Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes
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...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | Journal of Immunology Research |
| Online Access: | http://dx.doi.org/10.1155/2015/173593 |
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| _version_ | 1832565176582275072 |
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| author | Reiner Ribarics Michael Kenn Rudolf Karch Nevena Ilieva Wolfgang Schreiner |
| author_facet | Reiner Ribarics Michael Kenn Rudolf Karch Nevena Ilieva Wolfgang Schreiner |
| author_sort | Reiner Ribarics |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8aa547bc6b3d4ba2ba36b3b12fd04579 |
| institution | Kabale University |
| issn | 2314-8861 2314-7156 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Immunology Research |
| spelling | doaj-art-8aa547bc6b3d4ba2ba36b3b12fd045792025-02-03T01:08:59ZengWileyJournal of Immunology Research2314-88612314-71562015-01-01201510.1155/2015/173593173593Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility ComplexesReiner Ribarics0Michael Kenn1Rudolf Karch2Nevena Ilieva3Wolfgang Schreiner4Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, AustriaSection of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, AustriaSection of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, AustriaInstitute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 25A, 1113 Sofia, BulgariaSection of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, AustriaMHC 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.http://dx.doi.org/10.1155/2015/173593 |
| spellingShingle | Reiner Ribarics Michael Kenn Rudolf Karch Nevena Ilieva Wolfgang Schreiner Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes Journal of Immunology Research |
| title | Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes |
| title_full | Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes |
| title_fullStr | Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes |
| title_full_unstemmed | Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes |
| title_short | Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes |
| title_sort | geometry dynamics of α helices in different class i major histocompatibility complexes |
| url | http://dx.doi.org/10.1155/2015/173593 |
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