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Research article - Peer-reviewed, 2020

Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus

Agback, Peter; Shernyukov, Andrey; Dominguez, Francisco; Agback, Tatiana; Frolova, Elena I.

Abstract

In recent years, intrinsically disordered proteins (IDPs) and disordered domains have attracted great attention. Many of them contain linear motifs that mediate interactions with other factors during formation of multicomponent protein complexes. NMR spectrometry is a valuable tool for characterizing this type of interactions on both amino acid (aa) and atomic levels. Alphaviruses encode a nonstructural protein nsP3, which drives viral replication complex assembly. nsP3 proteins contain over 200-aa-long hypervariable domains (HVDs), which exhibits no homology between different alphavirus species, are predicted to be intrinsically disordered and appear to be critical for alphavirus adaptation to different cells. Previously, we have shown that nsP3 HVD of chikungunya virus (CHIKV) is completely disordered with low tendency to form secondary structures in free form. In this new study, we used novel NMR approaches to assign the spectra for the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV). The HVDs of CHIKV and VEEV have no homology but are both involved in replication complex assembly and function. We have found that VEEV nsP3 HVD is also mostly disordered but contains a short stable alpha-helix in its C-terminal fragment, which mediates interaction with the members of cellular Fragile X syndrome protein family. Our NMR data also suggest that VEEV HVD has several regions with tendency to form secondary structures.

Keywords

NMR; MUSIC pulse sequences; nsP3; IDP; VEEV

Published in

Molecules (Basel, Switzerland)
2020, volume: 25, number: 24, article number: 5824
Publisher: MDPI

Authors' information

Swedish University of Agricultural Sciences, Department of Molecular Sciences
Sherniukov, Andrei
Swedish University of Agricultural Sciences, Department of Molecular Sciences
Sherniukov, Andrei
Vorozhtsov Novosibirsk Institute of Organic Chemistry
Dominguez, Francisco
University of Alabama at Birmingham (UAB)
Swedish University of Agricultural Sciences, Department of Molecular Sciences
Frolova, Elena I.
University of Alabama at Birmingham (UAB)

UKÄ Subject classification

Biochemistry and Molecular Biology

Publication Identifiers

DOI: https://doi.org/10.3390/molecules25245824

URI (permanent link to this page)

https://res.slu.se/id/publ/110191