Table 3.
CD Analysis of α/β proteins. The DInaMo calculations are for the minimized or rebuilt structure using CDCALC or CAPPS. All RMSDs are calculated between 180 and 210 nm.
| CD Method | Wavelength (nm) | Δε (M−1·cm−1) | Wavelength (nm) | Δε (M−1·cm−1) | RMSD (M−1·cm−1) | Range RMSDs † (M−1·cm−1) |
|---|---|---|---|---|---|---|
| Monellin (Figure S47) | ||||||
| a SRCD (CD0000046000) [47] | 190 | 3.75 | 213 | −3.32 | 0.000 | |
| b 4000OL (PDB code 1MOL) | 191 | 4.37 | 212 | −2.08 | 0.876 | 0.876–2.234 |
| c SII (PDB code 1MOL) | 189 | 3.73 | 217 | −0.96 | 1.501 | 1.501–3.938 |
| Ferredoxin (Figure S49) | ||||||
| a SRCD (CD0000032000) [47] | 185 | 1.03 | 201 | −6.37 | 0.000 | |
| b 4000OL (PDB code 2FDN) | 189 | 6.66 | 205 | −5.19 | 4.627 | 1.388–5.076 |
| d MM2 (PDB code 2FDN) | 194 | 3.99 | 214 | −1.45 | 5.539 | 5.539–6.791 |
| Triose Phosphate Isomerase (Figure S51) | ||||||
| a SRCD (CD0000070000) [47] | 190 | 7.85 | 217 | −5.06 | 0.000 | |
| b 4000OL (PDB code 7TIM) | 192 | 10.70 | 207 | −8.80 | 3.037 | 1.840–3.768 |
| e 4000Hx (PDB code 7TIM) | 190 | 8.66 | 204 | −6.14 | 2.522 | 2.073–3.437 |
| f MM3 (PDB code 7TIM) | 192 | 7.54 | 211 | −4.90 | 1.230 | 1.230–2.193 |
| Crambin (Figure 5) | ||||||
| g Conventional CD [63] | 191 | 15.26 | 209 | −10.98 | 0.000 | |
| b 4000OL (PDB code 1AB1) | 192 | 13.66 | 207 | −10.93 | 0.776 | 0.776–7.515 |
| e 4000Hx (PDB code 1AB1) | 192 | 8.14 | 206 | −7.94 | 3.897 | 3.897–7.876 |
The DInaMo calculations are for the minimized or rebuilt structure using CDCALC or CAPPS. Example literature calculations are also listed when available. † The range of RMSDs if for all calculations including literature calculations is presented. For full RMSD information on all calculations including literature, please see the Supplementary Information for a full table of calculations with RMSDs for each protein. a SRCD from the PCDDB [44]; b CDCALC using PDB structure minimized via NAMD/CHARMM22; c Exciton Hamiltonian with electrostatic fluctuations based on 2000 MD snapshots that consider the electrostatic potential from all surroundings [29]; d Matrix method using including protein backbone and charge-transfer transitions [55]; e CAPPS using rebuilt secondary structures of PDB structure including hydrogens; f Matrix method on 7TIM [64] using ab intio parameters including protein backbone, charge-transfer and side chain transitions [55]; g Conventional CD for crambin in 60% ethanol [63].