Molecular dynamics of CBD3 peptide
We modeled the CBD3 peptide based on the X-ray diffraction structure of
CRMP2 (PDB: 5MKV) (Zheng et al., 2018). Three independent molecular
dynamics simulations (MDS) of both the CBD3 by itself and conjugated
with a blood-brain barrier-permeable peptide TAT-CBD3 were run with
pmemd.cuda (Case et al., 2018; Götz, Williamson, Xu, Poole, Le Grand &
Walker, 2012; Salomon-Ferrer, Götz, Poole, Le Grand & Walker, 2013)
from AMBER18 using AMBER ff14SB force field (Maier, Martinez,
Kasavajhala, Wickstrom, Hauser & Simmerling, 2015). We used tLeap
binary (AMBER18) for solvating the peptides in an octahedral TIP3P water
box with a 15 Å distance from structure surface to the box edges, and
closeness parameter of 0.75 Å. The neutralized system was solvated in a
solution of 150 mM NaCl. H-bonds were constrained using SHAKE algorithm
and integration time-step at 2 fs. Simulations were carried out
equilibrating the system for 1 ns at NPT using Berstein barostat to keep
constant pressure at 1 atm at 300K, followed by 300 ns NPT production at
300 K. The first 60 ns of each MDS were discarded as equilibration time.