Molecular Dynamics Simulations of Peptides

Simulations of Ala₅ were run using the simulation package Gromacs^{28 ,29} using a protocol similar to that used in our previous work,^{15 (link)} and with the implementation of the Amber force fields by Sorin and Pande.^{30 (link)} The peptide was unblocked and protonated at both N and C termini, corresponding to the experimental conditions of pH 2.^{14 (link)} Molecular dynamics simulations of each peptide in a 30 Å cubic simulation box of explicit TIP3P water³¹ were run at a constant temperature of 300 K and a constant pressure of 1 atm, with long range electrostatic terms evaluated using particle-mesh Ewald (PME) using a 1.0 Å grid spacing and a 9 Å cutoff for short-range interactions. For each force field, four runs of 50 ns each were initiated from different starting configurations. Further details of the simulation protocols are as published.^{15 (link)}Replica exchange molecular dynamics (REMD) simulations of the blocked peptide Ac-(AAQAA)₃-NH₂ were run using Gromacs^{28 ,29} with 32 replicas spanning a temperature range of 278 K to 595 K. The peptide was solvated in a truncated octahedron simulation cell of 1022 TIP3P water molecules with an initial distance of 35 Å between the nearest faces of the cell. This cell was equilibrated for 200 ps at 300 K and a constant pressure of 1 atm. Subsequently, all REMD simulations were done at constant volume, with long range electrostatics calculated using PME with a 1.2 Å grid spacing and 9 Å cutoff. Dynamics was propagated with a Langevin integration algorithm using a friction of 1 ps⁻¹, and replica exchange attempts every 1 ps (every 500 steps with a time step of 2 fs). Typical acceptance probabilities for the replica exchange were in the range 0.1–0.5. All replica exchange runs used the same set of initial configurations, which were taken from the final configurations of a preliminary replica exchange simulation with ff99SB. The simulations were run for at least 30 ns per replica, of which the first 10 ns were discarded in the analysis (with an aggregate of ≈ 1 µs for each force field). To test for possible system size dependence, additional simulations of Ac-(AAQAA)₃-NH₂ in a 45 Å truncated octahedron box solvated by 2268 water molecules were run for 30 ns using a similar protocol, in this case with 32 replicas at 5 K intervals between 278 and 433 K.
Additional simulations were performed for the unblocked peptide HEWL19, derived from hen egg-white lysozyme with sequence KVFGRC(SMe)ELAAAMKRHGLDN. The structure and parameters for the S-methylated Cys 6 were adapted from those for methionine and are given in Supporting Information (SI) Figure 1 and Table 1 respectively. Both termini as well as all acidic side chains were protonated, corresponding to the experimental conditions of pH 2.^{14 (link)} The peptide was solvated in a truncated octahedron simulation cell with a 42 Å distance between nearest faces, and equilibrated at constant pressure for 200 ps at 300 K. Constant volume REMD was run with 32 replicas spanning the temperature range 278 K to 472 K, for 27 ns, of which the first 10 ns were discarded in the analysis. All other parameters were the same as for Ac-(AAQAA)₃-NH₂.
Native state simulations of ubiquitin were run starting from the crystal structure 1UBQ.^{32 (link)} The protein was solvated by 2586 explicit TIP3P water molecules in a cubic simulation box of 45 Å length with long range electrostatics calculated using PME with a 1.2 Å grid spacing and 9 Å cutoff. To neutralize the system charge, 7 sodium and 8 chloride ions were added. Dynamics was propagated for 30 ns at constant pressure (1 atm) and temperature (300 K) using a Nosé-Hoover thermostat³³ and Parrinello-Rahman barostat.³⁴