Figure 1

HIV-1 gp120 V3 loop structure visualization, Delaunay tessellation, and variant representation. (a) Ribbon diagram and (b) C_α trace of the V3 loop peptide structure (PDB ID: 1ce4, NMR model 1). (c) Delaunay tessellation of the V3 loop superimposed over the trace. (d) 3D-1D potential profiles for both the native R5-tropic V3 loop sequence corresponding to PDB structure file 1ce4, as well as an R5-tropic variant V3 loop sequence defined by the five substitutions N5G, H13R, R18Q, T22A, and I26V threaded onto the native structure tessellation. The variant residual profile is defined as the difference between the variant and native 3D-1D potential profiles and measures environmental perturbations at all 35 V3 loop positions due to the substitutions.