Achievement

Alpna Agarwal, in collaboration with her advisor Timothy Cardozo (Sackler), has worked to elucidate a 3D structural model of the chemokine receptor-binding surface of HIV-1 gp120. Although several X-ray crystallographic structures of the HIV-1 gp120 surface protein have been solved, a complete 3D visualization of gp120 in its infective, or chemokine receptor binding, form remains elusive. Agarwal integrated several independent sources of data (X-ray crystal structures of gp120 and the V3 loop crown complexed with various antibodies) with various computational methods, such as docking, loop modeling, and homology modeling, to generate this model of gp120 containing the co-receptor binding conformation of the V3 loop. Model validation will be done through in silico design of short peptides sequences that potentially bind the chemokine co-receptor surface, and successive in vitro neutralization assays to test viral inhibition by these peptides.