Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers

Journal of Molecular Modeling
Ali RahimiHamid Modarress

Abstract

Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

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Citations

Feb 25, 2018·Journal of Molecular Modeling·Abbas YousefpourSepideh Amjad-Iranagh
Jun 13, 2018·Scientific Reports·Nadezhda N ShevelevaErkki Lähderanta
Apr 6, 2019·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Hatem BesrourMajdi Hochlaf
May 2, 2021·Journal of Molecular Modeling·Xiangyao PengDavid R M Williams
Mar 18, 2020·The Journal of Physical Chemistry. B·Piotr BatysMaria Sammalkorpi
Nov 24, 2021·The Journal of Physical Chemistry. B·Parham Khoshbakht MarviRouein Halladj

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