Table 4.
CD Analysis of Other 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) |
|---|---|---|---|---|---|---|
| Insulin (Figure S56) | ||||||
| a SRCD (CD0000040000) [47] | 192 | 16.75 | 221 | −8.08 | 0.000 | |
| b 6000OL (PDB code 3INC) | 192 | 11.08 | 210 | −4.68 | 3.253 | 0.945–7.731 |
| c 6000Jy (PDB code 3INC) | 195 | 8.59 | 2.10 | −5.85 | 1.129 | 1.129–9.930 |
| d 6000Jy (PDB code 3INC) | 196 | 7.08 | 212 | −4.46 | 1.061 | 1.061–9.018 |
| e MM3 (PDB code 1TRZ) | 192 | 7.59 | 210 | −4.45 | 2.072 | 2.072–3.639 |
| Bovine Pancreatic Trypsin Inhibitor (Figure S60) | ||||||
| a SRCD (CD0000007000) [47] | 187 | 4.52 | 202 | −7.67 | 0.000 | |
| b 6000OL (PDB code 5PTI) | 189 | 3.86 | 207 | −3.42 | 3.056 | 1.669–4.954 |
| d 6000Jy (PDB code 5PTI) | 196 | 1.14 | 210 | −2.24 | 4.352 | 3.634–4.687 |
| f RH04:3 (PDB code 5PTI) | 187 | 6.72 | 205 | −6.48 | 1.629 | 1.629–7.100 |
| Light-Harvesting Protein Complex II (Figure 6) | ||||||
| a SRCD (CD0000114000) [59] | 191 | 18.12 | 210 | −6.97 | 0.000 | |
| b 6000OL (PDB code 1NKZ) | 192 | 13.81 | 211 | −8.90 | 4.503 | 4.503–10.390 |
| d 6000Jy (PDB code 1NKZ) | 196 | 9.98 | 214 | −13.83 | 7.054 | 6.349–10.537 |
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 CDALC using PDB structure minimized via Insight®II/Discover/CVFF; d CAPPS with rebuilt secondary structures of the PDB structure including all hydrogens; e Matrix method including ab initio protein backbone, charge-transfer and side chain transitions [55]; f Matrix method on including ab initio protein backbone and ab initio side chain parameters [68].