Molecular dynamics was
propagated via the Langevin dynamics integrator in GROMACS (version
4.5.5 or 4.6.5),
30 using a time step of
2 fs, and a friction coefficient of 1 ps
–1. Langevin
dynamics was used because it is a very effective thermostat and correctly
samples the canonical ensemble. The friction used here will have only
a small effect on the dynamics,
31 and no
effect on most of the observables we are concerned with, because these
are almost all equilibrium configurational averages. Lennard-Jones
pair interactions were cut off at 1.4 nm, electrostatic energies were
computed via particle-mesh Ewald
32 with
a grid spacing of ∼0.1 nm and a real-space cutoff of 0.9 nm.
The force field in all cases was a derivative of Amber ff03:
33 (link) either Amber ff03*
6 (link) in conjunction with the TIP3P water model
11 or Amber ff03w
20 (link) in conjunction with
the TIP4P/2005 water model.
13 (link) The force
field for the chromophores Alexa 488 and Alexa 594 will be described
in a future publication, and has been extensively validated against
experimental data.
In certain cases, temperature replica exchange
simulations were performed (for Csp M34, ACTR, Ac-(AAQAA)
3-NH
2, GB1 hairpin, chignolin, and Trp cage). The protocol
for these is the same as above, with exchanges attempted every 1 ps.
Further details on the temperature ranges and simulation lengths for
each case are included in the
Results section.
We eliminate from the analysis any configurations in which the proteins
make van der Waals contact with their periodic image, defined by a
closest approach of any atom with an image atom of less than 0.3 nm.
22 Nativeness of proteins and peptides was
assessed by computing the
dRMS over native
contacts, defined as the mean-square
difference between the distances d
ij0 between residue pairs (
i,
j) in contact in the reference (native)
state, and the corresponding distance
dij(
x) in a given configuration
x The list of the
Nij native contacts, {native}, is defined
as all pairs
of heavy atoms (
i,
j) within 4.5
Å in the native structure, excluding pairs for which |Res(
i) – Res(
j)| ≤ 2, where the
function Res(
k) gives the residue number of atom
k.
Best R.B., Zheng W, & Mittal J. (2014). Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. Journal of Chemical Theory and Computation, 10(11), 5113-5124.