Abstract

Research Article

Utilization of Molecular Simulation Applications for Stability Testing of Anthocyanin Compounds in Black Elderberry

Richard Benedict*

Published: 01 September, 2023 | Volume 7 - Issue 1 | Pages: 012-017

Recently, many studies on the molecular activity of compounds have been carried out using simulations through computer programs or in silico simulations. Anthocyanins are one of the compounds that are often used as food coloring agents and can function as antioxidants to prevent blockage of blood vessels, as an anti-cancer that can prevent the development of cancer cells and tumors and have anti-inflammatory effects. The purpose of the research is to determine the stability of anthocyanins using molecular simulations and determine the best mixing sequence of ingredients to produce the most stable anthocyanin mixture. 
Based on the results of the simulations carried out, it can be proven that the final 3 sets (the modeled compound belonging to namely AP and AZ followed by a number based on the simulation order) selected are AP17, AP18, and AZ17. The AP17 set had the lowest potential energy at the end of molecular dynamics simulations, but molecular visualization showed structural instability indicated by the formation of gaps in the molecular conformation. The AP18 set had the second lowest potential energy at the end of molecular dynamics simulations and molecular visualization showed molecular conformation that tended to be stable during molecular simulations with no change in structure. The AZ17 set had the highest potential energy of the final 3 sets selected and molecular visualization showed a gap in the conformation at the beginning of the simulation, but over time the gap became denser, indicating that the molecule became more stable over time. 
Based on the research results, the AP18 set was chosen because it has relatively low potential energy and it can be proven that the structure visualization of this set tends to be more stable over time during molecular dynamics simulations.

Read Full Article HTML DOI: 10.29328/journal.abb.1001035 Cite this Article Read Full Article PDF

Keywords:

Anthocyanins; Molecular simulation; Stability

References

  1. Palsson B. The challenges of in Silico Biology. Nature Biotechnology. 2000; 18(11):1147-1150. https://doi.org/10.1038/81125
  2. van Gunsteren WF, Dolenc J, Mark AE. Molecular simulation as an aid to experimentalists. Curr Opin Struct Biol. 2008 Apr;18(2):149-53. doi: 10.1016/j.sbi.2007.12.007. Epub 2008 Feb 14. PMID: 18280138.
  3. Milbury PE, Cao G, Prior RL, Blumberg J. Bioavailablility of elderberry anthocyanins. Mech Ageing Dev. 2002 Apr 30;123(8):997-1006. doi: 10.1016/s0047-6374(01)00383-9. PMID: 12044949.
  4. Hubbermann EM, Heins A, Stöckmann H, Schwarz K. Influence of acids, salt, sugars, and hydrocolloids on the color stability of anthocyanin-rich black currant and elderberry concentrates. European Food Research and Technology. 2005; 223(1): 83–90. https://doi.org/10.1007/s00217-005-0139-2
  5. Baeza R, Sánchez V, Salierno G, Molinari F, López P, Chirife J. Storage stability of anthocyanins in freeze-dried elderberry pulp using low proportions of encapsulating agents. Food Sci Technol Int. 2021 Mar;27(2):135-144. doi: 10.1177/1082013220937867. Epub 2020 Jul 12. PMID: 32659122.
  6. Levitt M, Lifson S. Refinement of protein conformations using a macromolecular energy minimization procedure. J Mol Biol. 1969 Dec 14;46(2):269-79. doi: 10.1016/0022-2836(69)90421-5. PMID: 5360040.
  7. Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006 May;106(5):1589-615. doi: 10.1021/cr040426m. PMID: 16683746; PMCID: PMC2547409.
  8. Padmavathi DA. Potential Energy Curves & AMP; material properties. Materials Sciences and Applications. 2011; 02(02): 97–104. https://doi.org/10.4236/msa.2011.22013
  9. Byška J, Trautner T, Marques SM, Damborský J, Kozlíková B, Waldner M. Analysis of long molecular dynamics simulations using interactive focus+context visualization. Computer Graphics Forum. 2019; 38(3): 441–453. https://doi.org/10.1111/cgf.13701
  10. Biswas R, Ghosh S, Bagchi A. A structural perspective on the interactions of TRAF6 and Basigin during the onset of melanoma: A molecular dynamics simulation study. J Mol Recognit. 2017 Nov;30(11). doi: 10.1002/jmr.2643. Epub 2017 Jun 14. PMID: 28612997.

Figures:

Figure 1

Figure 1

Figure 1

Figure 2

Figure 1

Figure 3

Figure 1

Figure 4

Figure 1

Figure 5

Similar Articles

Recently Viewed

Read More

Most Viewed

Read More

Help ?