Table 1.
Peptides and Proteins subjected to MD simulations.
| Protein | PDB ID/Reference | Box size (Å) | ions | Simulation details |
|---|---|---|---|---|
| (Ala)5 | -- | 31.8 | -- | Hamiltonian Replica Exchange |
| Acetyl-(Ala)7-amide | -- | -- | Gas-Phase Temp. Replica Exchange | |
| A) GB1 hairpin (residues 41–56 of protein G | 100 ns MD with C36 FF | |||
| GEWTYDDATKTFTVTE | 50.0 | -- | 150 ns MD with Drude FF | |
| B) Dimeric coiled coil, 2×21 aa | 58.7 0.15 | M KCl | 200 ns MD with C36 FF5 | |
| 1u0i132 | 100 ns with Drude FF | |||
| C) Crambin, 46 aa | 52.0 | -- | 100 ns with C36 FF | |
| 1ejg133 | 2 × 100 ns with Drude FF | |||
| D) Protein GB1 domain, 56 aa | 56.7 | K+ | 100 ns with C36 FF | |
| 1p7e134 | 100 ns with Drude FF | |||
| E) Cold-shock protein A, 69 aa | 52.4 | K+ | 100 ns with C36 FF | |
| 1mjc135 | 100 ns with Drude FF | |||
| F) Ubiquitin, 76 aa | 58.4 | -- | 100 ns with C36 FF | |
| 1ubq136 | 100 ns with Drude FF | |||
| G) Circular permutant of ribosomal proteion S6, 77 aa | 100 ns with C36 FF | |||
| 3zzp137 | 61.0 | Na+ | 2×100 ns with Drude FF | |
| H) DNA methyltransferase associated protein (DMAP1) | 100 ns with C36 FF | |||
| 4iej (to be published), 93 aa, | 59.0 | -- | 2 ×100 ns with Drude FF | |
| I) PDZ domain from tight junction regulatory protein, 94 aa | 100 ns with C36 FF | |||
| 3vqf (to be published) | 58.0 | Na+ | 2 ×100 ns with Drude FF | |
| J) Lysozyme, 129 aa | 69.8 | Cl− | 200 ns with C36 FF | |
| 135l138 | 93 and 100 ns with Drude FF | |||
| K) Fatty acid binding protein, 132 aa | 63.4 | -- | 100 ns with C36 FF | |
| 1ifc139 | 100 ns with Drude FF | |||
| L) Dethiobiotin synthase, 224 aa | 72.4 | Na+ | 90 ns with C36 FF | |
| 1byi140 | 2 × 90 ns with Drude FF | |||
-- indicates no ions or periodic conditions were not used. Number of counterions added were enough the neutralize the system unless the concentration is presented.