Nef

The accessory protein Nef is essential for high-level viremia and progression to AIDS in infected patients. Nef is targeted, via myristylation and a cholesterol recognition motif, to lipid rafts in cellular membranes and interacts with partner proteins to perform diverse functions, including host cell activation and stimulation of viral replication, and promoting internalization of host cell surface molecules, such as CD4, MHC class I and T cell receptors. We are interested in structures of Nef complexes as well as understanding possible allosteric effects that regulate binding and assembly.

The HARC Center Nef project, headed by Dr. B. Matija Peterlin and Dr. Thomas Alber, combines Dr. Peterlin's biochemical and biophysical characterization of Nef with the structural and computational techniques utilized by Dr. Alber and other HARC Center members. Work in Dr. Peterlin's lab has shown, in part, that Nef binds the PI3K signalosome containing PI3K, the guanine nucleotide exchange factor Vav1, small GTPases CDC42/Rac1 and p21 activated kinase PAK2. The HARC Center Nef project studies the structure of Nef in complex with its various partners individually and within an intact signalosome.

In addition, Nef binds with cell surface receptors (e.g. CD4, MHC class I) and bridges their binding to armadillo repeat (ARM repeat) proteins such as AP complexes, βCOP and the V1H subunit of the vacuolar ATPase. Another component of the HARC Center Nef Project is aimed at structurally characterizing this bridging role, by studying complexes between Nef and its receptor and ARM repeat partners.

In essence, the different interactions of Nef not only bring together functional partners, but also activate targets through allosteric effects. Thus, an important component of the Nef project is also to understand how such effects are mediated, which is addressed using computational biological approaches.