Computational protocol: Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

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Protocol publication

[…] For the NS5A-OAS1 docking, the crystal structure of the NS5A domain I of a subtype 1b strain (PDB: 1ZH1) and the structure of human OAS1 (PDB: 4IG8) were obtained from the Protein Data Bank (PDB) (; ). The 1b subtype was used in the original study describing interaction between OAS1 and NS5A (). Two docking methods were applied and their results compared for consistency. Specifically, we used the PatchDock server () and imposed that the F37 residue in NS5A is located at the binding interface, as described (). We next used ClusPro (; ) without any assumption on the residues involved in binding. The best models from ClusPro and Patchdock were superimposed and revealed an almost identical binding pose. We next checked that the two OAS1 regions necessary for NS5A binding () were located at the interface: one of these two regions (amino acids 235-275) defines most of the contact area in the models. Overall, these observations indicate that the binding interaction pose obtained with the two docking methods is reliable.The C19 sphingomyelin ligand structure was prepared for simulation using the LigPrep module of Maestro (Schrodinger Release, 2016-4: Maestro Schrodinger, LLC, New York, NY, United States, 2016) to determine the 3D structure and ionization states at pH 7.0 ± 0.2. The NS5B structure of a subtype 1b strain (PDB ID: 4MK7 chain A) was processed with Protein Preparation Wizard module of Maestro to remove crystal water molecules, add hydrogen atoms, assign bond orders, and optimize the orientation of hydroxyl groups. Docking simulation was carried out with IFD protocol () in Extra Precision mode. The receptor grid was generated around the Sphingomyelin Binding Domain (residues E230 to G263). All the simulations were performed using the OPLS3 force field (). The docked ligand-receptor poses were analyzed in terms of Glide Score, a scoring function that estimate protein-ligand binding affinities ().The 3D structures were rendered using PyMOL (The PyMOL Molecular Graphics System, Version 1.8.4.0 Schrödinger, LLC). […]

Pipeline specifications

Software tools PatchDock, Cluspro, LigPrep, OPLS3, Glide, PyMOL
Applications Drug design, Protein interaction analysis
Organisms Equus caballus, Equus asinus, Homo sapiens
Diseases Hepatitis C, Infection