Browsing by Author "Yuca, Esra"

Filter results by typing the first few letters
Now showing 1 - 4 of 4
  • Thumbnail Image
    ItemOpen Access
    Autonomous synthesis of fluorescent silica biodots using engineered fusion proteins
    (American Chemical Society, 2018) Ölmez, Tolga T.; Yuca, Esra; Eyüpoğlu, Erol; Çatalak, Hazal B.; Şahin, Özgür; Şeker, Urartu Özgür Şafak
    Formation of biological materials is a well-controlled process that is orchestrated by biomolecules such as proteins. Proteins can control the nucleation and mineralization of biomaterials, thereby forming the hard tissues of biological organisms, such as bones, teeth, and shells. In this study, the design and implementation of multifunctional designer proteins are demonstrated for fluorescent silica micro/nanoparticle synthesis. The R5 motif of silaffin polypeptide, which is known for its silicification capability, was fused genetically into three spectrally distinct fluorescent proteins with the intention of forming modified fluorescent proteins. The bifunctional R5 peptide domain served as a tag to provide silica synthesis at ambient conditions. Three functional fusion constructs have been prepared, including GFPmut3-R5, Venus YFP-R5, and mCherry-R5. Recombinant fluorescent proteins were purified using silica-binding peptide tag through silica gel resin. Purified proteins were tested for their binding affinity to silica using quartz crystal microbalance with dissipation monitoring to make sure they can interact strong enough with the silica surfaces. Later, engineered fluorescent proteins were used to synthesize silica nano/microparticles using silica precursor materials. Synthesized silica particles were investigated for their fluorescence properties, including time-resolved fluorescence. Additionally, elemental analysis of the particles was carried out using electron energy loss spectroscopy and energy-filtered transmission electron microscopy. Last, they were tested for their biocompatibility. In this study, we aimed to provide a biomimetic route to synthesize fluorescent silica nanoparticles. Recombinant fluorescent proteins-directed silica nanoparticles synthesis offers a one-step, reliable method to produce fluorescent particles both for biomaterial applications and other nanotechnology applications.
  • Thumbnail Image
    ItemOpen Access
    Biomineralization of calcium phosphate crystals controlled by protein-protein interactions
    (American Chemical Society, 2019) Duman, Elif; Şahin-Kehribar, Ebru; Ahan, Recep Erdem; Yuca, Esra; Şeker, Urartu Özgür Şafak
    Hydroxyapatite (HAP) is the major biomineral of bone. Despite the large number of studies addressing HAP formation, a fundamental understanding of the critical roles of HAP-forming proteins in vitro is needed. Effects of two HAP-interacting proteins, osteocalcin (OCN) and osteopontin (OPN), on HAP formation was investigated via in vitro biomineralization experiments, and their outcomes on the crystal structure of calcium phosphate (CaP) was revealed. Our data suggest that OCN concentration is negatively correlated with crystal formation rate and crystal size, yet the presence of OCN leads to a more ordered HAP crystal formation. On the other hand, OPN protein promotes faster formation of CaP crystals potentially working as a growth site for mineral formation, and it decreases the Ca:P ratio. This effect results in a shift from HAP-type minerals to less ordered crystals. The crystal size, shape, and Ca:P ratio can be tuned to design improved mammalian hard tissue environment-mimicking matrices by taking advantage of the OCN and OPN proteins on crystal formation. We believe our current findings will lead to innovative approaches for bone biomineralization in regenerative medicine.
  • Thumbnail Image
    ItemOpen Access
    Design and construction of protein and peptide-based self-assembled nanostructures
    (Elsevier, 2022-01-01) Yuca, Esra; Khan, Anooshay; Hacıosmanoğlu, Nedim; Şeker, Urartu Özgür Şafak; Pandya, A.; Singh, V.; Bhosale, R. S.
    Self-assembly is the driving force for the formation of biological materials. From nucleic acid conformations to more complex cellular organizations, self-assembling structures shape biological functionality. So, the design of self-assembling biomolecular structures holds a great advantage for enhanced material properties. In biological processes, inorganic structures are created in a hierarchical fashion utilizing biomolecule-based templates. Since they have recognition and self-assembly properties, biomolecules can control highly organized inorganic material formation in nature. The bio-templating approach takes advantage of biomolecules’ self-assembly properties to develop new nanostructures with superior chemical and physical properties. Here, peptides and proteins including β-sheets, β-hairpins, α-helix, amyloid, capsid, ferritin, and albumin, used in the formation of nanostructures with desired functionality under mild environmental conditions, and their applications are discussed.
  • Thumbnail Image
    ItemOpen Access
    Self-assembly of bacterial amyloid protein nanomaterials on solid surfaces
    (Academic Press, 2018) Onur, Tuğçe; Yuca, Esra; Ölmez, Tolga Tarkan; Şeker, Urartu Özgür Şafak
    Hypothesis: Amyloid-forming biofilm proteins of Escherichia coli, namely CsgA and CsgB, can form self-assembled nanofibers on solid surfaces. These proteins can be programmed to form bio-nanomaterials for functional applications. Experiments: In this study, the assembly of the CsgA and CsgB protein on solid surfaces was investigated in real time using a quartz crystal microbalance instrument with dissipation monitoring. The assembly kinetics of the CsgA and CsgB proteins in various settings on solid surfaces were investigated. Protein nanowires were investigated using electron microscopy. Findings: CsgA protein polymers and CsgB-added CsgA polymers form densely packed biofilm on gold surfaces, whereas CsgB polymers and CsgA-added CsgB polymers form biofilms with high water-holding capacity according to the dissipation data. Electron microscopy images of nanofibers grown on gold surfaces showed that CsgA and CsgB polymers include thicker nanofibers compared to the nanofibers formed by CsgA-CsgB protein combinations. The resulting nano/microstructures were found to have strong fluorescence signals in aqueous environments and in chloroform while conserving the protein nanowire network.