Effect of Mutations in the N-Terminal Peptide of the Coat Protein on the Structure of Potato Virus X According to Small-Angle X-Ray Scattering and Molecular Dynamics

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Alexander L. Ksenofontov^1,a*, Maxim V. Petoukhov², Alexander M. Arutyunyan¹, Ilya P. Oleynikov¹, Georgy S. Peters³, Lyudmila A. Baratova¹, Marina V. Arkhipenko⁴, Nikolai A. Nikitin⁴, Olga V. Karpova⁴, and Eleonora V. Shtykova²

¹Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

²Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia

³National Research Center “Kurchatov Institute”, 123182 Moscow, Russia

⁴Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia

^* To whom correspondence should be addressed.

Received: December 24, 2025; Revised: February 9, 2026; Accepted: February 10, 2026

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Mutations in the N-terminal peptide (Ser-Thr to Ala-Gly substitution) of the coat protein (CP) of potato virus X (PVX-ST) render its genomic RNA translationally competent, unlike in the wild-type PVX virions. Consequently, RNA within the PVX-ST virions can be translated without additional triggers (such as phosphorylation or interaction with the triple gene block 1 protein), unlike the encapsidated RNA of the wild-type virus. Comprehensive structural analysis using molecular dynamics (MD), small-angle X-ray scattering (SAXS), and tritium planigraphy revealed differences in the virion organization. The mutations were shown to increase hydrophobicity and induce partial folding of the N-terminal peptides. This triggers structural rearrangement in the PVX-ST virion: packing density of the coat proteins within the helical capsid is altered. This conclusion is supported by the SAXS data, increased accessibility for tritium labeling of the key CP domains (including the RNA-binding region), and reduced stability against the action of the sodium dodecyl sulfate detergent. The obtained results provide explanation for the mechanism by which the encapsidated RNA of the PVX-ST mutant becomes accessible to ribosomes. This mechanism is associated with structural rearrangement of the N-terminal coat protein peptide and change in the packing density of the helical capsid.

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KEY WORDS: potato virus X, coat protein, N-terminal peptide, translational activation of virion RNA, small-angle X-ray scattering, circular dichroism, molecular modeling, tritium planigraphy

DOI: 10.1134/S0006297925604472

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