Changes in the structure of potato virus A virions during limited proteolysis <i>in situ</i> according to tritium labeling data and computer simulation

Abstract

The coat proteins (CP) of potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. A comparative analysis of the structures of coat proteins (CPs) in intact PVA virions and in virus particles lacking the N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using the atomic resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/ interhelix contacts were determined. For this purpose, the approach of Lee and Richards (Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400) was used. Comparison of the incorporation profiles of the tritium label in intact and trypsin-degraded PVA∆32 revealed the position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. The presence of channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ∆N-peptide, a decrease in the label within the virion (a.a. 184-200) was also observed, indicating a possible structural transition leading to virion compactization. Based on the data obtained, we can conclude that part of the surface ∆N-peptide is located between the coils of the virion helix, which increases the helix pitch and provides greater flexibility of the virion, which is important for the intercellular transport of the viruses in the plants.