Computational Chemical Physics Group

Exploring Nature With Computer Simulations

April 20, 2017
by Danilo Roccatano

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.


April 19, 2017
by Danilo Roccatano

Citrate Synthase a Pac-Enzyme

Citrate Synthase (CS) is an enzyme localized in the mitochondria of our cells where it plays an important role in the aerobic respiration cycle by transforming oxaloacetate molecules (on the right side of the picture) in citrate (on the top left side) with the assistance of the acetyl-coenzyme A (CoA) molecule. As the pac-man in the famous computer game, this Pac-Enzyme diffuse along the space between the convolute cristae of mitochondria “chomping” at its encounter oxaloacetates that activate the enzyme to bind the CoA (ghosts in the playground). For each captured CoA, a new citrate molecule is then produced (score). This complex mechanism requires large conformation changes of parts of the protein (domains) whose molecular details are not yet clarified. Using molecular dynamics simulations on the ARCHER supercomputer, I am studying in collaboration with Dr. S. Hayward of the University of UEA (Norwich, UK) this enzyme to garner novel insights on structural, dynamics and thermodynamics of its functional mechanisms.
The following image was submitted to ARCHER Image Competition 2016
and it was selected for the September picture in the ARCHER calendar 2017.