High-resolution yeast actin structures indicate the molecular mechanism of actin filament stiffening by cations

• Published in: Communications chemistry 2024-07, Vol.7 (1), p.164-10, Article 164
• Main Authors: Xu, Xiao-Ping, Cao, Wenxiang, Swift, Mark F., Pandit, Nandan G., Huehn, Andrew E., Sindelar, Charles V., De La Cruz, Enrique M., Hanein, Dorit, Volkmann, Niels
• Format: Article
• Language: English
• Subjects: 101/28; 631/535/1258/1259; 631/535/1267; 631/92/612/1228; Alanine; Assembly; Binding sites; Cations; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Cryoforming; Cryogenic properties; Filaments; Glutamic acid; High resolution; Magnesium; Mechanical properties; Residues; Stiffening; Stiffness; Vertebrates; Vitrification; Workflow; Yeast
• ISSN: 2399-3669; 2399-3669
• DOI: 10.1038/s42004-024-01243-x

Actin filament assembly and the regulation of its mechanical properties are fundamental processes essential for eukaryotic cell function. Residue E167 in vertebrate actins forms an inter-subunit salt bridge with residue K61 of the adjacent subunit. Saccharomyces cerevisiae actin filaments are more flexible than vertebrate filaments and have an alanine at this position (A167). Substitution of this alanine for a glutamic acid (A167E) confers Saccharomyces cerevisiae actin filaments with salt-dependent stiffness similar to vertebrate actins. We developed an optimized cryogenic electron microscopy workflow refining sample preparation and vitrification to obtain near-atomic resolution structures of wild-type and A167E mutant Saccharomyces cerevisiae actin filaments. The difference between these structures allowed us to pinpoint the potential binding site of a filament-associated cation that controls the stiffness of the filaments in vertebrate and A167E Saccharomyces cerevisiae actins. Through an analysis of previously published high-resolution reconstructions of vertebrate actin filaments, along with a newly determined high-resolution vertebrate actin structure in the absence of potassium, we identified a unique peak near residue 167 consistent with the binding of a magnesium ion. Our findings show how magnesium can contribute to filament stiffening by directly bridging actin subunits and allosterically affecting the orientation of the DNase-I binding loop of actin, which plays a regulatory role in modulating actin filament stiffness and interactions with regulatory proteins. Actin filament assembly and the regulation of its mechanical properties are fundamental processes essential for eukaryotic cell function, however, the molecular mechanisms that govern the mechanical properties of the actin filaments formed from different species are not fully understood. Here, the authors report high-resolution cryo-EM reconstructions of yeast actin from Saccharomyces cerevisiae and propose how the mechanism of the stiffening of the actin filament is affected by magnesium cations.