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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 most frequently highlighted regions.White and solid: TCR. White and transparent: MHC. Red: peptide. Green: top 5 most frequently highlighted regions per threshold (i.e. 20 regions where several of them are identical). If the whole TCR beta chain was within the top regions it was not coloured in green for reasons of visibility. (A) Direct-method. (B) Median-method. (C) Square-method.
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pone-0064464-g006: Illustration of the most frequently highlighted regions.White and solid: TCR. White and transparent: MHC. Red: peptide. Green: top 5 most frequently highlighted regions per threshold (i.e. 20 regions where several of them are identical). If the whole TCR beta chain was within the top regions it was not coloured in green for reasons of visibility. (A) Direct-method. (B) Median-method. (C) Square-method.

Mentions: Among all 94 investigated regions in the TCR most regions with the largest number of differences over time form parts of the TCR beta chain. Out of the top 10 regions (the 10 regions with the highest amount of differences over time) for each of the 4 thresholds (i.e. 40 in total) 34 regions form parts of the TCR beta chain while 6 formparts of the TCR alpha chain (Figure 3 and Table 1). Among the top 20 regions over all 4 thresholds (i.e. 80 in total) 67 regions formparts of the TCR beta chain while 13 form parts of the TCR alpha chain. These findings are in agreement with Armstrong et al. who suggested that the beta-chain may play an important role in ligand recognition [32]. In Figure 6 the spatial arrangement of the top 5 regions per threshold and method are illustrated.


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 most frequently highlighted regions.White and solid: TCR. White and transparent: MHC. Red: peptide. Green: top 5 most frequently highlighted regions per threshold (i.e. 20 regions where several of them are identical). If the whole TCR beta chain was within the top regions it was not coloured in green for reasons of visibility. (A) Direct-method. (B) Median-method. (C) Square-method.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0064464-g006: Illustration of the most frequently highlighted regions.White and solid: TCR. White and transparent: MHC. Red: peptide. Green: top 5 most frequently highlighted regions per threshold (i.e. 20 regions where several of them are identical). If the whole TCR beta chain was within the top regions it was not coloured in green for reasons of visibility. (A) Direct-method. (B) Median-method. (C) Square-method.
Mentions: Among all 94 investigated regions in the TCR most regions with the largest number of differences over time form parts of the TCR beta chain. Out of the top 10 regions (the 10 regions with the highest amount of differences over time) for each of the 4 thresholds (i.e. 40 in total) 34 regions form parts of the TCR beta chain while 6 formparts of the TCR alpha chain (Figure 3 and Table 1). Among the top 20 regions over all 4 thresholds (i.e. 80 in total) 67 regions formparts of the TCR beta chain while 13 form parts of the TCR alpha chain. These findings are in agreement with Armstrong et al. who suggested that the beta-chain may play an important role in ligand recognition [32]. In Figure 6 the spatial arrangement of the top 5 regions per threshold and method are illustrated.

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