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Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium
Author(s) -
Shishkov Alexander,
Bogacheva Elena,
Fedorova Natalia,
Ksenofontov Alexander,
Badun Gennadii,
Radyukhin Victor,
Lukashina Elena,
Serebryakova Marina,
Dolgov Alexey,
Chulichkov Alexey,
Dobrov Evgeny,
Baratova Lyudmila
Publication year - 2011
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2011.08392.x
Subject(s) - chemistry , tritium , domain (mathematical analysis) , crystallography , c terminus , proteolysis , protein structure , protein domain , matrix (chemical analysis) , biophysics , amino acid , biochemistry , physics , chromatography , biology , mathematical analysis , mathematics , nuclear physics , gene , enzyme
The structure of the C‐terminal domain of the influenza virus A matrix M1 protein, for which X‐ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally‐activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C‐terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C‐terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C‐terminal domain is an almost flat layer with a three‐α‐helical structure. To explain the high level of tritium label incorporation into the C‐terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI‐TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C‐terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell.