2.3 | Molecular Dynamics Simulation
In order to explore the structural and dynamic characteristics of the
modeled complexes (OsL1/OsS1-ATP and OsL1:OsS1 heterotetramer),
molecular dynamics (MD) simulations were conducted using GROMACS
5.139 with CHARRM36 force field40and periodic boundary conditions. The topology parameters for ATP were
generated using the SwissParam server.41 The
simulation systems were solvated using TIP3P water models and
neutralized by adding Na+ and Cl-ions at a physiological concentration of 0.15 M to achieve
electro-neutrality (Table. S1). Energy minimization of the systems were
conducted using the steepest-descent method to avoid steric clashes and
high energy interactions.42 Particle-mesh Ewald (PME)
method was employed to handle long-range electrostatic
interactions.43 Subsequently, the energy-minimized
systems were position-restrained (equilibrated) in two different phases;
NVT (constant volume and temperature) and NPT (constant pressure and
temperature) for 0.1 and 1 ns, respectively. Then, the equilibrated
monomeric systems (OsL1-/OsS1-ATP) were simulated up to 70 ns, and the
heterotetrameric systems (C-I, C-II, and C-III) were subjected to 100 ns
production run (in duplicate). The temperature and pressure of all
simulation systems were maintained at 300 K and 1 bar, respectively. The
built-in GROMACS tools were used for trajectory analysis. PDBe-PISA web
interface (https://www.ebi.ac.uk/pdbe/pisa/picite.html) was used
to analyze protein-protein interactions. PyMOL
(https://pymol.org/) was used for structural visualization. 2D
graphs were plotted in Grace 5.1.2
(http://plasma‐gate.weiz-mann.ac.il/Grace/).