Characterization of intramolecular interactions of HIV-1 accessory protein Nef by differential scanning calorimetry

The interactions between the N-terminal arm and the structural core of Nef, an HIV-1 accessory protein, have been studied by high sensitivity differential scanning calorimetry. Critical interactions have been identified by measuring the structural energetics of both truncation and point mutants of the protein. These studies demonstrate that the N-terminal arm of Nef strongly interacts with the core and that it contributes close to 4.3 kcal/mol to the stability of the entire protein. The interactions are not evenly distributed through the N-terminal arm. Two strongly interacting regions have been identified: the region between residues 1 and 40 that contributes 1.6 kcal/mol to the stability of Nef; and, the region between residues 50 and 61 that contributes 2.7 kcal/mol. Other regions (e.g. residues 41 to 49) appear to contribute little to the interaction. The identification of these, until now, elusive interactions provides a physical foundation for allosteric effects between N-terminal arm and protein core elicited by different binding partners.