Table 1.
Intra- and intermolecular hydrogen bonds as a function of conformational state and solvent environment
| Simulation | Number of hydrogen bonds
|
||
|---|---|---|---|
| N | TS | D | |
| Pure water | |||
| 60°C | |||
| Water–protein | 96 | NA | NA |
| Protein–protein | 53 | NA | NA |
| 125°C | |||
| Water–protein | 82 | 119 (6) | 118 (6) |
| Protein–protein | 55 | 36 (2) | 33 (3) |
| 8 M urea, 60°C | |||
| UR1 | |||
| Water–protein | 70 | 102 (4) | 108 (7) |
| Urea–protein | 30 | 32 (2) | 41 (7) |
| Protein–protein | 49 | 26 (2) | 25 (2) |
| UR2 | |||
| Water–protein | 70 | 94 (5) | 103 (7) |
| Urea–protein | 30 | 37 (3) | 40 (5) |
| Protein–protein | 48 | 30 (1) | 26 (2) |
| UR3 | |||
| Water–protein | 74 | 109 (3) | 110 (7) |
| Urea–protein | 22 | 43 (3) | 52 (7) |
| Protein–protein | 52 | 24 (3) | 23 (2) |
Hydrogen bonds were considered to be intact when donor and acceptor atoms were within 2.6 Å and 35° of linearity. The N values are for t = 0 ns for each simulation. The TS values are averages over the following time intervals: UR1, 2.085–2.090 ns; UR2, 1.845–1.850 ns; UR3, 1.805–1.810 ns; and 125°C in pure water, 8.245–8.250 ns. The TS ensemble regions were identified by using a conformational clustering procedure described by Li and Daggett (23, 24). The D values are averages from 15–20 ns. SDs are given in parentheses. NA, not applicable.