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The Structure of the Potato Virus A Particles Elucidated by Small Angle X-Ray Scattering and Complementary Techniques

Eleonora V. Shtykova1,a, Maxim V. Petoukhov1, Natalia V. Fedorova2, Alexander M. Arutyunyan2, Eugene V. Skurat3, Larisa V. Kordyukova2 , Andrey V. Moiseenko3, and Alexander L. Ksenofontov1,2,b*

1Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences, 119333 Moscow, Russia

2Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia

3Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia

* To whom correspondence should be addressed.

Received August 26, 2020; Revised September 27, 2020; Accepted September 27, 2020
Potato virus A (PVA) protein coat contains on its surface partially unstructured N-terminal domain of the viral coat protein (CP), whose structural and functional characteristics are important for understanding the mechanism of plant infection with this virus. In this work, we investigated the properties and the structure of intact PVA and partially trypsinized PVAΔ32 virions using small-angle X-ray scattering (SAXS) and complimentary methods. It was shown that after the removal of 32 N-terminal amino acids of the CP, the virion did not disintegrate and remained compact, but the helical pitch of the CP packing changed. To determine the nature of these changes, we performed ab initio modeling, including the multiphase procedure, with the geometric bodies (helices) and restoration of the PVA structure in solution using available high-resolution structures of the homologous CP from the PVY potyvirus, based on the SAXS data. As a result, for the first time, a low-resolution structure of the filamentous PVA virus, both intact and partially degraded, was elucidated under conditions close to natural. The far-UV circular dichroism spectra of the PVA and PVAΔ32 samples differed significantly in the amplitude and position of the main negative maximum. The extent of thermal denaturation of these samples in the temperature range of 20-55°C was also different. The data of transmission electron microscopy showed that the PVAΔ32 virions were mostly rod-shaped, in contrast to the flexible filamentous particles typical of the intact virus, which correlated well with the SAXS results. In general, structural analysis indicates an importance of the CP N-terminal domain for the vital functions of PVA, which can be used to develop a strategy for combating this plant pathogen.
KEY WORDS: potyviruses, coat protein, potato virus A, N-terminal disordered domains, small-angle X-ray scattering, structural modeling

DOI: 10.1134/S0006297921020115