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. 2023 May 31;13(1):8841.
doi: 10.1038/s41598-023-34814-4.

Molecular structure of soluble vimentin tetramers

Affiliations

Molecular structure of soluble vimentin tetramers

Pieter-Jan Vermeire et al. Sci Rep. .

Erratum in

Abstract

Intermediate filaments (IFs) are essential constituents of the metazoan cytoskeleton. A vast family of cytoplasmic IF proteins are capable of self-assembly from soluble tetrameric species into typical 10-12 nm wide filaments. The primary structure of these proteins includes the signature central 'rod' domain of ~ 300 residues which forms a dimeric α-helical coiled coil composed of three segments (coil1A, coil1B and coil2) interconnected by non-helical, flexible linkers (L1 and L12). The rod is flanked by flexible terminal head and tail domains. At present, the molecular architecture of mature IFs is only poorly known, limiting our capacity to rationalize the effect of numerous disease-related mutations found in IF proteins. Here we addressed the molecular structure of soluble vimentin tetramers which are formed by two antiparallel, staggered dimers with coil1B domains aligned (A11 tetramers). By examining a series of progressive truncations, we show that the presence of the coil1A domain is essential for the tetramer formation. In addition, we employed a novel chemical cross-linking pipeline including isotope labelling to identify intra- and interdimeric cross-links within the tetramer. We conclude that the tetramer is synergistically stabilized by the interactions of the aligned coil1B domains, the interactions between coil1A and the N-terminal portion of coil2, and the electrostatic attraction between the oppositely charged head and rod domains. Our cross-linking data indicate that, starting with a straight A11 tetramer, flexibility of linkers L1 and L12 enables 'backfolding' of both the coil1A and coil2 domains onto the tetrameric core formed by the coil1B domains. Through additional small-angle X-ray scattering experiments we show that the elongated A11 tetramers dominate in low ionic strength solutions, while there is also a significant structural flexibility especially in the terminal domains.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
SEC-MALS profiles of vimentin tetramers and its progressive truncations on a Superdex 200 Increase column. Across each elution peaks, MALS-derived molecular weight profiles are also shown (right axis). (A) Elution of FL vimentin in LS buffer (2 mM HEPES, pH 8.2). (B) Elution of different truncations in HS buffer (10 mM HEPES, 150 mM NaCl, pH 7.5).
Figure 2
Figure 2
Chemical cross-linking of vimentin samples. (A) Reducing SDS-PAGE analysis of the FL vimentin in LS buffer before (control, ctrl) and after chemical cross-linking with DSG, DSPU and DSBU. Molar excess of the cross-linker over the protein is indicated. M stands for a molecular weight marker. The likely composition of different bands is given at the left-hand side of the gels. The original uncropped gels for panels (A) and (B) are presented in Supplementary Fig. 1. (B) Reducing SDS-PAGE of vimentin truncation constructs cross-linked with DSG in either LS or HS conditions. (C) Classification of the FL vimentin XLs as intra- or interdimeric using the α-ratio calculated from the 14N/15N data. The yellow zone corresponds to intradimeric XLs between close-by residues.
Figure 3
Figure 3
Vimentin tetramer models. (A) Elongated A11 tetramer. Coil1A is shown in orange, coil1B in green, coil2 in blue. Satisfied XLs are shown as solid red lines and the XLs exceeding the distance cut-offs are shown as red dashed lines. For clarity, only one instance of each unique XL is drawn (for instance, the XL connecting residue K143 in dimer1 and residue K223 in dimer2 is present, while the XL connecting K223 in dimer1 and K143 in dimer2 is not shown). (B) Backfolded, compact tetramer. (C) AlphaFold modelling of the terminal domains. The upper part shows the head in red together with the beginning of the rod domain (coil1A and part of coil1B) in grey. The lower part shows the tail in magenta together with the end of the rod domain (part of coil2). N- and C-termini of the rod are labelled. (D) Elongated tetramer with head and tail domains. For clarity, only the terminal domains for a single dimer are displayed. Here, one of the head domains (Head1) is modelled to mainly interact with coil1B, while the other one (Head2) is mainly interacting with coil1A. (E) Compact tetramer model with terminal domains.
Figure 4
Figure 4
SEC-SAXS analysis. (A) SAXS curves for the FL vimentin corresponding to the beginning (red), center (green) and end (blue) of the elution. The SAXS curve for the elution peak of Vim93-302-Eb1 is overlaid in black. (B) Top: Elution profile of the FL vimentin tetramer from a Superose 6 Increase 3.2/300 column in 2 mM HEPES pH 8.2, 1% sucrose. The frames taken for the beginning, center and end of the elution peak are indicated below the curve. Across the elution peak, the Rg values per frame are plotted as black dots. Bottom: Elution profile for the Vim93-302-Eb1 fragment from a BioSEC-3 300 Å column in 10 mM HEPES buffer, 150 mM NaCl, pH 7.5. (C) Guinier analysis for the end of the elution peak of the FL vimentin (blue, top) and for the Vim93-302-Eb1 fragment (black, bottom). (D) The corresponding intraparticle distance distribution functions P(r). (E) Atomic model of Vim93-302-Eb1 shown as ribbon. The capping motif is colored red. (F) Scattering calculated from the Vim93-302Eb1 model (red line) fitted to experimental data for this fragment (open circles). (G) Low-resolution model of FL vimentin tetramer (semi-transparent spheres) obtained using SAXS data. The model is superimposed with the elongated vimentin tetramer model (ribbon). (H) Calculated scattering from the elongated tetramer model (green line) and compact tetramer model (orange line) fitted to experimental data for the end of SEC elution peak (open circles).

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