Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)

Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, A.; Ożyhar, Andrzej; Dobryszycki, Piotr

doi:10.1016/j.bbapap.2017.08.019

Cited by 19 publications

(37 citation statements)

References 71 publications

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“…The MW determined by AUC for both proteins (approximately 26.0 kDa for 44K and 35.6 kDa for 56K) were slightly higher than the masses determined by ESI‐MS (22.8 kDa and 34.0 kDa, respectively). A similar discrepancy was previously observed in our laboratory for highly charged IDPs: Starmaker from zebrafish, Starmaker‐like from medaka, and otolith matrix macromolecule‐64 (OMM‐64) from rainbow trout . We conclude that this abnormal behavior, especially evident for a 44K fragment, may be caused by sedimentation non‐ideality, which for most globular proteins becomes significant above 1 mg/mL .…”

Section: Resultssupporting

confidence: 73%

“…The sedimentation velocity AUC is complementary to the SEC and makes it possible to determine if a protein is oligomeric, disordered, or both, because the mass‐ and shape‐dependent rate of sedimentation and the mass‐dependent rate of diffusion are simultaneously measured. Both the analytical techniques have been shown to be useful for identifying IDPs …”

Section: Resultsmentioning

confidence: 99%

“…Relationship of fractional ratio f / f 0 on log ( MW ) for reference proteins (filled symbols), DMP1 44K and 56K fragments and acidic IDPs: Starmaker from zebrafish (Stm), Starmaker‐like from medaka (Stm‐l), and otolith matrix macromolecule 64 from rainbow trout (OMM64) . The lines represent the models estimated for native proteins, natively unfolded pre‐molten globule‐like proteins (NU PMG‐like) and natively unfolded coil‐like proteins (NU coil‐like).…”

Section: Resultsmentioning

confidence: 99%

“…Interestingly, a lot of proteins involved in the biomineralization of calcium phosphate and calcium carbonate are IDPs . These include, for example, mammalian proteins: osteopontin (OPN), bone sialoprotein (BSP), dentin sialophosphoprotein (DSPP), as well as a zebrafish otolith matrix protein Starmaker (Stm), and its homologs from other fish species . However, more ordered proteins are also involved, for example: otoconin‐90 (OC90), amorphous calcium carbonate‐binding protein (ACCBP), otolin‐1 …”

Section: Introductionmentioning

confidence: 99%

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Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

et al. 2020

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Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.

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Section: Resultssupporting

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

et al. 2020

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“…A similar regulation of nucleation and mineral growth through phosphorylation has been shown in amelogenin in enamel [60,61]. It has also been shown that, with IDPs, an increased degree of calcium binding leads to greater compaction of the protein, allowing for closer packing and thereby regulating the extent of crystal growth [45,59].…”

Section: The Importance Of Phosphorylation In Nucleation and Polymorpmentioning

confidence: 55%

The inner ear proteome of fish

et al. 2018

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The mechanisms that underpin the formation, growth and composition of otoliths, the biomineralized stones in the inner ear of fish, are largely unknown, as only a few fish inner ear proteins have been reported. Using a partial transcriptome for the inner ear of black bream (Acanthopagrus butcheri), in conjunction with proteomic data, we discovered hundreds of previously unknown proteins in the otolith. This allowed us to develop hypotheses to explain the mechanisms of inorganic material supply and daily formation of growth bands. We further identified a likely protein mediator of crystal nucleation and an explanation for the apparent metabolic inertness of the otolith. Due to the formation of both daily and annual increments, otoliths are routinely employed as natural chronometers, being used for age and growth estimation, fisheries stock assessments, and the reconstruction of habitat use, movement, diet and the impacts of climate change. Our findings provide an unprecedented view of otolith molecular machinery, aiding in the interpretation of these essential archived data.

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Diversity of hydrodynamic radii of intrinsically disordered proteins

Białobrzewski,

Klepka,

Michaś

et al. 2023

Eur Biophys J

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Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.

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Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)

Cited by 19 publications

References 71 publications

Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

The inner ear proteome of fish

Diversity of hydrodynamic radii of intrinsically disordered proteins

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