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Int. J. Mol. Sci. 2018, 19(9), 2772; https://doi.org/10.3390/ijms19092772

Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study

1
Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium
2
Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium
3
Ludwig Institute for Cancer Research, de Duve Institute and Université Catholique de Louvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
*
Author to whom correspondence should be addressed.
Received: 8 June 2018 / Revised: 6 September 2018 / Accepted: 10 September 2018 / Published: 14 September 2018
(This article belongs to the Section Molecular Biophysics)
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Abstract

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called “peptergents”) have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with “peptergency” properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for “peptergency”. View Full-Text
Keywords: peptide; self-assembly; molecular dynamic simulations; peptergent peptide; self-assembly; molecular dynamic simulations; peptergent
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Crowet, J.M.; Nasir, M.N.; Dony, N.; Deschamps, A.; Stroobant, V.; Morsomme, P.; Deleu, M.; Soumillion, P.; Lins, L. Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study. Int. J. Mol. Sci. 2018, 19, 2772.

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