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Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.

Knapp B, Dorffner G, Schreiner W - PLoS ONE (2013)

Bottom Line: The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology.In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system.Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.

View Article: PubMed Central - PubMed

Affiliation: Center for Medical Statistics, Informatics and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria. bernhard.knapp@meduniwien.ac.at

ABSTRACT
The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology. Although several different models for the activation process of the T cell via the T cell receptor have been proposed, it could not be shown that a structural mechanism, which discriminates between peptides of different immunogenicity levels, exists within the T cell receptor. In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system. Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.

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Illustration of the overall TCRpMHC complex.Blue: MHC alpha chain. Red: Beta-2 microglobulin. Green: Presented Peptide in the MHC binding groove. Orange: TCR alpha chain. Yellow: TCR beta chain.
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pone-0064464-g001: Illustration of the overall TCRpMHC complex.Blue: MHC alpha chain. Red: Beta-2 microglobulin. Green: Presented Peptide in the MHC binding groove. Orange: TCR alpha chain. Yellow: TCR beta chain.

Mentions: The structure of the investigated TCRpMHC complex is shown in Figure 1. To systematically investigate the TCR we grouped all residues according to the secondary structure labelling and complementary determining regions (CDR) labelling from [35], as well as the secondary structure labelling provided by the program VMD [51]. In total we investigated 94 different residue groups (see Table 1 for a detailed list).


Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.

Knapp B, Dorffner G, Schreiner W - PLoS ONE (2013)

Illustration of the overall TCRpMHC complex.Blue: MHC alpha chain. Red: Beta-2 microglobulin. Green: Presented Peptide in the MHC binding groove. Orange: TCR alpha chain. Yellow: TCR beta chain.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3675092&req=5

pone-0064464-g001: Illustration of the overall TCRpMHC complex.Blue: MHC alpha chain. Red: Beta-2 microglobulin. Green: Presented Peptide in the MHC binding groove. Orange: TCR alpha chain. Yellow: TCR beta chain.
Mentions: The structure of the investigated TCRpMHC complex is shown in Figure 1. To systematically investigate the TCR we grouped all residues according to the secondary structure labelling and complementary determining regions (CDR) labelling from [35], as well as the secondary structure labelling provided by the program VMD [51]. In total we investigated 94 different residue groups (see Table 1 for a detailed list).

Bottom Line: The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology.In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system.Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.

View Article: PubMed Central - PubMed

Affiliation: Center for Medical Statistics, Informatics and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria. bernhard.knapp@meduniwien.ac.at

ABSTRACT
The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology. Although several different models for the activation process of the T cell via the T cell receptor have been proposed, it could not be shown that a structural mechanism, which discriminates between peptides of different immunogenicity levels, exists within the T cell receptor. In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system. Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.

Show MeSH