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

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• 作者：Ali Rahimi ; Sepideh Amjad-Iranagh ; Hamid Modarress
• 关键词：Coarse grained simulation ; Drug delivery ; Molecular dynamics ; Poly(L ; lysine) dendrimer
• 刊名：Journal of Molecular Modeling
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：22
• 期：3
• 全文大小：730 KB
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• 作者单位：Ali Rahimi (1)
  Sepideh Amjad-Iranagh (1)
  Hamid Modarress (1)
  
  1. Department of Chemical Engineering, Amirkabir University of Technology, Tehran, Iran
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Biomedicine
  Molecular Medicine
  Health Informatics and Administration
  Life Sciences
  Computer Application in Life Sciences
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：0948-5023

文摘

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.