Mechanistic insights into Zika virus NS3 helicase inhibition by Epigallocatechin-3-gallate: Supplementary Files

Deepak Kumar; Nitin Sharma; Murali Aarthy; Sanjeev Singh; Rajanish Giri

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/530600 doi: bioRxiv preprint 5000 steps is used until a gradient threshold (25 kcal/mol/Ã…) were reached. The constant NPT (number of atoms, Pressure P and temperature T) ensemble condition is incorporated to relax the simulation system to generate simulation data for post analyses. The overall simulation process is performed using the Nose-Hoover thermostats, and stable atmospheric pressure (1atm) carried out by Martina-Tobias-Klein barostat method, and the 300K was assigned as the temperature value. In order to investigate the equation of motion throughout the dynamics, the multi-time step RESPA integrator algorithm was used (42, 43) . The bonded, near non-bonded and far nonbonded interactions, were assigned at the time steps of 2,2 and 6fs respectively. The atoms involved in the hydrogen bond interaction were constrained with the SHAKE algorithm. A cut-off value of 9 Ã… radius was set up to estimate the longrange electrostatic interactions and Lennard-Jones interactions. The Particle Mesh Ewald (PME) method was used to evaluate the long-range electrostatic interactions along with the simulation process using the periodic boundary conditions (PBC). During the intervals of 1.2 and 4.8ps, the trajectory data and the energy analysis were recognized. The final production molecular dynamics were carried out for 100ns for both the apoprotein and protein complex. The results were analyzed using the simulation event analysis and simulation interaction diagram available in Desmond module (44) .