Structure of the HIV-1 gag polyprotein in solution

Human immunodeficiency virus type 1 (HIV-1) belongs to a family of enveloped retroviruses that cause fatal diseases in humans. The Gag polyprotein is the main structural element of HIV-1. In the viral lifecycle, it is responsible for the assembly and release of virions from the host cell. In this study, small-angle X-ray scattering (SAXS) was used to provide a high-resolution structure of recombinant non-myristoylated Gag lacking the p6 domain (Gag-Δp6) in solution at three different concentrations. To ensure the reliability of the results and conclusions, various independent approaches to SAXS data interpretation were used along with modern computational methods, such as the AlphaFold3 and molecular dynamics (MD). At low concentration of 2 mg/ml only Gag-Δp6 monomers were observed in solution, while at a concentration of 8 mg/ml the SAXS invariants calculated from the scattering curves definitely corresponded to a trimeric polyprotein organization. Larger oligomers and any virus-like particles were not observed. Subsequent structural modeling revealed that Gag-Δp6 is highly labile and lacks a stable, well-defined three-dimensional structure in either monomeric or trimeric state in solution. These unique structural properties - flexibility, lability, and the relative positions of the Gag polyprotein chains within the trimer, first identified in this study - may be crucial for the formation of new virions.