Molecular Dynamics Simulations of Folded Proteins

Simulations using Gromacs 4.5.3 were carried out for the following four folded globular proteins: bovine pancreatic trypsin inhibitor (BPTI), ubiquitin, GB3 and hen Lysozyme, starting from the published experimental structures (PDB entries 5PTI^{48 (link)}, 1UBQ^{49 (link)}, 1P7E^{50 (link)}, 6LYT⁵¹ respectively). Each protein was solvated in a truncated octahedron simulation cell filled with TIP3P water, with nearest distance between images of 45 Å for all proteins except for lysozyme, for which the distance was 60 Å. Sodium and chloride ions were added as needed to yield a final salt concentrations of ~100 mM, with adjustments to ensure charge neutrality. For each protein, a 100-step SD energy minimization of the whole system was performed, followed by 200 ps of MD at a constant pressure of 1 bar and temperature of 300 K, in which harmonic positional restraints of 2.39 kcal/mol/Ų were applied to each Cartesian component of each protein non-hydrogen atom using the minimized structure as a reference. Each protein was then simulated at a constant pressure of 1 bar and a temperature of 300 K for 200 ns. Pressure was regulated by a Parinello-Rahman barostat⁵² with a coupling time of 2.5 ps; otherwise all details were as described for Ac-(AAQAA)₃-NH₂ above.