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Effect of the Coat Protein N-Terminal Domain Structure on the Structure and Physicochemical Properties of Virions of Potato Virus X and Alternanthera Mosaic Virus

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Abstract

The amino acid sequences of the coat proteins (CPs) of the potexviruses potato virus X (PVX) and alternanthera mosaic virus (AltMV) share ~40% identity. The N-terminal domains of these proteins differ in the amino acid sequence and the presence of the N-terminal fragment of 28 residues (∆N peptide) in the PVX CP. Here, we determined the effect of the N-terminal domain on the structure and physicochemical properties of PVX and AltMV virions. The circular dichroism spectra of these viruses differed significantly, and the melting point of PVX virions was 10-12°C higher than that of AltMV virions. Alignment of the existing high-resolution 3D structures of the potexviral CPs showed that the RMSD value between the Cα-atoms was the largest for the N-terminal domains of the two compared models. Based on the computer modeling, the ∆N peptide of the PVX CP is fully disordered. According to the synchrotron small-angle X-ray scattering (SAXS) data, the structure of CPs from the PVX and AltMV virions differ; in particular, the PVX CP has a larger portion of crystalline regions and, therefore, is more ordered. Based on the SAXS data, the diameters of the PVX and AltMV virions and helix parameters in solution were calculated. The influence of the conformation of the PVX CP N-terminal domain and its position relative to the virion surface on the virion structure was investigated. Presumably, an increased thermal stability of PVX virions vs. AltMV is provided by the extended N-terminal domain (ΔN peptide, 28 amino acid residues), which forms additional contacts between the adjacent CP subunits in the PVX virion.

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Abbreviations

AltMV:

alternanthera mosaic virus

cryo-EM:

cryo-electron microscopy

CP:

coat protein

PVX:

potato virus X

RNP:

ribonucleoprotein

SAXS:

small-angle X-ray scattering

TMV:

tobacco mosaic virus

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Acknowledgments

The experiments on the isolation and characterization of viral particles were performed with the assistance of the Interdisciplinary Research and Education School “Molecular Technologies of Living Systems and Synthetic Biology”, Lomonosov Moscow State University, using the equipment purchased under the Program of Development of Lomonosov Moscow State University.

Funding

The work was supported by the Ministry of Science and Higher Education within the framework of the State Assignment for the Federal Scientific Research Center “Crystallography and Photonics”, Russian Academy of Sciences (SAXS experiments).

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Authors and Affiliations

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

    Alexander L. Ksenofontov, Natalia V. Fedorova, Pavel I. Semenyuk & Alexander M. Arutyunyan

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

    Maxim V. Petoukhov, Vladimir V. Matveev & Eleonora V. Shtykova

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

    Maxim V. Petoukhov

  4. Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia

    Tatiana I. Manukhova, Ekaterina A. Evtushenko, Nikolai A. Nikitin & Olga V. Karpova

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  1. Alexander L. Ksenofontov
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  2. Maxim V. Petoukhov
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  3. Vladimir V. Matveev
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  4. Natalia V. Fedorova
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  5. Pavel I. Semenyuk
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  6. Alexander M. Arutyunyan
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  7. Tatiana I. Manukhova
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  8. Ekaterina A. Evtushenko
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  9. Nikolai A. Nikitin
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  10. Olga V. Karpova
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  11. Eleonora V. Shtykova
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Contributions

A. L. Ksenofontov and E. V. Shtykova developed the concept and supervised the study; A. L. Ksenofontov, M. V. Petoukhov, V. V. Matveev, N. V. Fedorova, A. M. Arutyunyan, T. I. Manukhova, and E. A. Evtushenko performed the experiments; M. V. Petoukhov, O. V. Karpova, and P. I. Semenyuk discussed research results; A. L. Ksenofontov, M. V. Petoukhov, and E. V. Shtykova wrote the article; N. A. Nikitin and O. V. Karpova edited the manuscript.

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Correspondence to Alexander L. Ksenofontov.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain description of studies with human participants or animals performed by any of the authors.

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Ksenofontov, A.L., Petoukhov, M.V., Matveev, V.V. et al. Effect of the Coat Protein N-Terminal Domain Structure on the Structure and Physicochemical Properties of Virions of Potato Virus X and Alternanthera Mosaic Virus. Biochemistry Moscow 88, 119–130 (2023). https://doi.org/10.1134/S0006297923010108

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