Background/Objectives: Cows produce antibodies with ultralong CDRH3 segments (ulCABs) that contain a disulfide-stabilized knob domain. This domain is connected to the globular core of the antibody by a β-strand stalk. In the crystal structures, the stalk protrudes from the core in an extended conformation and presents the knob at its distal end. However, the rigidity of this topology has been questioned due to the extensive crystal packing present in most ulCAB crystal structures. To gain more insight into the dynamics of ultralong CDRH3s, we performed a comparative molecular dynamics (MD) study of 19 unique ulCABs. Methods: For all 19 systems, one-microsecond MD simulations were performed in explicit solvent. The analyses included an investigation of the systems’ conformational stability and the dynamics of the knob domain as well as an energetic analysis of the intramolecular knob interactions. Results: The simulations show that the extended stalk–knob conformation observed in the crystal structures is not preserved in solution. There are significant differences in the degree of knob dynamics, the orientations of the knobs, the number of flexible stalk residues, and the frequency of the motions. Furthermore, interactions between the knob and the light chain (LC) of the ulCABs were observed in about half of the systems. Conclusions: The study reveals that pronounced knob dynamics is a general feature of ulCABs rather than an exception. The magnitude of knob motions depends on the system, thus reflecting the high sequence diversity of the CDRH3s in ulCABs. The observed knob–LC interactions might play a role in stabilizing distinct knob orientations. The MD simulations of ulCABs could also help to identify suitable knob fragments as mini-antibodies by suggesting appropriate truncation points based on flexible sites in the stalks.
Denysenko et al. (Wed,) studied this question.