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Różycka MO, Bielak K, Ptak M, Jost B, Melo Rodriguez G, Schoelkopf J, Stolarski J, Dobryszycki P, Ożyhar A. Effect of Gel Exposition on Calcium and Carbonate Ions Determines the Stm-l Effect on the Crystal Morphology of Calcium Carbonate. Biomacromolecules 2023; 24:4042-4050. [PMID: 37605889 PMCID: PMC10498444 DOI: 10.1021/acs.biomac.3c00395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/22/2023] [Indexed: 08/23/2023]
Abstract
Biomineralization of fish otoliths is regulated by macromolecules, such as proteins, whose presence is crucial for the functionality and properties of these mineralized structures. Special regulatory effects are exerted by intrinsically disordered proteins, such as the polyanionic Starmaker-like protein from medaka, a homolog of zebrafish Starmaker. In this study, we employed a set of bioinspired mineralization experiments with a single diffusion system to investigate the effect of the Starmaker-like protein on calcium carbonate biominerals with regards to the prior exposition of the protein to calcium or carbonate ions. Interestingly, the bioinspired minerals grown in the presence of the Starmaker-like protein in calcium- or carbonate-type experiments differ significantly in terms of morphology and protein distribution within the crystals. Our deeper analysis shows that the Starmaker-like protein action is a result of the environmental conditions to which it is exposed. These findings may be of special interest in the areas of biomineralization process pathways and biomaterial sciences.
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Affiliation(s)
- Mirosława O. Różycka
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Klaudia Bielak
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Maciej Ptak
- Institute
of Low Temperature and Structure Research, Polish Academy of Sciences, Wroclaw 50-422, Poland
| | | | | | | | - Jarosław Stolarski
- Institute
of Paleobiology, Polish Academy of Sciences, Warsaw 00-818, Poland
| | - Piotr Dobryszycki
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Andrzej Ożyhar
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
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2
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Tarczewska A, Bielak K, Zoglowek A, Sołtys K, Dobryszycki P, Ożyhar A, Różycka M. The Role of Intrinsically Disordered Proteins in Liquid–Liquid Phase Separation during Calcium Carbonate Biomineralization. Biomolecules 2022; 12:biom12091266. [PMID: 36139105 PMCID: PMC9496343 DOI: 10.3390/biom12091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Some animal organs contain mineralized tissues. These so-called hard tissues are mostly deposits of calcium salts, usually in the form of calcium phosphate or calcium carbonate. Examples of this include fish otoliths and mammalian otoconia, which are found in the inner ear, and they are an essential part of the sensory system that maintains body balance. The composition of ear stones is quite well known, but the role of individual components in the nucleation and growth of these biominerals is enigmatic. It is sure that intrinsically disordered proteins (IDPs) play an important role in this aspect. They have an impact on the shape and size of otoliths. It seems probable that IDPs, with their inherent ability to phase separate, also play a role in nucleation processes. This review discusses the major theories on the mechanisms of biomineral nucleation with a focus on the importance of protein-driven liquid–liquid phase separation (LLPS). It also presents the current understanding of the role of IDPs in the formation of calcium carbonate biominerals and predicts their potential ability to drive LLPS.
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3
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Kalka M, Markiewicz N, Ptak M, Sone ED, Ożyhar A, Dobryszycki P, Wojtas M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization. FASEB J 2019; 33:6877-6886. [PMID: 30840836 DOI: 10.1096/fj.201802268r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Otoliths are one of the biominerals whose formation is highly controlled by proteins. The first protein discovered to be involved in otolith biomineralization in zebrafish was starmaker (Stm). Previously, Stm was shown to be responsible for the preferential formation of aragonite, a polymorph of calcium carbonate, in otoliths. In this work, proteomic analysis of adult zebrafish otoliths was performed. Stm is the only highly phosphorylated protein found in our studies. Besides previously studied otolith proteins, we discovered several dozens of unknown proteins that reveal the likely mechanism of biomineralization. A comparison of aragonite and vaterite otoliths showed similarities in protein composition. We observed the presence of Stm in both types of otoliths. In vitro studies of 2 characteristic Stm fragments indicated that the DS-rich region has a special biomineralization activity, especially after phosphorylation.-Kalka, M., Markiewicz, N., Ptak, M., Sone, E. D., Ożyhar, A., Dobryszycki, P., Wojtas, M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.
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Affiliation(s)
- Marta Kalka
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Natalia Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Maciej Ptak
- Division of Optical Spectroscopy, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Wrocław, Poland; and
| | - Eli D Sone
- Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
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4
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Poznar M, Hołubowicz R, Wojtas M, Gapiński J, Banachowicz E, Patkowski A, Ożyhar A, Dobryszycki P. Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1358-1371. [PMID: 28866388 DOI: 10.1016/j.bbapap.2017.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/28/2017] [Indexed: 01/28/2023]
Abstract
Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed.
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Affiliation(s)
- Monika Poznar
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Rafał Hołubowicz
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Wojtas
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jacek Gapiński
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Ewa Banachowicz
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Adam Patkowski
- A. Mickiewicz University, Faculty of Physics, Molecular Biophysics Division, Umultowska 85, 61-614, Poznań, Poland
| | - Andrzej Ożyhar
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Piotr Dobryszycki
- Wrocław University of Science and Technology, Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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5
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Yarawsky AE, English LR, Whitten ST, Herr AB. The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. J Mol Biol 2017; 429:261-279. [PMID: 27890783 PMCID: PMC5363081 DOI: 10.1016/j.jmb.2016.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022]
Abstract
Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a 135-aa-long, proline/glycine-rich region (PGR) that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the PGR using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide with unusually high polyproline type II helix propensity. In contrast to many intrinsically disordered polypeptides, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon the addition of the osmolyte trimethylamine N-oxide or the cosolvent 2,2,2-trifluoroethanol. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B Herr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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6
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Borgia A, Zheng W, Buholzer K, Borgia MB, Schüler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, Schuler B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc 2016; 138:11714-26. [PMID: 27583570 PMCID: PMC5597961 DOI: 10.1021/jacs.6b05917] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) have reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.
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Affiliation(s)
- Alessandro Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Karin Buholzer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madeleine B. Borgia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anja Schüler
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Klaus Gast
- Physical Biochemistry, University of Potsdam, 14476 Potsdam, Germany
| | - Alexander Grishaev
- National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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7
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Loewen TN, Carriere B, Reist JD, Halden NM, Anderson WG. Linking physiology and biomineralization processes to ecological inferences on the life history of fishes. Comp Biochem Physiol A Mol Integr Physiol 2016; 202:123-140. [PMID: 27328377 DOI: 10.1016/j.cbpa.2016.06.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/07/2023]
Abstract
Biomineral chemistry is frequently used to infer life history events and habitat use in fishes; however, significant gaps remain in our understanding of the underlying mechanisms. Here we have taken a multidisciplinary approach to review the current understanding of element incorporation into biomineralized structures in fishes. Biominerals are primarily composed of calcium-based derivatives such as calcium carbonate found in otoliths and calcium phosphates found in scales, fins and bones. By focusing on non-essential life elements (strontium and barium) and essential life elements (calcium, zinc and magnesium), we attempt to connect several fields of study to synergise how physiology may influence biomineralization and subsequent inference of life history. Data provided in this review indicate that the presence of non-essential elements in biominerals of fish is driven primarily by hypo- and hyper-calcemic environmental conditions. The uptake kinetics between environmental calcium and its competing mimics define what is ultimately incorporated in the biomineral structure. Conversely, circannual hormonally driven variations likely influence essential life elements like zinc that are known to associate with enzyme function. Environmental temperature and pH as well as uptake kinetics for strontium and barium isotopes demonstrate the role of mass fractionation in isotope selection for uptake into fish bony structures. In consideration of calcium mobilisation, the action of osteoclast-like cells on calcium phosphates of scales, fins and bones likely plays a role in fractionation along with transport kinetics. Additional investigations into calcium mobilisation are warranted to understand differing views of strontium, and barium isotope fractionation between calcium phosphates and calcium carbonate structures in fishes.
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Affiliation(s)
- T N Loewen
- Interdisciplinary Studies (Geological Sciences), University of Manitoba, Winnipeg, MB, Canada; Freshwater Institute, Fisheries & Oceans, Winnipeg, MB, Canada.
| | - B Carriere
- Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - J D Reist
- Freshwater Institute, Fisheries & Oceans, Winnipeg, MB, Canada
| | - N M Halden
- Geological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - W G Anderson
- Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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8
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Wojtas M, Hołubowicz R, Poznar M, Maciejewska M, Ożyhar A, Dobryszycki P. Calcium ion binding properties and the effect of phosphorylation on the intrinsically disordered Starmaker protein. Biochemistry 2015; 54:6525-34. [PMID: 26445027 DOI: 10.1021/acs.biochem.5b00933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Starmaker (Stm) is an intrinsically disordered protein (IDP) involved in otolith biomineralization in Danio rerio. Stm controls calcium carbonate crystal formation in vivo and in vitro. Phosphorylation of Stm affects its biomineralization properties. This study examined the effects of calcium ions and phosphorylation on the structure of Stm. We have shown that CK2 kinase phosphorylates 25 or 26 residues in Stm. Furthermore, we have demonstrated that Stm's affinity for calcium binding is dependent on its phosphorylation state. Phosphorylated Stm (StmP) has an estimated 30 ± 1 calcium binding sites per protein molecule with a dissociation constant (KD) of 61 ± 4 μM, while the unphosphorylated protein has 28 ± 3 sites and a KD of 210 ± 22 μM. Calcium ion binding induces a compaction of the Stm molecule, causing a significant decrease in its hydrodynamic radius and the formation of a secondary structure. The screening effect of Na(+) ions on calcium binding was also observed. Analysis of the hydrodynamic properties of Stm and StmP showed that Stm and StmP molecules adopt the structure of native coil-like proteins.
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Affiliation(s)
- Magdalena Wojtas
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Rafał Hołubowicz
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Monika Poznar
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marta Maciejewska
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Andrzej Ożyhar
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Piotr Dobryszycki
- Wrocław University of Technology , Faculty of Chemistry, Department of Biochemistry, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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9
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Różycka M, Wojtas M, Jakób M, Stigloher C, Grzeszkowiak M, Mazur M, Ożyhar A. Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PLoS One 2014; 9:e114308. [PMID: 25490041 PMCID: PMC4260845 DOI: 10.1371/journal.pone.0114308] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/07/2014] [Indexed: 01/31/2023] Open
Abstract
Fish otoliths, biominerals composed of calcium carbonate with a small amount of organic matrix, are involved in the functioning of the inner ear. Starmaker (Stm) from zebrafish (Danio rerio) was the first protein found to be capable of controlling the formation of otoliths. Recently, a gene was identified encoding the Starmaker-like (Stm-l) protein from medaka (Oryzias latipes), a putative homologue of Stm and human dentine sialophosphoprotein. Although there is no sequence similarity between Stm-l and Stm, Stm-l was suggested to be involved in the biomineralization of otoliths, as had been observed for Stm even before. The molecular properties and functioning of Stm-l as a putative regulatory protein in otolith formation have not been characterized yet. A comprehensive biochemical and biophysical analysis of recombinant Stm-l, along with in silico examinations, indicated that Stm-l exhibits properties of a coil-like intrinsically disordered protein. Stm-l possesses an elongated and pliable structure that is able to adopt a more ordered and rigid conformation under the influence of different factors. An in vitro assay of the biomineralization activity of Stm-l indicated that Stm-l affected the size, shape and number of calcium carbonate crystals. The functional significance of intrinsically disordered properties of Stm-l and the possible role of this protein in controlling the formation of calcium carbonate crystals is discussed.
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Affiliation(s)
- Mirosława Różycka
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Michał Jakób
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
| | - Christian Stigloher
- Division of Electron Microscopy, Biocenter, University of Würzburg, Würzburg, Germany
| | - Mikołaj Grzeszkowiak
- NanoBioMedical Centre and Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Maciej Mazur
- Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
- * E-mail:
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10
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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11
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Abstract
The notion that human α-synuclein is an intrinsically disordered monomeric protein was recently challenged by a postulated α-helical tetramer as the physiologically relevant protein structure. The fact that this alleged conformation had evaded detection for so many years was primarily attributed to a widely used denaturation protocol to purify recombinant α-synuclein. In the present paper, we provide in-cell NMR evidence obtained directly in intact Escherichia coli cells that challenges a tetrameric conformation under native in vivo conditions. Although our data cannot rule out the existence of other intracellular protein states, especially in cells of higher organisms, they indicate clearly that inside E. coli α-synuclein is mostly monomeric and disordered.
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12
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Wojtas M, Kapłon TM, Dobryszycki P, Ożyhar A. The effect of counter ions on the conformation of intrinsically disordered proteins studied by size-exclusion chromatography. Methods Mol Biol 2012; 896:319-330. [PMID: 22821534 DOI: 10.1007/978-1-4614-3704-8_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Counter ions are able to change the conformation of intrinsically disordered proteins (IDPs) to a more compact structure via the reduction of electrostatic repulsion. When the extended IDP conformation is transformed into a more ordered one, the value of the Stokes radius should decrease. Size-exclusion chromatography is a simple method for the determination of the Stokes radius, which describes the hydrodynamic properties of protein molecules. In our paper size-exclusion chromatography experiments of Starmaker (a highly acidic IDP), in the presence of various counter ions, are presented as an example of a simple experimental method, which provides valuable information about subtle counter ions-induced conformational changes in IDP.
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Affiliation(s)
- Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland
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13
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Abbas L, Whitfield TT. The zebrafish inner ear. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1546-5098(10)02904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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