Computational Chemical Physics Group

Exploring Nature With Computer Simulations

Modular Assembly of Proteins on Nanoparticles

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I have recently contributed to a proof of concept study published in the prestigious  Nature Communication Journal (doi:10.1038/s41467-018-03931-4) [1]. The study involved collaborations with experimental groups across University of Lincoln (UoL), University of Molise (Italy) and the Royal Holloway University of London coordinated by Dr. Enrico Ferrari (UoL).

The motivation for this is that, generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Enrico had the smart idea to design a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. For this purpose, the N-terminal part is Glutathione S-Transferase (GST, a protein ubiquitously present in both eukaryotes and prokaryotes  with the ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification) from Schistosoma japonicum was bound covalently bound to gold nanoparticles (GNPs) by gold-sulfur bonds. The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag (see Figure 1).

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Figure 1: Crystal structure of the SpyCatcher/SpyTag complex (PDB code: 4MLI). The image was created using the Chimera software.

In this work, it was shown that Spy- Catcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.

In this paper, Molecular Dynamics (MD) simulations have been used to study the absorption of the protein on the surface of the gold nanoparticles coated with citrate molecules. In the simulation, the nanoparticle surface is approximated as a flat gold surface. An atomistic simulation of the entire particle would be challenging since the NP used in the experimental study (~40 nm in diameter) is too large (only the NP would consist of 2 millions of atoms, see Figure 2).

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Figure 2: A 40 nm particle compared to the size of the GST protein. If not differently indicated, all the pictures on this blog have been generated using the VMD software.

Gold nanoparticles are easily produced by reduction of gold salts in the presence of a citrate solution whose concentration determines the diameter of the nanoparticle. The citrate molecules absorbed on the nanoparticle surface negatively charge it. To reproduce this effect, the gold surface used for the MD simulation was prepared by letting citrate molecules to be absorbed on it. In this way, the citrate molecules in complex with Na counterions coat the gold surface as a molecular quill (see Figure 3)!

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Figure 3: planar (10×10 nm) Au layer with citrate molecules absorbed used in the simulations.

The result of the simulations clearly indicates the tendency of the protein to bind the coated layer driven by electrostatic interactions with the negative carboxylates of the citrate with the side chain of the arginine residues on the protein surface. In Figure 4, conformations of the protein bonded to the layer at the end of three 20 ns simulations starting from different velocities are shown. The results support the experimental finding on the possible mechanism of absorption of the protein on the nanoparticles.

ProteinLayerBinding20ns

REFERENCE

  1. Ma, A. Saccardo, D. Roccatano, D. Aboagye-Mensah, M. Alkaseem, M. Jewkes, F. Di Nezza, M. Baron, M. Soloviev, E. Ferrari. Modular assembly of proteins on nanoparticles. Nature Communication.9, 1489 (2018).

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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