Open AccessMolecular Basis of Peptide Recognition by the TCR: Affinity Differences Calculated Using Large Scale Computing
Author(s) -
Shunzhou Wan,
Peter V. Coveney,
Darren R. Flower
Publication year - 2005
Publication title -
the journal of immunology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.737
H-Index - 372
eISSN - 1550-6606
pISSN - 0022-1767
DOI - 10.4049/jimmunol.175.3.1715
Subject(s) - massively parallel , t cell receptor , basis (linear algebra) , molecular dynamics , peptide , energy (signal processing) , scale (ratio) , exploit , computer science , computational science , parallel computing , statistical physics , physics , chemistry , t cell , biology , computational chemistry , mathematics , immunology , quantum mechanics , biochemistry , geometry , immune system , computer security
Free energy calculations of the wild-type and the variant human T cell lymphotropic virus type 1 Tax peptide presented by the MHC to the TCR have been performed using large scale massively parallel molecular dynamics simulations. The computed free energy difference (-1.86 +/- 0.44 kcal/mol) using alchemical mutation-based thermodynamic integration agrees well with experimental data (-2.9 +/- 0.2 kcal/mol). Our simulations exploit state-of-the-art hardware and codes whose algorithms have been optimized for supercomputing platforms. This enables us to simulate larger, more realistic biological systems for longer durations without the imposition of artificial constraints.
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