Determining structure and action mechanism of LBF14 by molecular simulation

A computational algorithm to assess the physiochemical determinants of T cell receptor dissociation kinetics

“…Nonetheless, these results increase attention to the CDR2 regions in the future of TCR design. Finally, in contrast to previous reports [28] , [59] , peptide radius of gyration and CDR3⍺-CDR3β distance were not selected in the top ten predictive features. This is likely due to the artificial pMHC unfolding by pulling from TCR-pMHC termini 27 and the lack of diversity in TCR-pMHC pairs evaluated [28] , [59] , respectively.…”

“…This characterization provides an overall assessment of the physiochemical features that might impact bond lifetime and is consistent with the quaternary structure of globular proteins. We considered features likely to impact dissociation kinetics and thus included H-bonds (58) , LJ- contacts (59) , distance between the TCR and pMHC [60] , [61] , solvent accessible surface area (SASA) (62) , root mean square fluctuations (RMSF) (63) , and the gyration tensor of the TCR and pMHC. This approach resulted in 18 features for the first set, and we dubbed these quaternary features ( Table S2 ).…”

The Atomic-Level Physiochemical Determinants of T Cell Receptor Dissociation Kinetics

“…This characterization provides an overall assessment of the physiochemical features that might impact bond lifetime and is consistent with the quaternary structure of globular proteins. We considered features likely to impact dissociation kinetics and thus included Hbonds 56 , LJ-contacts 57 , distance between the TCR and pMHC 58,59 , solvent accessible surface area (SASA) 60 , root mean square fluctuations (RMSF) 61 , and the gyration tensor of the TCR and pMHC. This approach resulted in 18 features for the first set, and we dubbed these quaternary features (Figure 1-supplement 2).…”