Simulation Protocol
All the systems were simulated using the CHARMM-36M [71] forcefield,
which is an improved forcefield for MD simulations for intrinsically
distorted proteins and accurately define carbohydrates [71]. Each of
the systems were solvated using the TIP3 water model in a rectangular
box of dimensions 115 Å ⨯75 Å ⨯50 Å, and neutralized by adding
Na+ and Cl- ions using the Monte
carlo [72] ion placing method. Each system was later energy
minimized using the steepest descent algorithm for 10000 steps, with
bonds having H constrained using the LINCS algorithm [73]. This was
followed by a 1 ns equilibration step using Nose-Hoover [74]
temperature coupling with the temperature kept at 303.15 K and pressure
at 1 atm. Later each system was subjected to isobaric-isothermal ( NPT)
ensemble MD production stimulation for 1 microsecond length under
periodic boundary conditions having isotropic Parrinello -Rahman
pressure coupling [75], with pressure kept at 1 atm. The leapfrog
algorithm was used for integrating the Newtonian equations of motions.
Coulombic interactions were calculated using the particle-mesh Ewald
[76] method having a 1.2 Å cutoff. Lennard-Jones or van der Waals
interactions were calculated using 1.2 Å cutoff. All stimulations were
performed using GROMACS 2020.3 [77, 78].