Table 1.
Characteristic Time Scales for Protein Motions
| event | spatial extent (nm) | amplitude (nm) | time (s) | appropriate simulations |
|---|---|---|---|---|
| bond-length vibration | 0.2–0.5 | 0.001–0.01 | 10−14-10−13 | QM methods |
| elastic vibration of globular domain | 1.0–2.0 | 0.005–0.05 | 10−12-10−11 | conventional MD |
| rotation of solvent-exposed side chains | 0.5–1.0 | 0.5–1.0 | 10−11-10−10 | conventional MD |
| torsional libration of buried groups | 0.5–1.0 | 0.05 | 10−11-10−9 | conventional MD |
| hinge bending (relative | 1.0–2.0 | 0.1–0.5 | 10−11-10−7 | Langevin dynamics, enhanced |
| motion of globular domains) | sampling MD methods? | |||
| rotation of buried side chains | 0.5 | 0.5 | 10−4-1 | enhanced sampling MD methods? |
| allosteric transitions | 0.5–4.0 | 0.1–0.5 | 10−5-1 | enhanced sampling MD methods? |
| local denaturation | 0.5–1.0 | 0.5–1.0 | 10−5-101 | enhanced sampling MD methods? |
| loop motions | 1.0–5.0 | 1.0–5.0 | 10−9-10−5 | Brownian dynamics? |
| rigid-body (helix) motions | 1.0–5.0 | 10−9-10−6 | enhanced sampling MD methods? | |
| helix-coil transitions | >5.0 | 10−7-104 | enhanced sampling MD methods? | |
| protein association | ≫1.0 | Brownian dynamics |