DynaDom: Structure-based prediction of TCR inter-domain and TCR- pMHC association angles
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چکیده
The theoretical framework of the present modeling pipeline follows the methodology introduced in our former analysis study of the Vα/Vβ association angles in TCR complexes [1]. In that former analysis, the structure with the PDB-ID 2bnu was used as an arbitrary reference to superimpose all TCR structures in the data set on the Vα domain and thus the 2bnu coordinate system is further used as reference. The work performed in ref. [1] can be briefly summarized as follows: First, the TCR Vα:Vβ structures were superimposed onto conserved residues of the Vα domain. Second, unified cuboids were placed around the two variable domains based on the backbone atoms of the conserved residues. Third, a pairwise Euler angle distance matrix was computed for all Vβ cuboids with respect to the position of the fixed Vα domain. Clustering of the matrix elements led to six major structural clusters. Fourth, a Center of Rotation was identified by embedding grids into the Vβ cuboids and determining the grid point with the lowest deviation. The position of this center of rotation, denoted as CoRβ, is found in the 2bnu coordinate at: 28.5, -37.6, 55.5 Å, and is stabilized by two interacting Q residues.
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تاریخ انتشار 2017