Table 1.
HLA class II binding of RA-associated epitopes1.
Table 2.
Predicted HLA DR binding cores of four known citrullinated RA-associated epitopes.
Fig 1.
Comparison of binding affinity of wild-type and citrullinated versions of vimentin peptides.
Each data point indicates the DRB1*01:01 (left panel) or DRB1*04:01 (right panel) binding capacity of WT vimentin peptides with the corresponding citrullinated version. Effects greater or less than 3-fold are demarcated by the diagonal dashed red lines and highlighted by red fill. Points to the lower right indicate instances where the citrullinated peptide binds with higher affinity that the WT peptide, and vice versa.
Fig 2.
Prediction of the DRB1*01:01 and DRB1*04:01 binding capacity of citrullinated peptides.
The DRB1*01:01 (left panel) and DRB1*04:01 (right panel) binding capacity of citrullinated peptides were predicted using NetMHCIIpan version 3.1 predictions by substituting the citrullinated residues with the wildcard “X”. Trend lines are show in red.
Fig 3.
Increases in binding capacity due to citrullination is associated with modification at both anchor and non-anchor positions.
The number of instances of increased DRB1*01:01 (left panel) or DRB1*04:01 (right panel) binding associated with citrullination of arginine at specific peptide positions relative to predicted core region frames is shown. Anchor positions are highlighted with red bars and non-anchor by blue bars. Light filled bars show the total number of increases attributed to anchor (white filled red bars) and non-anchor (blue hatched bars) positions. Tabulations are shown for two different approaches to defining the core residues, as described in the text.