PMC:2728246 / 20026-21917
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/2728246","sourcedb":"PMC","sourceid":"2728246","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2728246","text":"A Matlab7 (Mathworks, MA) script was designed to perform a grid search in order to model the full side chain rotameric sampling of valines (V5, V70), isoleucines (I3, I36, I44, and I61) and leucines (L8, L67) over the fs-ms time range based on two average spherical harmonics sets (ten parameters) from their Cγ and/or Cδ RDCs. The protocol searches populations of ideal rotamers in trans (tr), gauche+ (g+) and gauche− (g−) of χ1 and χ2 angles and computes the average spherical harmonics based on the following expressions:7 8 where the terms p1xx represent populations between 0 and 1 for torsion angle χ1 in ideal rotamer xx = [tr, g+, g−] and the terms p2yy|1xx represent populations of χ2 in ideal rotamer yy when χ1 is in ideal rotamer xx. The isotropic general order parameters Sγ and Sδ are terms representing local small-scale fluctuations specific to Cγ and Cδ, and all spherical harmonics, and are generated from the N–Cα–Cβ bond of the reference crystal structure pdb:1ubi and represent the idealised rotameric geometries for methyls at Cγ and Cδ positions. Due to the fact that the = 1 − ptr − for all χ angle, the grid search was performed for valines on three variables (p1tr, Sγ) in increment steps of (0.02, 0.02, 0.01) and on isoleucines on 10 variables (p1tr,p1tr|2tr, , , , , , Sγ, Sδ) in increments steps of (0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.05, 0.05). The grid search on leucines was performed as for isoleucines, except that the two isotropic order parameters were combined into a single one. In certain cases, where relaxation-based order parameters were available from (Lee et al. 1999) and did not suggest any rotameric exchange , these values were used directly in the result of the grid search as . The minimized target function is the squared sum of differences (ssd) of the real and imaginary terms of the average spherical harmonics, defined as:9","divisions":[{"label":"label","span":{"begin":525,"end":526}},{"label":"label","span":{"begin":527,"end":528}}],"tracks":[]}