Molecular Dynamics Simulation
Molecular dynamics (MD) simulations were performed and analyzed with the
Molecular Operating Environment (MOE) (Chemical Computing Group, Canada)
and NAMD 2.7 suite [http://www.ks.uiuc.edu/Research/namd] (Phillips
et al., 2005). For molecular dynamics simulation with the
antibody-ligand complexes, starting coordinates were from homology
modeled structures. Hydrogen atoms were added to the starting structures
using the LigX protonation tool of the MOE 2016.08 suite. Using the
solvation algorithm in MOE, a 10 Å region around the protein-ligand
complex was immersed in a TIP3P water droplet such that protein atoms
outside the droplet were fixed to dampen long range dynamic effect.
Sodium cations were added for electroneutrality. Additional Sodium and
Chloride ions were added to a final concentration of 0.15 M. This
resulted in systems consisting of 18,780 atoms for the mAb1,17,788 atoms for mAb2, and 16,469 atoms for mAb3. Dynamics simulations
were then performed using NAMD, with parameters from the Amber10:EHT
forcefield set. Equilibration consisted of 15, 000 steps of conjugate
gradient energy minimization, followed by 50 ps of MD with restraints
applied to the protein to equilibrate the water. The systems were then
warmed to 300 K over a total of 18 ns with a 50 K increment and
equilibration at each temperature step. This was followed by
unrestrained production run of 30 ns, which is enough for the
determination of empirically relevant binding affinities (Salvalaglio,
Zamolo, Busini, Moscatelli, & Cavallotti, 2009). The SHAKE algorithm
was used, allowing a 2 fs time-step. Long-range electrostatics were
treated via the particle mesh Ewald method. Trajectory analysis was
carried out with the MOE analysis tool and in-house scripts.