Fig. 5: Molecular dynamics simulations of variants with swapped ulCDRs.
From: Stability convergence in natural antibodies with ultra-long hypervariable loops
a Simulation snapshots of variants with a zoom-in in the stalk region. The stalk is marked in blue with distinctive residues visualized as single residues and the respective residues marked in bold in ascending and descending stalk representations. The knob region is marked in red, the rest of the VH in green, and the VL in gray. b Probability density functions (pdf) for the fraction of native contacts. c Root mean square fluctuation (RMSF) per residue of the VL. d RMSF per residue of the VH. The knob region from the CDR-H3 is excluded from the sequence numbering and comparison.
