Docking Simulation of CNTs and TLRs

The docking simulation of CNTs to TLRs was performed using the AutoDock Vina software⁷⁵. The 3D structures of model nanotubes, i.e., zigzag nanotubes with chirality parameters (14,0) and a corresponding diameter of 1.1 nm were generated using the TubeGen 3.4 tool⁷⁶. The length of each CNT was 8 nm. For oxidized CNTs, carboxylated groups were added on both ends (until saturation) and on the surface of the nanotube (randomly) using the Molfacture plugin in VMD visualization software^{77 (link)}. The target structure was taken from the x-ray crystal structure of TLR4 (PDB code: 3fxi, chain A) and a 1 Å-spaced grid map with 200 × 200 × 200 points was built around the protein to search for possible binding sites over the entire surface of the target. Gasteiger partial atom charges in both protein and nanotube structures were assigned by using the AutoDock Tools suite program^{78 (link)}. Docking simulations were carried out with a maximum number of 1000 generated binding modes. The top orientations were selected with a maximum energy difference of 10 kcal/mol between the best and worst retained binding modes.

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Mukherjee S.P., Bondarenko O., Kohonen P., Andón F.T., Brzicová T., Gessner I., Mathur S., Bottini M., Calligari P., Stella L., Kisin E., Shvedova A., Autio R., Salminen-Mankonen H., Lahesmaa R, & Fadeel B. (2018). Macrophage sensing of single-walled carbon nanotubes via Toll-like receptors. Scientific Reports, 8, 1115.

Publication 2018

AutoDock Vina software AutoDock Tools suite

Binding sites Modes Orientations Protein X ray

Corresponding Organization :

Other organizations : Karolinska Institutet, University of Cologne, University of Rome Tor Vergata, National Institute for Occupational Safety and Health, Tampere University, University of Turku, Åbo Akademi University, Turku Centre for Biotechnology

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Variable analysis

independent variables

Type of carbon nanotubes (zigzag nanotubes with chirality parameters (14,0) and a corresponding diameter of 1.1 nm)
Oxidation of carbon nanotubes (carboxylated groups added on both ends and on the surface)

dependent variables

Binding interactions between carbon nanotubes and Toll-like receptor 4 (TLR4)

control variables

Length of each carbon nanotube (8 nm)
Grid map size (200 × 200 × 200 points, 1 Å-spaced) around the TLR4 protein
Gasteiger partial atom charges assigned to both protein and nanotube structures
Maximum number of generated binding modes (1000)
Maximum energy difference between the best and worst retained binding modes (10 kcal/mol)

controls

No positive or negative controls were explicitly mentioned in the provided information.

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