Computational Chemical Physics Group

Exploring Nature With Computer Simulations

Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study


 Danilo Roccatano, Edita Sarukhanyan, and Ronen Zangi
The Journal of Chemical Physics 146, 074703 (2017); doi:
jcp_146_7_cover1    Cover Page

Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptake by living cells, and their high surface to volume ratio facilitates the adsorption of molecules of different nature. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutically agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A – Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surface through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalize Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to a loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus, into the interior of the CNT was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.


Profile photo of Danilo Roccatano

Author: Danilo Roccatano

Danilo Roccatano received his PhD in chemistry in 1997 at the University of Rome “La Sapienza”, Italy. From 1996, he worked as a postdoc in the group of Prof. H.J.C. Berendsen at the Chemistry department of the University of Groningen in the Netherlands. In 2001, he moved back in his home country with a research associate fellowships, first at the University of Rome “La Sapienza” and later at the University of L’Aquila. In 2003, he started a position of senior research associate position in Germany at the International University Bremen. In July 2005, he was promoted to Lecturer, and, later in 2009, he got the assistant professor position in Biochemical Engineering at the same university (then renamed as Jacobs University Bremen). Since then, he is leading a computational chemistry and biochemistry group, which attracted funding and students from different Germany national research agencies (DFG, BMBF, DAAD), EU, and biotech companies (EVONIK, BASF, BRAIN). In October 2015, he started a Senior Lecturer position in the School of Mathematics and Physics of the University of Lincoln.

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