Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations

Abstract

CD147 functions as the receptor of extracellular cyclophilin A (CypA) in various diseases, and CD147-CypA binding ulteriorly underlies the pathological process of various viral infections including HIV-1, SARS, and SARS-CoV-2....

Identification of Potential Lead Compounds Targeting Novel Druggable Cavity of SARS-CoV-2 Spike Trimer by Molecular Dynamics Simulations

“…All MD simulations were performed with periodic boundary conditions and the Newton-equations were integrated with a 2.0 fs time step using the Verlet algorithm. A cut-off distance of 10 Å was used for the van der Waals and electrostatic interactions [ 64 ]. Note: each complex was performed over two replicate simulations to ensure consistency.…”

Surface/interfacial transport through pores control desalination mechanisms in 2D carbon-based membranes

“…32,33 The simulated box containing Carzeo-ANG, graphene pistons, salt solution (4467 water molecules, 80 Na + , and 80 Cl − ), and pure water had the dimensions of 52 Å × 50 Å × 120 Å. The simulated system could satisfy the equilibrium state at an NVT (constant pressure condition) of 300 K. 34 The analog experiments were completed by applying periodic boundary conditions to the x , y , and z directions of the simulation box. To eliminate the influence of random factors and improve the result accuracy of the desalination properties, three MD simulations were performed for each system, and the data reported below are the average of the three duplicate simulations.…”

Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry

“…Principal component analysis (PCA) [54] , [55] was used to analyze the collective motions of proteins, which was able to provide insights into the dynamic conformational differences upon binding with ligand [56] . The dynamic cross-correlation matrices (DCCM) [57] , [58] for the Ca atoms of each residue was used to calculate the fluctuating cross-correlation coefficients of Cα atomic positions during the simulation, which provides the information on the relevant movements of proteins on a large scale.…”