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The Nef protein from human or simian immunodeficiency virus enhances viral replication, downregulates immune cell receptors, and activates multiple host cell signaling pathways. Conformational information about full-length Nef has been difficult to obtain as the full-length protein is not readily amenable to NMR or X-ray crystallography due to aggregation at high concentrations. As an alternative, full-length HIV and SIV Nef were probed with hydrogen exchange mass spectrometry, a method compatible with the low concentration requirements of Nef. The results showed that HIV Nef contains a solvent-protected core, as previously demonstrated with both NMR and X-ray crystallography. SIV Nef, for which there is no structural information, had a similar protected core, although it was more flexible and dynamic than its HIV counterpart. Many of the regions outside the core in both SIV and HIV Nef were highly solvent exposed. However, limited protection from exchange was observed in both N- and C-terminal regions, suggesting the presence of structured elements. Protection from exchange was also observed in a large loop emanating from the core that was deleted for NMR and X-ray analysis. These data show that while the majority of Nef was highly solvent exposed, regions outside the core may have structural attributes which may contribute to Nef functions known to map to these regions.

Nef is an HIV accessory protein required for high-titer viral replication and AIDS progression. Previous studies have shown that the SH3 domains of Hck and Lyn bind to Nef via proline-rich sequences in vitro, identifying these Src-related kinases as potential targets for Nef in vivo. Association of Nef with Hck causes displacement of the intramolecular interaction between the SH3 domain and the SH2-kinase linker, leading to kinase activation both in vitro and in vivo. In this study, we investigated whether interaction with Nef induces activation of other Src family kinases (Lyn, Fyn, Src, and Lck) following coexpression with Nef in Rat-2 fibroblasts. Coexpression with Nef induced Hck kinase activation and fibroblast transformation, consistent with previous results. In contrast, coexpression of Nef with Lyn was without effect, despite equivalent binding of Nef to full-length Lyn and Hck. Furthermore, Nef was found to suppress the kinase and transforming activities of Fyn, the SH3 domain of which exhibits low affinity for Nef. Coexpression with Nef did not alter c-Src or Lck tyrosine kinase or transforming activity in this system. Differential modulation of Src family members by Nef may produce unique downstream signals depending on the profile of Src kinases expressed in a given cell type.