| simulated annealing |
The symmetric, tetrameric bundle model of M2-TMP was constructed from the monomer structure (1MP6). The M2-TMP monomer coordinates were obtained by a geometrical search using a search algorithim to obtain a minimum of the global penalty function that incorporates all the orientational restraints and the CHARMM empirical function. The orientational restraints imposed on the structure during refinement are 15 15N chemical shifts and 15 15N-1H dipolar couplings from PISEMA experiments. The refinement was carried out in vacuo with the initial coordinates of an ideal a-helix structure (3.6 residues per turn) having a range of tilt and rotational orientations with respect to the bilayer spanning the values obtained from the PISA wheels.
The resulting tetrameric bundle model was used to search the side chain orientations in accord with the experimentally measured distance between 15ND1 His37 and 13CG Trp41. Both chi 1 and chi 2 angles of the residues were searched extensively using 10 increments to discern whether the interaction was intramolecular or intermolecular and to find out which residues accounted for the observed spin interaction before characterizing the rotameric states of the sidechains. Note that while the His37 and Trp41 sidechain rotameric states are defined by the distance restraint, the rotameric states of other residues are taken from the backbone dependent sidechain rotamer library. |
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