* Corresponding Author
Estimating Factors Determining Emulsification Capability of Surfactant-Like Peptide with Coarse-Grained Molecular Dynamics Simulation
https://doi.org/10.22146/ijc.34547 Tegar Wijaya(1), Rukman Hertadi(2*)
(1) Department of Chemistry, Faculty of Science and Computer, University of Pertamina, Jl. Teuku Nyak Arief, Simprug, Kebayoran Lama, Jakarta 12220, Indonesia
(2) Biochemistry Research Division, Bandung Institute of Technology, Jl. Ganesa No. 10 Bandung 40132, Indonesia
(*) Corresponding Author
Abstract
The ability of surfactant-like peptides to emulsify oil has become the main focus of our current study. We predicted the ability of a series of surfactant-like peptides (G6D, A6D, M6D, F6D, L6D, V6D, and I6D) to emulsify decane molecules using coarse-grained molecular dynamics simulations. A 1-μs simulation of each peptide was carried out at 298 K and 1 atm using MARTINI force field. Simulation system was constructed to consist of 100 peptide molecules, 20 decane molecules, water, antifreeze particles and neutralizing ions in a random configuration. Out of seven tested peptides, M6D, F6D, L6D, V6D, and I6D were able to form emulsion while G6D and A6D self-assembled to order b-strands. A higher hydropathy index of amino acids constituting the hydrophobic tail renders the formation of an emulsion by peptides more likely. By calculating contact number between peptides and decanes, we found that emulsion stability and geometry depends on the structure of amino acids constituting the hydrophobic tail. Analysis of simulation trajectory revealed that emulsions are formed by small nucleation following by fusion to form a bigger emulsion. This study reveals the underlying principle at the molecular level of surfactant peptide ability to form an emulsion with hydrophobic molecules.
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[1] Arima, K., Kakinuma, A., and Tamura, G., 1968, Surfactin, a crystalline peptide-lipid surfactant produced by Isolation, characterization and its inhibition of fibrin clot formation, Biochem. Biophys. Res. Commun., 31 (3), 488–494.
[2] Adjonu, R., Doran, G., Torley, P., and Agboola, S., 2013, Screening of whey protein isolate hydrolysates for their dual functionality: Influence of heat pre-treatment and enzyme specificity, Food Chem., 136 (3-4), 1435–1443.
[3] Zheng, X., Dong, S., Zheng, J., Li, D., Li, F., and Luo, Z., 2014, Expression, stabilization, and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants, Biotechnol. Adv., 32 (3), 564–574.
[4] Hamley, I.W., 2014, Peptide Nanotubes, Angew. Chem. Int. Ed., 53 (27), 6866–6881.
[5] Santoso, S., Hwang, W., Hartman, H., and Zhang, S., 2002, Self-assembly of surfactant-like peptides with variable glycine tails to form nanotubes and nanovesicles, Nano Lett., 2 (7), 687–691.
[6] Vauthey, S., Santoso, S., Gong, H., Watson, N., and Zhang, S., 2002, Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles, Proc. Natl. Acad. Sci. U.S.A., 99 (8) 5355–5360.
[7] Zhao, X., 2009, Design of self-assembling surfactant-like peptides and their applications, Curr. Opin. Colloid In., 14 (5) 340–348.
[8] Youssef, N., Simpson, D.R., Duncan, K.E., McInerney, M.J., Folmsbee, M., Fincher, T., and Knapp, R.M., 2007, In situ biosurfactant production by Bacillus strains injected into a limestone petroleum reservoir, Appl. Environ. Microbiol., 73 (4), 1239–1247.
[9] Youssef, N.H., Nguyen, T., Sabatini, D.A., and McInerney, M.J., 2007, Basis for formulating biosurfactant mixtures to achieve ultra-low interfacial tension values against hydrocarbons, J. Ind. Microbiol. Biotechnol., 34 (7), 497–507.
[10] Simpson, D.R., Natraj, N.R., McInerney, M.J., and Duncan, K.E., 2011, Biosurfactant-producing Bacillus are present in produced brines from Oklahoma oil reservoirs with a wide range of salinities, Appl. Microbiol. Biotechnol., 91 (4), 1083–1093.
[11] Adjonu, R., Doran, G., Torley, P., and Agboola, S., 2014, Whey protein peptides as components of nanoemulsions: A review of emulsifying and biological functionalities, J. Food Eng., 122 (1), 15–27.
[12] Singh, P., and Cameotra, S.S., 2004, Potential applications of microbial surfactants in biomedical sciences, Trends Biotechnol., 22 (3), 142–146.
[13] Panda, J.J., and Chauhan, V.S., 2014, Short peptide-based self-assembled nanostructures: Implications in drug delivery and tissue engineering, Polym. Chem., 5 (15), 4418–4436.
[14] Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., and de Vries, A.H., 2007, The MARTINI force field: A coarse-grained model for biomolecular simulations, J. Phys. Chem. B, 111 (27), 7812–7824.
[15] Monticelli, L., Kandasamy, S.K., Periole, X., Larson, R.G., Tieleman, D.P., and Marrink, S.J., The MARTINI coarse-grained force field: Extension to proteins, J. Chem. Theory Comput., 4 (5), 819–834.
[16] Humphrey, W., Dalke, A., and Schulten, K., 1996, VMD: Visual molecular dynamics, J. Mol. Graphics., 14 (1), 33–38.
[17] MacKerell, A.D., Bashford, D., Bellot, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wirkiewicz-Kuczera, J., Yin, D., and Karplus, M., 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, 102 (18), 3586–3616.
[18] MacKerell, A.D., Feig, M., and Brooks, C.L., 2004, Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, J. Comput. Chem., 25 (11), 1400–1415.
[19] Lindahl, E., Hess, B., and van der Spoel, D., 2001, GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Model., 7 (8), 306–317.
[20] Berendsen, H.J.C., van der Spoel, D., and van Drunen, R., 1995, GROMACS: A message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91 (1-3), 43–56.
[21] van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., Berendsen, H.J., 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26 (16), 1701–1718.
[22] Kyte, J., and Doolittle, R.F., 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol., 157 (1), 105–132.
[23] Middleton, D.A., Madine, J., Castelletto, V., and Hamley, I.W., 2013, Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample, Angew. Chem. Int. Ed., 52 (40), 10537–10540.
[24] Qiu, F., Chen, Y., and Zhao, X., 2009, Comparative studies on the self-assembling behaviors of cationic and catanionic surfactant-like peptides, J. Colloid Interface Sci., 336 (2), 477–484.
[25] Hudiyanti, D., Radifar, M., Raharjo, T.J., Narsito, N., and Noegrohati, S., 2014, A Coarse-grained molecular dynamics simulation using NAMD package to reveal aggregation profile of phospholipid self-assembly in water, J. Chem., 2014, 273084.
[26] Dwiastuti, R., Radifar, M., Marchaban, M., Noegrohati, S., and Istyastono, E.P., 2016, Molecular dynamics simulations and empirical observations on soy lecithin liposome preparation, Indones. J. Chem., 16 (2), 222–228.
[27] Koshiyama, K., and Wada, S., 2016, Collapse of a lipid-coated nanobubble and subsequent liposome formation, Sci. Rep., 6, 28164.
DOI: https://doi.org/10.22146/ijc.34547
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