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Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation

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Abstract

Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the 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 incorporation profiles of the tritium label in the intact and trypsin-degraded PVA∆32 revealed 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. Presence of the channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ∆N-peptide, decrease in the label incorporation within the virion (a.a. 184-200) was also observed, indicating possible structural transition leading to the virion compactization. Based on the obtained data, we can conclude that part of the surface ∆N-peptide is inserted between the coils of the virion helix thus increasing the helix pitch and providing greater flexibility of the virion, which is important for intercellular transport of the viruses in the plants.

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Abbreviations

CP:

coat proteins

EM:

electron microscopy

PVA:

potato virus A

PVA∆32:

PVA virion lacking 32 amino acids at N-terminus

PVY:

potato virus Y

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Acknowledgments

The authors are grateful to Dr. E. V. Shtykova (Shubnikov Institute of Crystallography) for fruitful discussions.

Funding

This work was financially supported in part by the Russian Foundation for Basic Research (grant 18-04-00525a).

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Authors and Affiliations

  1. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia

    Alexander L. Ksenofontov, Ludmila A. Baratova, Pavel I. Semenyuk & Natalia V. Fedorova

  2. Faculty of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia

    Gennadii A. Badun

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  1. Alexander L. Ksenofontov
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Contributions

A.L.K. and L.A.B. concept of the study and supervision; A.L.K., G.A.B., N.V.F., and P.I.S. conducting experiments, discussion of the results of the study; A.L.K., L.A.B., and G.A.B. writing and editing of the manuscript.

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Correspondence to Alexander L. Ksenofontov.

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Ksenofontov, A.L., Baratova, L.A., Semenyuk, P.I. et al. Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation. Biochemistry Moscow 88, 2146–2156 (2023). https://doi.org/10.1134/S0006297923120167

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