Table 1. Summary of system parameters and perturbation scenarios.
| Starting Conformation | Perturbation Scenarioa | Ionic strength (mM) | Number of atoms | Equilibrated Box size (Å) | Simulation length (ns) | System labelb |
| Extended (3CLN) | – | 150 | 33835 | 82×84×90 | 150 |
|
| 50 | ||||||
| Compact (1PRW) | – | 161 | 20330 | 58×57×60 | 200 |
|
| 200 | ||||||
| Extended (3CLN) | – | 82 | 37099 | 62×87×69 | 400 |
|
| 50 | ||||||
| Extended (3CLN) | 11, 31, 67, 84, 93, 104, 107, 122, 133, 140 are protonated | 43 | 31660 | 64×81×60 | 200 |
|
| 100 | ||||||
| Extended (3CLN) | E31 is protonated | 91 | 31652 | 63×81×60 | 400 |
|
| 150 | ||||||
| Extended (3CLN) | E31A mutation | 94 | 31645 | 60×83×62 | 400 |
|
| 400 | ||||||
| 400 |
= 7.4 using pKa values calculated in ref 22. These systems are assumed to be at physiological pH.a Unless otherwise indicated, residues are assigned charge states according to pH
IS-p: physiological ionic strength, IS-l: low ionic strength, E31+: residue E31 is protonated, E31A: residue E31 is mutated to A, pH – l: low pH.b Abbreviations: E: Extended, C: Compact;