TABLE 2.
Summary of modeling procedures for the MBL oligomers
| Oligomer | Search | Conformational variable | Conclusion |
|---|---|---|---|
| Monomer | 1 | Randomized CRD region at the swivel | 12 best-fit modelsa were identified from 5,000 trials |
| 2, 3, 4 | Randomized N terminus at the hub | Not used further | |
| Dimer | 1 | Two monomers rotated in 10° increments; bases separated by 0 nm | Not used further |
| 2 | Two monomers rotated in 10° increments; bases separated by 3.3 nm | 12 best-fit modelsa were identified from 6,859 trials | |
| 3 | Two monomers rotated in 10° increments; bases separated by 4.8 nm | Not used further | |
| 4 | Two monomers rotated in 10° increments; bases separated by 6.6 nm | Not used further | |
| Trimer | 1 | Rotated a monomer relative to the best-fit dimer which was kept fixed | Not used further |
| 2 | Monomer 1 fixed; monomers 2 and 3 subjected to 10° and 20° rotational increments respectively | 12 best-fit modelsa were identified from 2,028 trials | |
| Tetramer | 1 | Monomer 1 fixed; monomers 2–4 subjected to 10, 20, and 30° rotational increments, respectively | 10 best-fit modelsa were identified from 900 trials |
a PDB-formatted coordinates for the best-fit oligomer models are provided in the supplemental material.