Enzyme Inspired Catalysts
The uploaded files include prep libraries required for building polystyrene system:
* STY: styrene monomer
* HST: terminal (head) styrene monomer capped with methyl group
* TST: terminal (tail) styrene monomer capped with methyl group
* CAT: styrene residue with catalytic moiety attached
* SPA: styrene residue with C16 alkyl chain attached
* SCL: cross-linking residue (p-divinylbenzene) with 1 additional branching point
* SDB: cross-linking residue (p-divinylbenzene) with 2 additional branching points (double-branch)
Six fragments
containing catalyst and hydrophobic residue separated by 0 to 5
styrene units (EIC-0 to EIC-5) were built, with three additional
styrene units added on each side of catalyst and hydrophobic residue.
These fragments were then solvated with TIP3P waters in a truncated
octahedron box with 10 Å buffer in each direction from the solute.
The solvated fragments were relaxed in 4 steps: 1) steepest descent
minimization was performed with maximum of 10 000 cycles; 2) slow
heating of the system from 0 to 300 K in 100 ps with harmonic
position restraints on solute (2.5 kcal/mol Å2)
under constant volume (NVT); 3) constant pressure (NPT) dynamics at
300 K for 1 ns with harmonic position restraints placed on solute
(2.5 kcal/mol Å2);
4) constant pressure (NPT) dynamics at 300 K without restraints for
another 1 ns. After relaxation (total of 2.1 ns), each system was
simulated for 100 ns at 300 K under constant volume (NVT).
Periodic boundary conditions were used and long range electrostatic interactions were calculated with the Particle-Mesh Ewald (PME) technique with a cutoff of 8.0 Å. The temperature in all simulations was set to 300 K and controlled by Langevin thermostat combined with random seed generator.[6] The SHAKE algorithm[7] was employed to constrain bonds involving hydrogen atoms during dynamics and an integration time step of 2 fs was used. The simulations were carried out using GPU version of PMEMD program implemented in the Amber16 package, saving snapshots every 10 ps. Analysis was performed using cpptraj module available in AmberTools. For clustering, all-atom RMS deviations of catalyst and hydrophobic residues (styrene residues were not included) was used in conjunction with k-means algorithm with maximum number of clusters set to 20.
An example input file to build a fragment with these residues using LEaP module of Amber package is provided (build_example.leap), as well as the input files for running molecular dynamics (min.in, heat.in, npt-restr.in, npt.in, nvt.in).
Conformations representing the two most populated clusters for each fragments is shown in figure named top2clusters_EIC0-5.png. Distances calculated between CAT and SPA residues, as well as the distances measured between head and tail atoms for each of these two residues is shown in figure named Distances&initial_conformations.png.
Finally, the system topologies and resulting trajectories with stripped solvent are provided (eic-N.prmtop and eic-N.nc files).