Display options
Cite
Pérez-Rodríguez G, Pérez-Pérez M, Glez-Peña D, et al. Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. Biomed Res Int. 2015;2015:769471doi: 10.1155/2015/769471.
Pérez-Rodríguez, G., Pérez-Pérez, M., Glez-Peña, D., Fdez-Riverola, F., Azevedo, N. F., & Lourenço, A. (2015). Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. BioMed research international, 2015769471. https://doi.org/10.1155/2015/769471
Pérez-Rodríguez, Gael, et al. "Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework." BioMed research international vol. 2015 (2015): 769471. doi: https://doi.org/10.1155/2015/769471
Pérez-Rodríguez G, Pérez-Pérez M, Glez-Peña D, Fdez-Riverola F, Azevedo NF, Lourenço A. Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework. Biomed Res Int. 2015;2015:769471. doi: 10.1155/2015/769471. Epub 2015 Mar 22. PMID: 25874228; PMCID: PMC4385633.
Copy Download .nbib Format: NLM
Share it on

Biomed Res Int. 2015;2015:769471. doi: 10.1155/2015/769471. Epub 2015 Mar 22.

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

BioMed research international

Gael Pérez-Rodríguez, Martín Pérez-Pérez, Daniel Glez-Peña, Florentino Fdez-Riverola, Nuno F Azevedo, Anália Lourenço

Affiliations

  1. Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain.
  2. LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rúa Dr. Roberto Frias, 4200-465 Porto, Portugal.
  3. Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain ; Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.

PMID: 25874228 PMCID: PMC4385633 DOI: 10.1155/2015/769471

Abstract

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.

References

  1. Front Psychol. 2014 Jul 14;5:668 - PubMed
  2. Bioinformatics. 2012 Nov 15;28(22):2971-8 - PubMed
  3. Curr Opin Biotechnol. 2014 Dec;30:101-6 - PubMed
  4. Biomed Res Int. 2013;2013:780145 - PubMed
  5. Mol Genet Genomics. 2014 Oct;289(5):727-34 - PubMed
  6. Gene. 2013 May 25;521(1):1-14 - PubMed
  7. Nat Chem Biol. 2012 Jun;8(6):536-46 - PubMed
  8. PLoS One. 2013;8(10):e78011 - PubMed
  9. Theor Biol Med Model. 2013;10:41 - PubMed
  10. ACS Synth Biol. 2012 Nov 16;1(11):514-25 - PubMed
  11. Theor Biol Med Model. 2013;10:23 - PubMed
  12. FEBS Lett. 2013 Sep 2;587(17):2725-30 - PubMed
  13. Math Biosci. 2015 Feb;260:16-24 - PubMed
  14. Brief Bioinform. 2015 Jan;16(1):137-52 - PubMed
  15. Biotechnol J. 2013 Sep;8(9):1043-57 - PubMed
  16. Methods Mol Biol. 2013;930:399-426 - PubMed
  17. Biosystems. 2004 Aug-Oct;76(1-3):89-100 - PubMed
  18. Methods Mol Biol. 2014;1151:233-53 - PubMed
  19. Bioinformatics. 2014 Nov 1;30(21):3101-8 - PubMed
  20. PLoS One. 2014;9(4):e94411 - PubMed
  21. Adv Wound Care (New Rochelle). 2013 Nov;2(9):510-526 - PubMed
  22. Proc Natl Acad Sci U S A. 2002 May 14;99 Suppl 3:7280-7 - PubMed
  23. Bioengineered. 2014 Jul-Aug;5(4):243-53 - PubMed
  24. Front Microbiol. 2013 Apr 04;4:75 - PubMed
  25. Adv Microb Physiol. 2014;64:65-114 - PubMed
  26. Biochemistry. 2011 Oct 4;50(39):8264-9 - PubMed
  27. Integr Biol (Camb). 2011 Feb;3(2):86-96 - PubMed
  28. J R Soc Interface. 2014 Feb 6;11(91):20130505 - PubMed
  29. Wiley Interdiscip Rev Syst Biol Med. 2009 Sep-Oct;1(2):159-71 - PubMed
  30. Biotechnol Adv. 2013 Nov;31(6):925-35 - PubMed
  31. Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6 - PubMed
  32. Curr Opin Biotechnol. 2013 Dec;24(6):965-72 - PubMed
  33. J Biotechnol. 2013 Jan 20;163(2):204-16 - PubMed
  34. Comput Struct Biotechnol J. 2012 Sep 28;2:e201209002 - PubMed
  35. Integr Biol (Camb). 2012 Jan;4(1):53-64 - PubMed
  36. Mol Syst Biol. 2013;9:641 - PubMed
  37. Biotechnol Adv. 2013 Nov;31(6):903-14 - PubMed

MeSH terms

Publication Types