Table 2.
CD Analysis of β-Sheet 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) |
|---|---|---|---|---|---|---|
| Concanavalin A (Figure S29) | ||||||
| a SRCD (CD 0000020000) [47] | 196 | 4.64 | 223 | −2.25 | 0.000 | |
| b 4000 Hy (PDB code 1NLS) | 199 | 3.09 | 211 | −1.19 | 1.574 | 1.574–3.253 |
| c 6000 Hy (PDB code 1NLS) | 198 | 4.53 | 216 | −0.14 | 0.681 | 0.681–2.669 |
| d MM1 (PDB code 1NLS) | 194 | 4.98 | 214 | −1.44 | 1.518 | 1.518–3.375 |
| Outer Membrane Protein OPCA (Figure 3) | ||||||
| a SRCD (CD0000119000) [59] | 199 | 4.72 | 218 | −1.56 | 0.000 | |
| b 4000Hy (PDB code 2VDF) | 198 | 3.00 | 214 | −0.322 | 1.625 | 1.526–2.959 |
| Jacalin (Figure S33) | ||||||
| a SRCD (CD0000119000) [47] | 192 | −3.87 | 202 | 3.33 | 0.000 | |
| b 4000 Hy (PDB code 1KU8) | 185 | −1.56 | 199 | 1.72 | 2.001 | 1.408–2.558 |
| e MM3 (PDB code 1KU8) | 183 | −4.24 | 203 | 3.81 | 2.284 | 2.284–3.672 |
| Rubredoxin (Figure S35) | ||||||
| aSRCD (CD0000064000) [47] | 191 | 1.47 | 202 | −6.23 | 0.000 | |
| b 4000Hy (PDB code 1R0I) | 189 | 3.21 | 206 | −3.52 | 2.144 | 1.900–3.924 |
| c 6000Hy (PDB code 1R0I) | 188 | 2.76 | 202 | −2.70 | 1.886 | 1.472–3.506 |
| f BA98:1 (PDB code 8RXN) | 192 | 4.30 | 210 | −0.78 | 3.916 | 3.916–5.662 |
| Lentil Lectin (Figure S38) | ||||||
| a SRCD (CD0000043000) [47] | 195 | 5.43 | 226 | −1.33 | 0.000 | |
| b 4000Hy (PDB code 1LES) | 197 | 3.81 | 210 | −1.29 | 1.887 | 1.887–3.571 |
| c 6000 Hy (1LES) | 196 | 4.12 | not observed | - | 1.232 | 1.232–3.160 |
| g MM2 (1LES) | 197 | 4.97 | 220 | −1.32 | 0.415 | 0.415–2.997 |
| Pea Lectin (Figure S41) | ||||||
| a SRCD (CD0000053000) [47] | 196 | 5.05 | 226 | −1.58 | 0.000 | |
| b 4000Hy (PDB code 1OFS) | 198 | 3.12 | 210 | −1.48 | 1.975 | 1.975–3.362 |
| d MM1 (PDB code 1OFS) | 197 | 5.17 | 220 | −1.35 | 0.373 | 0.373–2.084 |
| Avidin (Figure S43) | ||||||
| a SRCD (CD0000008000) [47] | 197 | 2.03 | 214 | −0.04 | 0.000 | |
| b 4000 Hy (PDB code 2A8G) | 200 | 5.04 | 211 | −1.42 | 2.462 | 2.238–3.699 |
| c 6000 Hy (PDB code 2A8G) | 200 | 3.36 | not observed | - | 2.435 | 2.092–3.421 |
| g MM2 (PDB code 1RAV) | 197 | 5.31 | 218 | −0.91 | 2.410 | 2.410–4.115 |
| Outer Membrane Protein G (Figure 4) | ||||||
| a SRCD (CD0000118000) [59] | 190 | 7.07 | 216 | −3.13 | 0.000 | |
| b 4000 Hy (PDB code 2IWV) | 203 | 2.51 | 213 | −0.59 | 4.301 | 3.973–4.798 |
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 is 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 CAPPS with rebuilt secondary structures including hydrogens; d Matrix method with ab initio parameters including only the protein backbone transitions [55]; 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 [60] including residues 4–6, 8–12, 14–18, 20–22, 24–28, 30–32, 34–37, 39–44, 46–51 with set Hy at 4000 cm−1 [3]; g Matrix method using ab initio parameters including protein backbone and charge-transfer transitions [55].