Initial helical conformations were defined as all amino acids having (φ, ψ)=(−60°, −40°). Initial extended conformations were defined as all (φ, ψ)=(180°, 180°). Native conformations, as appropriate, were defined for each system as below. Explicit solvation was achieved with truncated octahedra of TIP3P water16 with a minimum 8.0 Å buffer between solute atoms and box boundary. All structures were built via the LEaP module of Ambertools. Except where otherwise indicated, equilibration was performed with a weak-coupling (Berendsen) thermostat33 and barostat targeted to 1 bar with isotropic position scaling as follows. With 100 kcal mol−1 Å−2 positional restraints on protein heavy atoms, structures were minimized for up to 10000 cycles and then heated at constant volume from 100 K to 300 K over 100 ps, followed by another 100 ps at 300 K. The pressure was equilibrated for 100 ps and then 250 ps with time constants of 100 fs and then 500 fs on coupling of pressure and temperature to 1 bar and 300 K, and 100 kcal mol−1 Å−2 and then 10 kcal mol−1 Å−2 Cartesian positional restraints on protein heavy atoms. The system was again minimized, with 10 kcal mol−1 Å−2 force constant Cartesian restraints on only the protein main chain N, Cα, and C for up to 10000 cycles. Three 100 ps simulations with temperature and pressure time constants of 500 fs were performed, with backbone restraints of 10 kcal mol−1 Å−2, 1 kcal mol−1 Å−2, and then 0.1 kcal mol−1 Å−2. Finally, the system was simulated unrestrained with pressure and temperature time constants of 1 ps for 500 ps with a 2 fs time step, removing center-of-mass translation and rotation every picosecond.
SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
