Geometry Dynamics of α -Helices in Different Class I Major Histocompatibility Complexes.

ABSTRACT: MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, g

SUBMITTER: Ribarics R 

PROVIDER: S-EPMC4651647 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature