Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin

Takeda, Susumu; Fujiwara, Ikuko; Sugimoto, Yoshiaki; Oda, Tatsuya; Narita, Akihiro; Maéda, Yuichiro

doi:10.1007/s10974-019-09571-5

Cited by 7 publications

(4 citation statements)

References 41 publications

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“…Focusing on the SLC-corrected ensemble, the main contribution to the radius of gyration and the RMSF comes from the long N-terminal disordered region with significant fluctuations also found in the two main linkers connecting the G2 domain to the G3 domain and the G3 domain to the G4 domain ( Figure 6 ). Referring to high-resolution data for some of the isolated domains (also in the presence of Ca 2+ and/or actin), 76 − 78 GSN appears reasonably stable, suggesting that the model with smaller fluctuations is preferable.…”

Section: Resultsmentioning

confidence: 95%

Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

Ballabio,

Paissoni,

Bollati

et al. 2023

J. Chem. Theory Comput.

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Small-angle X-ray and neutron scattering (SAXS/ SANS) provide valuable insights into the structure and dynamics of biomolecules in solution, complementing a wide range of structural techniques, including molecular dynamics simulations. As contrastbased methods, they are sensitive not only to structural properties but also to solvent−solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. In this work, we demonstrate the feasibility of calculating SAXS and SANS intensities using a coarsegrained representation consisting of one bead per amino acid and three beads per nucleic acid, with form factors that can be corrected on the fly to account for solvation effects at no additional computational cost. By coupling this forward model with molecular dynamics simulations restrained with SAS data, it is possible to determine conformational ensembles or refine the structure and dynamics of proteins and nucleic acids in agreement with the experimental results. To assess the robustness of this approach, we applied it to gelsolin, for which we acquired SAXS data on its closed state, and to a UP1-microRNA complex, for which we used previously collected measurements. Our hybrid-resolution small-angle scattering (hySAS) implementation, being distributed in PLUMED, can be used with atomistic and coarse-grained simulations using diverse restraining strategies.

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Section: Resultsmentioning

confidence: 95%

Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

Ballabio,

Paissoni,

Bollati

et al. 2023

J. Chem. Theory Comput.

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“…The gel-filtrated actin samples used for the crystallization of cWT_ADP-Pi and Q137A_ADP-P i were further polished by one cycle of polymerization and depolymerization. The Physarum polycephalum fragmin F1 domain (residues 1–160), expressed using an Escherichia coli expression system, was purified as described previously ( Takeda et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis

Iwasa

Takeda

Narita

et al. 2023

Front. Cell Dev. Biol.

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The dynamic assembly of actin is controlled by the hydrolysis of ATP, bound to the center of the molecule. Upon polymerization, actin undergoes a conformational change from the monomeric G-form to the fibrous F-form, which is associated with the flipping of the side chain of His161 toward ATP. His161 flipping from the gauche-minus to gauche-plus conformation leads to a rearrangement of the active site water molecules, including ATP attacking water (W1), into an orientation capable of hydrolysis. We previously showed that by using a human cardiac muscle α-actin expression system, mutations in the Pro-rich loop residues (A108G and P109A) and in a residue that was hydrogen-bonded to W1 (Q137A) affect the rate of polymerization and ATP hydrolysis. Here, we report the crystal structures of the three mutant actins bound to AMPPNP or ADP-Pi determined at a resolution of 1.35–1.55 Å, which are stabilized in the F-form conformation with the aid of the fragmin F1 domain. In A108G, His161 remained non-flipped despite the global actin conformation adopting the F-form, demonstrating that the side chain of His161 is flipped to avoid a steric clash with the methyl group of A108. Because of the non-flipped His161, W1 was located away from ATP, similar to G-actin, which was accompanied by incomplete hydrolysis. In P109A, the absence of the bulky proline ring allowed His161 to be positioned near the Pro-rich loop, with a minor influence on ATPase activity. In Q137A, two water molecules replaced the side-chain oxygen and nitrogen of Gln137 almost exactly at their positions; consequently, the active site structure, including the W1 position, is essentially conserved. This seemingly contradictory observation to the reported low ATPase activity of the Q137A filament could be attributed to a high fluctuation of the active site water. Together, our results suggest that the elaborate structural design of the active site residues ensures the precise control of the ATPase activity of actin.

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“…Gelsolin is composed of six domains, which can severe actin filaments (Nag et al, 2013). It can cut the actin filaments released by dead cells in the plasma, thereby boosting metabolism (Takeda et al, 2020). Gelsolin severs actin filaments in a Ca 2+ -dependent manner and coats the barbed ends of F-actin (Takeda et al, 2020).…”

Section: Gelsolin Superfamilymentioning

confidence: 99%

“…It can cut the actin filaments released by dead cells in the plasma, thereby boosting metabolism (Takeda et al, 2020). Gelsolin severs actin filaments in a Ca 2+ -dependent manner and coats the barbed ends of F-actin (Takeda et al, 2020). The amino-terminal of gelsolin binds to two actin monomers, and F-actin can be severed without free calcium.…”

Section: Gelsolin Superfamilymentioning

confidence: 99%

Actin polymerization and depolymerization in developing vertebrates

Bai,

Zhao,

et al. 2023

Front. Physiol.

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Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.

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Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin

Cited by 7 publications

References 41 publications

Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations

Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis

Actin polymerization and depolymerization in developing vertebrates

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