TABLE V.
Molecular dynamics based findings for [GYGSG]5 (top) and [GLGSQ]5 (bottom) from 5°C to 60°C in A. aurantia (MaSp1) silk (the repeating motif [GLGSQ]5 also appears in N. Clavipes MaSp1)
| Temp (°C) | Rg (nm)A | SASA (nm2)B | Non Polar SASA (nm2)B | Side-Chain ContactsC | Number of Water MoleculesD | Peptide - Peptide H BondsE | Peptide - Water H BondsE |
|---|---|---|---|---|---|---|---|
| 5 | 1.27 ± 0.14 | 25.7 ± 0.90 | 13.2 ± 0.60 | 228.8 ± 10.9 | 16039.4 ± 467.6 | 0.43 ± 0.60 | 75.8 ± 4.48 |
| 25 | 0.87 ± 0.04 | 18.3 ± 0.64 | 9.75 ± 0.35 | 354.9 ± 13.8 | 11854.2 ± 380.1 | 8.08 ± 1.39 | 56.6 ± 4.21 |
| 30 | 0.76 ± 0.02 | 19.2 ± 0.61 | 10.2 ± 0.36 | 346.4 ± 11.7 | 12461.3 ± 398.6 | 4.53 ± 1.14 | 61.8 ± 4.07 |
| 35 | 0.77 ± 0.05 | 18.9 ± 0.52 | 10.3 ± 0.37 | 340.1 ± 10.8 | 11914.2 ± 331.9 | 8.33 ± 1.89 | 55.0 ± 4.29 |
| 40 | 0.90 ± 0.06 | 21.3 ± 0.74 | 10.9 ± 0.57 | 313.0 ± 14.4 | 13236.9 ± 431.2 | 3.44 ± 1.51 | 64.5 ± 4.51 |
| 60 | 0.72 ± 0.02 | 17.4 ± 0.58 | 9.69 ± 0.44 | 377.3 ± 11.7 | 10812.1 ± 378.2 | 9.96 ± 1.96 | 49.4 ± 4.04 |
| Temp (°C) | Rg (nm)A | SASA (nm2)B | Non Polar SASA (nm2)B | Side-Chain ContactsC | Number of Water MoleculesD | Peptide - Peptide H BondsE | Peptide - Water H BondsE |
|---|---|---|---|---|---|---|---|
| 5 | 1.21 ± 0.05 | 25.9 ± 0.60 | 13.4 ± 0.35 | 257.6 ± 12.1 | 17174.6 ± 354.9 | 4.28 ± 1.24 | 74.5 ± 4.20 |
| 25 | 0.81 ± 0.05 | 21.0 ± 0.84 | 10.9 ± 0.48 | 331.1 ± 12.1 | 14177.2 ± 494.9 | 7.65 ± 1.75 | 62.3 ± 4.46 |
| 30 | 0.96 ± 0.04 | 21.3 ± 0.57 | 11.4 ± 0.46 | 316.8 ± 13.1 | 14274.2 ± 401.2 | 7.45 ± 2.20 | 61.9 ± 5.06 |
| 35 | 1.15 ± 0.11 | 23.2 ± 1.08 | 12.3 ± 0.59 | 259.8 ± 11.4 | 15311.1 ± 589.2 | 5.92 ± 2.36 | 65.1 ± 5.04 |
| 40 | 0.79 ± 0.05 | 20.3 ± 1.07 | 10.3 ± 0.56 | 306.4 ± 19.9 | 13473.2 ± 670.2 | 5.57 ± 1.53 | 60.3 ± 5.09 |
| 60 | 0.74 ± 0.01 | 20.2 ± 0.72 | 10.9 ± 0.34 | 330.0 ± 11.0 | 12991.5 ± 456.8 | 8.63 ± 2.08 | 54.0 ± 4.39 |
radius of gyration averaged over all Cα
solvent accessible surface area (SASA) was computed with the minimum distance set to 0.14nm
side-chain contacts were counted when two neighboring aliphatic carbon atoms from neighboring residues were within 0.65nm of each other
number of water molecules were counted when a water molecule is within 0.6nm of any protein atoms
hydrogen bonds are defined as when the hydrogen and the acceptor atoms are within 0.35nm.
The errors shown in the table were determined by the standard deviation of the fluctuations observed over the 2 ns of data used in the analysis, as discussed in the text.