­
­
­
­

Inventi Impact: Infectious Diseases & Immunology

Articles

  • Inventi:hif/18333/15
    Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes
    01-Jan-1970 Research 2016 : January - March
    Reiner Ribarics, Michael Kenn, Rudolf Karch, Nevena Ilieva, Wolfgang Schreiner

    MHC

    How to Cite this Article
    MHC ????-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices\nin molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the ????-helices. Each\nresulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate\npolynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a\nhinge movement.We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative\nerror. From MD simulations we selected those parts of ????-helices that were stable and also close to the TCR/MHC interface. We\nmonitored the curvature integral, generated a ruled surface between the two MHC ????-helices, and computed interhelical area and\nsurface torsion, as they changed over time. We found that MHC ????-helices undergo rapid but small changes in conformation. The\ncurvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed\nby RMSD analysis. We speculate that small changes in the conformation of individual MHC ????-helices are part of the intrinsic\ndynamics induced by engagement with the TCR.
    Download Full Text