Table I.
General properties of the PIMT simulationsa
| General properties | Initialh | 119V PIMT | 119I PIMT |
|---|---|---|---|
| Total Cα-rmsd (Å) | NAi | 2.8 ± 0.2 | 3.0 ± 0.4 |
| N-terminus Cα-rmsd (Å)b | NAi | 2.3 ± 0.4 | 2.4 ± 0.2 |
| C-terminus Cα-rmsd (Å)c | NAi | 1.7 ± 1.1 | 1.5 ± 0.4 |
| Total SASA (Å2)d | 9937 | 10 696 ± 220 | 10 955 ± 172 |
| SAM-binding site SASA (Å2)e | 501 | 444 ± 78 | 668 ± 138j |
| Isoaspartate-binding site SASA (Å2)f | 900 | 588 ± 90 | 672 ± 55 |
| Polymorphic site | |||
| Polymorphic-site SASA (Å2)g | 232 | 241 ± 4 | 273 ± 29j |
| Residue 119 SASA (Å2) | 38 | 33 ± 6 | 40 ± 13 |
| V119 Cγ2/I119 Cγ1−V115 Cγ1 (Å) | 4.7 | 4.5 ± 0.4 | 6.2 ± 1.1j |
| V119 Cγ1/I119 Cδ1−L130 Cδ1 (Å) | 4.0 | 4.2 ± 0.4 | 4.9 ± 1.1 |
| V119 Cγ2/I119 Cγ2−V135 Cγ1 (Å) | 7.0 | 7.7 ± 1.0 | 7.3 ± 1.8 |
| V119 Cγ2/I119 Cγ1−L137 Cδ1 (Å) | 5.3 | 4.2 ± 0.5 | 5.3 ± 0.8j |
aAll values were calculated using structures from the last 5 ns (5000 structures) of each simulation. All values are expressed as means and standard deviations of the means from three independent simulations at 37°C.
bCα-rmsd of residues W2–S8.
cCα-rmsd of residues D217–W225.
dThe total solvent-accessible surface area (SASA) was determined using the NACCESS algorithm (Hubbard and Thornton, 1993).
eThe following residues were used to calculate the SASA of the SAM-binding site: I52, T57, I58, S59, H64, G86, G87, S88, D109, H110, L114, G140, D141, G142, R143, G158, A159, V213, L214 and Q221.
fThe following residues were used to calculate the SASA of the isoaspartate-binding site: P49, S51, Q55, T57, S59, A60, H62, M63, Y66, L191, M208, V210, I211, Y212, V213 and P214.
gThe following residues were used to calculate the SASA of the polymorphic site: V115, V122, R123, L130, L137 and residue 119.
hInitial refers to the minimized starting structure of the 119V protein.
iNot applicable.
jP < 0.1.