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Journal of Immunology Research
Volume 2015 (2015), Article ID 173593, 20 pages
http://dx.doi.org/10.1155/2015/173593
Research Article

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

1Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
2Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 25A, 1113 Sofia, Bulgaria

Received 27 July 2015; Revised 30 September 2015; Accepted 30 September 2015

Academic Editor: Francesco Pappalardo

Copyright © 2015 Reiner Ribarics et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR.