Why is Dimeric 3D Domain Swapping in Antibody Light Chains Missing from the Solution? Atomistic Insights Mechanisms.

Misfolding of antibody light chains can lead to systemic light chain amyloidosis, which is associated with misfolding and aggregation. The antibody light chain may engage in 3D domain swapping within the variable region (#4VL) through hydrogen bonding (HB) interactions, potentially forming the tetramer, as revealed in solution and crystal structures. However, the 3D-domain swapping (3D-DS) dimers could not be detected experimentally. This study investigates the absence of 3D-DS using computational approaches, focusing on structural dynamics, solvation effects, and stability relevant to the loss of 3D-DS. Microscale molecular dynamics simulations of #4VL and 3D-DS confirm that native HB interactions are essential to maintain β-sheet structures in both #4VL and 3D-DS. A flickering native HB interaction in the 3D-DS system, caused by repulsive interaction with water molecules in the hydrophobic region, leads to intramolecular breathing motions and oligomerization in another 3D-DS. Structural dynamics of the 3D-DS dimer in long-run simulations were analyzed using the newly developed integrated solvation-based principal component analysis (3D-RISM/PCA) and density-based spatial clustering of applications with noise, confirm that if the 3D-DS cannot form the tetramer within the breathing motion process, the 3D-DS will collapse. This finding provides insights into why the 3D-DS dimer is missing from the solution and can be used to design and develop 3D-DS in other antibodies.