Fig. 1.

A 2D cartoon representation of a tectosquare design (type V). The full tectosquare is an assembly of four L-shaped monomers, labeled A through D, connected with each other via the engineered HIV-1 kissing loop structures. The kissing loop sequences (color-coded in the same way throughout all the figures) were mutated to assure unique interactions and control of the orientations of the 3′ tails, which facilitate interactions with other tectosquares. The right angles within each L-shaped monomer incorporate a right angle junction extracted from the PDB structure 1JJ2 (see the text). Loop labels within each monomer indicate the hairpins at the end of the 5′ and 3′ helical arms of each monomer. Thus the A1-D2 interaction indicates the pairing of the 5′ H-loop from monomer A with the 3′ H-loop from monomer D. This labeling scheme is used in all the figures. The dashed-line boxes indicate the elements of the tectosquare subjected to MD simulations; red boxes for the four kissing loop complexes and the gray box for the monomer A.