparaginase activity. Acta Biochim Pol 48(4):893–902

  5. Michalska K, Jaskolski M (2006) Structural aspects of L-asparaginases, their friends and relations. Acta Biochim Pol 53(4):627–640

  6. Campbell HA, Mashburn LT, Boyse EA, Old LJ (1967) Two L-asparaginases from Escherichia coli B. Their separation, purification, and antitumor activity. Biochemistry 6(3):721–730

  7. Van Kerckhoven SH, de la Torre FN, Cañas RA, Avila C, Cantón FR, Cánovas FM (2017) Characterization of three L-asparaginases from maritime pine (Pinus pinaster Ait.). Front Plant Sci 8:1075

  8. Bruneau L, Chapman R, Marsolais F (2006) Co-occurrence of both l-asparaginase subtypes in Arabidopsis: At3g16150 encodes a K+-dependent l-asparaginase. Planta 224(3):668–679

  9. Credali A, Díaz-Quintana A, García-Calderón M, De la Rosa MA, Márquez AJ, Vega JM (2011) Structural analysis of K+ dependence in l-asparaginases from Lotus japonicus. Planta 234(1):109–122

  10. Krishnapura PR, Belur PD, Subramanya S (2016) A critical review on properties and applications of microbial l-asparaginases. Crit Rev Microbiol 42(5):720–737

  11. Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, Meyer F, Olsen G, Olson R, Osterman A, Overbeek R, McNeil L, Paarmann D, Paczian T, Parrello B, Pusch G, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9(1):75

  12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

  13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235–242

  14. Michalska K, Brzezinski K, Jaskolski M (2005) Crystal structure of isoaspartyl aminopeptidase in complex with l-aspartate. J Biol Chem 280(31):28484–28491

  15. Gouet P, Courcelle E, Stuart DI, Métoz F (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15(4):305–308

    Article  CAS  Google Scholar 

  16. Michalska K, Hernandez-Santoyo A, Jaskolski M (2008) The mechanism of autocatalytic activation of plant-type L-asparaginases. J Biol Chem 283(19):13388–13397

  17. Šali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815

  18. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen M-Y, Pieper U, Sali A (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Ch5:Unit5.6

  19. Martí Renom M, Stuart A, Fiser A, Sánchez R, Melo F, Šali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29(1):291–325

  20. Hintze BJ, Lewis SM, Richardson JS, Richardson DC (2016) Molprobity's ultimate rotamer-library distributions for model validation. Proteins 84(9):1177–1189

  21. Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404

  22. Engh RA, Huber R (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 47(4):392–400

  23. Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W (2008) PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res 36 (Suppl 2):W270–W275

  24. Larsen RA, Knox TM, Miller CG (2001) Aspartic peptide hydrolases in Salmonella enterica serovar Typhimurium. J Bacteriol 183(10):3089–3097

  25. Bolton E, Wang Y, Thiessen P, Bryant S (2008) Chapter 12—PubChem: integrated platform of small molecules and biological activities. Annu Rep Comput Chem 4:217–240

  26. Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49(11):3315–3321

  27. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688

  28. Martí-Renom MASA, Fiser A, Sánchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys 29:291–302

  29. Field MJ, Albe M, Bret C, Proust-De Martin F, Thomas A (2000) The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. J Comput Chem 21(12):1088–1100

  30. Price DJ, Brooks CL (2004) A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys 121(20):10096–10103

  31. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 10(5):449–461

  32. Xu L, Sun H, Li Y, Wang J, Hou T (2013) Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. J Phys Chem B 117(28):8408–8421

  33. Chance MR, Bresnick AR, Burley SK, Jiang J-S, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK (2002) Structural genomics: a pipeline for providing structures for the biologist. Protein Sci 11(4):723–738

  34. Cantor JR, Stone EM, Chantranupong L, Georgiou G (2009) The human asparaginase-like protein 1 hASRGL1 is an Ntn hydrolase with β-aspartyl peptidase activity. Biochemistry 48(46):11026–11031

  35. Tasi G, Palinko I, Nyerges L, Fejes P, Foerster H (1993) Calculation of electrostatic potential maps and atomic charges for large molecules. J Chem Inf Comput Sci 33(3):296–299

  36. Tasi G, Mizukami F (1998) Analysis of permanent electric dipole moments of aliphatic hydrocarbon molecules. 2. DFT results. J Chem Inf Comput Sci 38(2):313–316

  37. Hong D-S, Cho SG (1999) Ab initio study of chlorosilanes: dipole moments and charge distributions. J Chem Inf Comput Sci 39(3):537–542

  38. Azevedo RA, Lancien M, Lea PJ (2006) The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino Acids 30(2):143–162

    Article  CAS  Google Scholar 

  39. Hildebrandt Tatjana M, Nunes Nesi A, Araújo Wagner L, Braun H-P (2015) Amino acid catabolism in plants. Mol Plant 8(11):1563–1579

  40. Schwamborn M (1998) Chemical synthesis of polyaspartates: a biodegradable alternative to currently used polycarboxylate homo- and copolymers. Polym Degrad Stab 59:39–45

  41. Joentgen W, Groth T, Hai T, Oppermann-Sanio FB, Steinbu Èchel A (1998) Poster 51: Synthesis of poly-α-aspartic acid by hydrolysis of cyanophycin. In: Int Symp on Biochemical Principles and Mechanisms of Biosynthesis and Biodegradation of Polymers, University of Munster, Germany, 3–6 June 1998

  42. Sallam A, Kast A, Przybilla S, Meiswinkel T, Steinbüchel A (2009) Biotechnological process for production of β-dipeptides from cyanophycin on a technical scale and its optimization. Appl Environ Microbiol 75(1):29–38

  43. Sallam A, Steinbüchel A (2010) Dipeptides in nutrition and therapy: cyanophycin-derived dipeptides as natural alternatives and their biotechnological production. Appl Microbiol Biotechnol 87(3):815–828

  44. Yagasaki M, Hashimoto S-I (2008) Synthesis and application of dipeptides; current status and perspectives. Appl Microbiol Biotechnol 81(1):13

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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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Authors and Affiliations

  1. 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

    Ronaldo Correia da Silva, Andrei Santos Siqueira, Alex Ranieri Jerônimo Lima, Adonis de Melo Lima, Délia Cristina Figueira Aguiar & Evonnildo Costa Gonçalves

  2. Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular, Instituto de Ciências Exatas e Naturais (ICEN), Universidade Federal do Pará (UFPA), Belém, Pará, Brasil

    Alberdan Silva Santos

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  1. Ronaldo Correia da Silva
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  2. Andrei Santos Siqueira
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  3. Alex Ranieri Jerônimo Lima
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Correspondence to Ronaldo Correia da Silva.

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da Silva, R.C., Siqueira, A.S., Lima, A.R.J. et al. In silico characterization of a cyanobacterial plant-type isoaspartyl aminopeptidase/asparaginase. J Mol Model 24, 108 (2018). https://doi.org/10.1007/s00894-018-3635-6

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