Influence of in situ limited proteolysis of potato virus X on change in the structure of virions according to data small-angle X-ray scattering and tritium labeling

The viral capsids of the potexvirus family are characterized by the presence on the surface of virions of partially disordered N-terminal fragments of proteins of various lengths. The present study is devoted to studying the effect of in situ removal of the N-terminal domain of the coat protein (CP) on the structural organization and physicochemical properties of potato virus X (PVX) virions. The work considers PVX virions containing an intact Ps-form CP, as well as virions including an in situ degraded Pf-form devoid of 19/21 amino acid residues from the N-end (PVXΔN). Synchrotron small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), tritium bombardment, and several other physicochemical methods were used for the study. Analysis of images obtained using TEM revealed similarities in the architecture of filamentous PVX and PVXΔN virions. SAXS results demonstrated differences in the organization of the capsid of PVX and PVXΔN virions: the latter was characterized by a reduction in the size of ordered regions, indicating partial disruption of the structure of the viral protein framework. In addition, based on the SAXS scattering curves, parameters of the spiral packing of virions in solution were calculated, and structural modeling of particles was performed. Modeling results also indicate changes in the structure of the capsid due to the removal of the ΔN-peptide. Using information about the secondary structure of the PVX model (PDB ID: 6R7G) and data from our previous studies on tritium labeling of surface sites of PVX and PVXΔN virions, a comparative analysis of label incorporation profiles into elements of the protein's secondary structure was conducted. This approach made it possible to predict the localization of the ΔN-peptide above the amino acid residues of neighboring helical subunits (122-129 and 143-153) and demonstrate the stabilizing role of this peptide on the overall structure of the virion. An increase in the level of the label in the C-terminal region after removing the ΔN-peptide also indicates a decrease in the compactness of the virion. Overall, the knowledge gained will be useful when using virus-like nanoparticles in biotechnology.