Unusual Properties of Structural Characteristics of Potato Virus A Coat Protein in Solution Revealed by SAXS
- Dr. Eleonora SHTYKOVA
- Dr. A.L. KSENOFONTOV (Moscow State University, Moscow, Russia)
- Dr. N.V. FEDOROVA (Moscow State University, Moscow, Russia)
- Prof. L.A. BARATOVA (Moscow State University, Moscow, Russia)
- Prof. E.N. DOBROV (Moscow State University, Moscow, Russia)
- Dr. Eleonora SHTYKOVA (Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences)
Structural analysis of the Potato Virus A Coat Protein (PVA CP) in solution was performed by small angle X-ray scattering (SAXS). SAXS experiments were carried out using synchrotron radiation at the P12 beamline at the Petra III storage ring (DESY, Hamburg). Modern techniques for interpretation of scattering data and structural modeling, including ab initio protocol, have been applied in the present work . Obtained values of radii of gyration (Rg =8.9 ± 0.1 nm for PVA CP at pH 7.8 and Rg=8.5 ± 0.1 nm for this protein at pH10.5) are too large to be a characteristic of the isolated protein macromolecule with molecular mass of 30.26 kDa calculated from the amino acid sequence of PVA CP. The average molecular masses (MMs) of the solutes were obtained by us (i) from the extrapolated I(0) and (ii) from the excluded (Porod) volumes Vp of the species. MMs calculated by these 2 independent methods clearly indicate formation of large aggregates containing dozens (30-60) of individual PVA CP macromolecules. Thus, the overall parameters (Rg, excluded Porod volume, MMs) point to the existence in the solution of large particles consisting of many protein macromolecules. On the other hand, Porod plots as well as Kratky plots revealed rather compact particles with definite shapes though less expressed for PVA CP at higher pH. It means that possibly we observed not aggregates, which as a rule do not possess a certain shape, but we can see a formation of some kind of ordered structures, most possible short virus-like particles (VLPs). The structure and overall characteristics of the VLPs depend strongly on such solution condition as pH: while a scattering curve from the sample at pH 7.8 demonstrates intensity pattern characteristic for a specific compact scattering object, SAXS curve from PVA CP changes dramatically at pH 10.5 and corresponds to a partly disordered body without clearly defined boundaries: the CP associates at pH 7.8 are more compact then those at pH 10.8. The shape of PVA CP at lower pH obtained by ab initio method is closed to a cylinder, thereby reproducing the shape of the virus, i.e. this self-assembling in solution to short VLP is an intrinsic biological property of the PVA CP allowing it to create an envelope to protect genetic material of the virus. Increasing pH leads to a partial distortion of this virus-like ensemble: the whole shape of the PVA CP associates at pH 10.5 becomes loose and splits into separate spherical parts. Thus, according to McDonald and Bancroft [2, 3], PVY CP at pH 10.5 disintegrates into monomers, destroying the structure of the VLP and pointing to the way of the virus deactivation. This work was supported in part by Russian Foundation for Basic Researches (projects 15-54-74002 EMBL, 15-04-01406, 16-03-00375 and 16-04-00563). References  Blanchet, C.E. and Svergun, D.I. (2013), Annu. Rev. Phys. Chem. 64, 37-54  Mc Donald JG, Beveridge TJ, Bancroft JB.(1976), Virology, 69 (1), 327-331.  Mc Donald JG and Bancroft JB. (1977), J. Gen.Virol., 35, 261-263.