Homology Modeling of Circulating V2 Segments

The four-stranded β-sheet conformations of V1V2 domain from previously published co-crystal structures of V1V2 with mAbs PG9 and PG16 [19 (link), 20 (link)] and the α-helical conformation of V1V2 from the co-crystal structure of V1V2 with mAb CH58 [21 (link)] were used as crystallographic templates for the homology modeling of circulating V2 segments. 3D homology models of the V2 variants were built using the ICM Pro software (Molsoft, LLC, La Jolla, CA) according to the following protocol. First, the coordinates of backbone atoms of a V2 peptide were assigned to be equal to the corresponding backbone coordinates of a V2 template. Then, the V2 peptide was subjected to Biased-Probability Monte Carlo (BPMC) sampling of ICM-Pro to produce the lowest energy structure matching the template coordinates. Importantly, the backbone of the model was tethered to the template backbone during the BPMC sampling by imposing additional energy penalty for any backbone atoms deviations. Finally, the energy of the resulting V2 homology model was recorded. Terms for van der Waals, hydrogen bonding, electrostatics, dihedral angle deformation, entropy, and solvation were included in energy calculation.