Table 1.
CD Analysis of α-Helical Proteins. 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) |
|---|---|---|---|---|---|---|
| Lysozyme (Figure 1) | ||||||
| a SRCD (CD0000045000) [47] | 191 | 6.01 | 207 | −4.68 | 0.000 | |
| b 6000Ho (PDB code 2VB1) | 190 | 6.51 | 205 | −1.83 | 1.620 | 1.620–5.783 |
| c 6000OL (PDB code 2VB1) | 192 | 12.89 | 211 | −2.81 | 3.585 | 0.935–7.477 |
| d 6000Ho (PDB code 2VB1) | 190 | 6.49 | 208 | −4.03 | 1.061 | 1.061–4.068 |
| e MM3 (PDB code 7LYZ) | 192 | 5.37 | 210 | −4.23 | 0.930 | 0.930–3.194 |
| Cytochrome c (Figure S4) | ||||||
| a SRCD (CD0000021000) [47] | 195 | 4.30 | 210 | −4.29 | 0.000 | |
| c 6000OL (PDB code 1HRC) | 192 | 5.04 | 210 | −4.29 | 0.756 | 0.756–3.506 |
| d 6000Ho (PDB code 1HRC) | 190 | 8.00 | 208 | −6.52 | 3.036 | 0.886–7.617 |
| f BA98:2 (PDB code 1HRC) | 184 | 8.17 | 206 | −10.37 | 1.843 | 1.183–3.242 |
| Phospholipase A2 (Figure S7) | ||||||
| a SRCD (CD0000059000) [47] | 192 | 6.96 | 209 | −4.63 | 0.000 | |
| c 6000OL (PDB code 1UNE) | 191 | 8.54 | 210 | −5.92 | 0.994 | 0.994–5.435 |
| d 6000Ho (PDB code 1UNE) | 190 | 6.92 | 206 | −5.53 | 1.821 | 1.821–5.313 |
| e MM3 (PDB code 1UNE) | 191 | 9.37 | 209 | −7.25 | 1.831 | 1.831–2.557 |
| Rhomboid Peptidase (Figure 2) | ||||||
| a SRCD (CD0000109000) [59] | 193 | 13.20 | 210 | −5.77 | 0.000 | |
| c 6000OL (PDB code 2NR9) | 192 | 11.33 | 209 | −8.14 | 1.367 | 1.367–4.546 |
| d 6000Ho (PDB code 2NR9) | 190 | 9.14 | 208 | −7.47 | 4.526 | 3.704–7.959 |
| Calmodulin (Figure S12) | ||||||
| a SRCD (CD0000013000) [47] | 192 | 12.57 | 208 | −6.58 | 0.000 | |
| c 6000OL (PDB code 1LIN) | 192 | 9.30 | 209 | −6.51 | 1.734 | 1.734–5.278 |
| d 6000Ho (PDB code 1LIN) | 190 | 7.01 | 206 | −4.24 | 3.453 | 3.082–4.755 |
| g MM2 (PDB code 1LIN) | 192 | 11.93 | 210 | −8.21 | 0.933 | 0.933–1.281 |
| Leptin (Figure S15) | ||||||
| a SRCD (CD0000044000) [47] | 191 | 13.20 | 207 | −7.48 | 0.000 | |
| c 6000OL (PDB code 1AX8) | 192 | 12.16 | 210 | −7.17 | 2.071 | 2.071–8.142 |
| d 6000Ho (PDB code 1AX8) | 190 | 10.92 | 208 | −8.96 | 2.276 | 2.276–9.660 |
| h SI (PDB code 1AX8) | 192 | 13.40 | 209 | −10.85 | 2.437 | 2.437–8.328 |
| Bacteriorhodopsin (Figure S18) | ||||||
| a SRCD (CD0000101000) [59] | 195 | 15.67 | 214 | −5.20 | 0.000 | |
| c 6000OL (PDB code 1QHJ) | 192 | 14.27 | 210 | −9.63 | 4.469 | 2.424–10.337 |
| d 6000Ho (PDB code 1QHJ) | 190 | 10.45 | 208 | −9.20 | 7.195 | 5.484–11.252 |
| i 6000Hy (PDB code 2BRD) | 191 | 12.11 | 208 | −9.61 | 5.985 | 5.985–9.952 |
| Horse Myoglobin (Figure S21) | ||||||
| a SRCD (CD0000047000) [47] | 192 | 16.75 | 209 | −7.51 | 0.000 | |
| b 6000Ho (PDB code 3LR7) | 189 | 15.49 | 205 | −8.46 | 5.609 | 2.990–14.244 |
| c 6000OL (PDB code 2V1K) | 192 | 11.65 | 210 | −9.35 | 3.938 | 2.991–7.823 |
| d 6000Ho (PDB code 2V1K) | 190 | 10.78 | 208 | −8.29 | 4.946 | 4.946–8.261 |
| h MM1 (PDB code 1YMB) | 192 | 16.80 | 211 | −11.36 | 3.131 | 3.131–4.797 |
| Sperm Whale Myoglobin (Figure S25) | ||||||
| a SRCD (CD0000048000) [47] | 193 | 17.33 | 210 | −7.77 | 0.000 | |
| b 6000Ho(PDB code 2JHO) | 186 | 19.38 | 204 | −6.07 | 8.344 | 2.392–12.070 |
| c 6000OL (PDB code 2JHO) | 192 | 12.28 | 210 | −9.29 | 3.988 | 3.169–8.131 |
| d 6000Ho (PDB code 2JHO) | 188 | 10.88 | 208 | −9.02 | 5.779 | 5.742–9.444 |
| j OH06:2 (PDB code unspecified) | 191 | 16.86 | 209 | −12.00 | 3.192 | 3.192–8.851 |
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 of 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 Insight®II/Discover/CVFF; c CDCALC using PDB structure minimized via NAMD/CHARMM22; d CAPPS with rebuilt secondary structures including hydrogens; e Matrix method using ab initio parameters including protein backbone, charge-transfer and side chain transitions [55]; f Dipole interaction model of rebuilt PDB structure with set Hy at 6000 cm−1 [3]; g Matrix method using ab initio parameters including protein backbone and charge-transfer transitions [55]; h Matrix method using ab initio parameters including only the protein backbone transitions [55]; i Dipole interaction model with rebuilt PDB structure with set Hy at 6000 cm−1 [3]; j Matrix method using unspecified myoglobin structure including local transitions and charge-transfer parameters [57].