Top, Ayben
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Top, A.
Top, A
Top, A
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aybentop@iyte.edu.tr
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03.02. Department of Chemical Engineering
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23
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792
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30
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2
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676
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726
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9
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22.53
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24.20
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18
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12
| Journal | Count |
|---|---|
| Soft Matter | 2 |
| Applied Clay Science | 1 |
| Biomacromolecules | 1 |
| Brazilian Archives of Biology and Technology | 1 |
| Gazi Üniversitesi Mühendislik Mimarlık Fakültesi Dergisi | 1 |
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Article Citation - WoS: 2Citation - Scopus: 2Integration of Leu-Asp Cell Attachment Motif Into Self-Assembling Peptide Sequences for Nanofibrillar Hydrogel Formation in Wound Healing(Amer Chemical Soc, 2025) Tarim, Burcu Sirma; Sırma Tarım, Burcu; Tamburaci, Sedef; Top, Ayben; Uysal, Berk; Top, AybenFunctionalizing peptide sequences with cell adhesion motifs enhances their cellular bioactivity. Numerous studies have focused on incorporating the Arg-Gly-Asp (RGD) motif into peptide hydrogels; however, the integration of other bioactive domains has yet to be comprehensively investigated. In this study, one of the essential fibronectin-derived cell-binding domains, Leu-Asp-Val (LDV), was integrated into the self-assembling peptide to obtain extracellular matrix (ECM)-mimetic nanofibrillar hydrogelators. IBP1A (NH2-KLDVKLDVKLKV-CONH2) and IBP1B (NH2-KLDVKLDVKLDV-CONH2) peptides were designed accordingly. These peptides self-assemble into hydrogels in phosphate-buffered saline (PBS) at pH 7.4 and deionized water at neutral pH with storage modulus values between similar to 200 and similar to 2000 Pa. Flow curves and the cyclic strain sweep data confirmed that the hydrogels have shear thinning, injectability, and self-healing properties. Flexible nanofibrillar morphology was observed in the TEM images. Nanofibril widths of IBP1A and IBP1B networks were measured as 8.2 +/- 1.1 and 4.5 +/- 0.8 nm, respectively. In vitro tests were also conducted to evaluate these peptides in wound healing applications. The IBP1A peptide with a +3 charge at neutral pH exhibited modest antibacterial activity against Gram (+) and Gram (-) bacteria. In vitro cell culture experiments show that the IBP1A and IBP1B hydrogels promoted the growth of fibroblast cells and glycosaminoglycan secretion compared with the KLDL12 control peptide, which does not contain the LDV motif. The designed hydrogels induced cell attachment within 72 h by altering the cell morphology similar to their natural 3D microenvironment, whereas cells exhibited spindle-like morphology on the KLDL12 hydrogel and tissue culture polystyrene (TCP). Moreover, IBP1B accelerated in vitro wound healing by facilitating fibroblast migration. These results suggest that these bioactive injectable peptide hydrogels have potential in wound healing and skin tissue regeneration.Article Citation - WoS: 25Citation - Scopus: 25Conformational and Aggregation Properties of a Pegylated Alanine-Rich Polypeptide(American Chemical Society, 2011) Top, Ayben; Roberts, Christopher J.; Kiick, Kristi L.The conformational and aggregation behavior of PEG conjugates of an alanine-rich polypeptide (PEG-c17H6) were investigated and compared to that of the polypeptide equipped with a deca-histidine tag (17H6). These polypeptides serve as simple and stimuli-responsive models for the aggregation behavior of helix-rich proteins, as our previous studies have shown that the helical 17H6 self-associates at acidic pH and converts to β-sheet structures at elevated temperature under acidic conditions. In the work here, we show that PEG-c17H6 also adopts a helical structure at ambient/subambient temperatures, at both neutral and acidic pH. The thermal denaturation behavior of 17H6 and PEG-c17H6 is similar at neutral pH, where the alanine-rich domain has no self-association tendency. At acidic pH and elevated temperature, however, PEGylation slows β-sheet formation of c17H6, and reduces the apparent cooperativity of thermally induced unfolding. Transmission electron microscopy of PEG-c17H6 conjugates incubated at elevated temperatures showed fibrils with widths of ∼20-30 nm, wider than those observed for fibrils of 17H6. These results suggest that PEGylation reduces β-sheet aggregation in these polypeptides by interfering, only after unfolding of the native helical structure, with interprotein conformational changes needed to form β-sheet aggregates.Article Citation - WoS: 12Citation - Scopus: 12Controlling Assembly of Helical Polypeptides Via Pegylation Strategies(Royal Society of Chemistry, 2011) Top, Ayben; Zhong, Sheng; Yan, Congqi; Roberts, Christopher J.; Pochan, Darrin J.; Kiick, Kristi L.Recent studies in our laboratories have demonstrated that a helical polypeptide (17H6), equipped with a histidine tag and a helical alanine-rich, glutamic-acid-containing domain, exhibits pH-responsive assembly behavior useful in the production of polymorphological nanostructures. In this study, the histidine tag in these polypeptides was replaced by polyethylene glycol (PEG) with different molecular masses (5 kDa, or 10 kDa), and the self-association behavior of 17H6 and the PEGylated conjugates was characterized via dynamic light scattering (DLS), small angle neutron scattering (SANS), and cryogenic transmission electron microscopy (cryo-TEM). DLS experiments illustrated that the polypeptide and its PEG-conjugates undergo reversible assembly under acidic conditions, suggesting that the aggregation state of the polypeptide and the conjugates is controlled by the charged state of the glutamic acid residues. Nanoscale aggregates were detected at polypeptide/conjugate concentrations as low as 20 μM (∼0.3-0.5 mg ml -1) at physiological and ambient temperatures. Scattering and microscopy results showed that the size, the aggregation number, and the morphology of the aggregates can be tuned by the size and the nature of the hydrophilic tag. This tunable nature of the morphology of the aggregates, along with their low critical aggregation concentration, suggests that PEG-alanine-rich polypeptide conjugates may be useful as drug delivery vehicles in which the alanine-rich block serves as a drug attachment domain.Article Development of Self-Assembled Peptide Hydrogels Containing Matrix-Metalloproteinase Degradable Motifs for 3D Lung Cancer Models(Royal Society of Chemistry, 2026) Tarim, Burcu Sirma; Tamburaci, Sedef; Top, AybenHydrogel-forming peptides, including matrix metalloproteinase (MMP)-degradable motifs, have been employed to investigate cell-extracellular matrix interactions in vitro. However, their potential in 3D cancer models has been explored only in a few studies. In this study, we used modified MMP-2 degradable motifs (VSLRA or ASLRA) in the design of EDP1 (RVSLRADARVSLRADA) and EDP2 (RASLRADARASLRADA) peptide hydrogelators. The peptides self-assembled into nanofibrillar hydrogels with storage moduli between similar to 300 and similar to 400 Pa. MMP-2 degradation properties of the peptides were confirmed, and a slightly higher MMP-2 responsiveness of the EDP1 hydrogel was observed. The hydrogels were used in the encapsulation of A549 lung adenocarcinoma cancer cells and MRC-5 human lung fibroblast cells. The designed hydrogels supported the proliferation of these cells with high viability and induced cluster formation of encapsulated A549 cells similar to that observed with the RADA hydrogel. However, the hydrogel network structure affected the morphology of the migrated cells in the absence of curcumin. The addition of curcumin decreased the migration and invasion of A549 cells, resulting in a round cell morphology independent of the hydrogel matrices. Anticancer drug tests indicated that cell viability after drug treatment was higher in the 3D hydrogels than in 2D cultures. It was also confirmed that the combinational therapy of doxorubicin and curcumin decreased the cell proliferation and colonization to a greater extent compared to doxorubicin monotherapy. Thus, the hydrogels developed in this study can be used for 3D cancer models or other tissue engineering applications as an alternative to the RADA hydrogel by exploiting the MMP-2 degradation properties.Conference Object Bioactive Self-Assembled Peptide Hydrogels for 3d Cancer Model Applications(Wiley, 2024) Tarim, Burcu Sirma; Tamburaci, Sedef; Top, AybenArticle Poly(Ethylene Glycol)-Keratin Hydrogels Prepared Via Thiol-Maleimide Reaction(Polymer Soc Korea, 2025) Yalcin, Damla; Top, AybenThe mechanical properties of hydrogels have a profound effect on cellular responses in tissue engineering applications. In this study, poly(ethylene glycol)-keratin (PEG-KRTN) hydrogels with tunable mechanical properties were prepared by varying molar mass of the maleimide functionalized PEG in the thiol-maleimide chemistry. Reduced keratins were reacted with PEG-maleimides having 2000 Da and 6000 Da molar masses. Viscoelastic and physiochemical properties and cytocompatibility of these hydrogels were tested. Storage modulus values were obtained as 2613 +/- 254 Pa and 1313 +/- 345 Pa for PEG2000-KRTN and PEG6000-KRTN hydrogels, respectively. Strain sweep data indicate that the linear viscoelastic region (LVER) of the PEG6000-KRTN hydrogel spans up to 40% strain value, whereas it is limited to 10% critical strain for the PEG2000-KRTN hydrogel. PEG6000-KRTN hydrogel presented higher swelling ratios and porosity. CCK-8 test showed that both hydrogels promoted the proliferation of L929 mouse fibroblast cells and, hence, can be applied in soft tissue engineering.Doctoral Thesis Biyoaktif Motifler İçeren Kendiliğinden Düzenlenen Peptit Hidrojellerin Geliştirilmesi(2025) Tarım, Burcu Sırma; Top, AybenAlternatif hidrofobik ve hidrofilik amino asitlere ve spesifik yük dağılımlarına sahip peptitler, kendiliğinden düzenlenerek bir araya gelerek hücre dışı matrise (ECM) benzer yapılar oluşturabilir. Peptit hidrojelatörlere hücre yapışma ve enzimatik olarak bozunabilir motifler gibi biyoaktif ipuçları eklenerek ECM benzeri özellikler geliştirilebilir. Çok sayıda çalışma, RGD hücre bağlanma motifi ile işlevselleştirilmiş peptit hidrojellere odaklanmıştır. Bu çalışmanın amacı, peptit hidrojelatörlere alternatif biyoaktif motifler ekleyerek, bu yapıların fizikokimyasal ve biyolojik özelliklerini değerlendirmektir. Bölüm 2'de, yara iyileşmesini hızlandırma potansiyeline sahip α4β1 integrin bağlayıcı LDV dizini ile işlevselleştirilmiş, enjekte edilebilir ve kendi kendini iyileştiren peptit hidrojeller yara iyileştirme uygulamaları için test edilmiştir. Bölüm 3 ve 4'te, hücre yapışma motiflerine (LDV+IKVAV) ve matris metalloproteinaz-2 bozunur dizinlere (VSLRA veya ASLRA) sahip peptit hidrojeller geliştirilmiş ve bu hidrojeller kanser hücrelerinin antikanser ilaç yanıtını değerlendirmek amacıyla 3B akciğer kanseri modelleri olarak incelenmiştir. Peptitler, katı faz peptit sentezi yöntemiyle sentezlenmiş ve saflıkları doğrulanmıştır. Hidrojellerin yapısal, morfolojik ve viskoelastik özellikleri belirlenmiştir. İn vitro hücre kültürü çalışmaları, LDV içeren hidrojellerin fibroblast hücrelerinin büyümesini, yapışmasını, migrasyonunu ve glikozaminoglikan salgılanmasını artırmıştır ve bu hidrojellerin yara iyileşmesini destekleyici potansiyellerini göstermektedir. Bölüm 3 ve 4'te geliştirilen hidrojeller, içerisinde enkapsüle edilen A549 akciğer kanseri hücrelerinin çoğalmasını, sferoid oluşumunu ve invazyonunu desteklemiştir. 3B matrislerde kültive edilen hücreler gelişmiş hücre-hücre etkileşimlerine sahip oldukları için yüksek antikanser ilaç direnci sergilemişlerdir. Dolayısıyla, bu biyoaktif hidrojeller kanser mekanizmalarının in vitro olarak incelenmesi ve antikanser ilaç taramaları için umut verici bir platform sunmaktadır.Master Thesis Peptide Hydrogels Containing Cell Attachment Molecules(Izmir Institute of Technology, 2019) Uysal, Berk; Top, Ayben; Top, AybenIn this study, peptides with sequences and notations as KLELKLELKLEL (KLEL), KLDVKLDVKLDV (KLDV), KLDVKLDVKLKV (KLKV1), KLKVKLDVKLKV (KLKV2), KLKVKLKVKLKV (KLKV3) were synthesized using solid phase peptide synthesis (SPPS) method based on Fmoc chemistry. Reverse phase HPLC and MALDI-TOF mass spectroscopy characterization methods were used to assess the purity of the peptides. Three different synthesis procedures were tested, and it was found that employing DMF:DMSO at 1:1 ratio as a solvent increased purity of the resultant peptide. FTIR results indicated the presence of expected β-sheet secondary structure, as well as an interference band from TFA salts for all of the peptides. All the peptides formed hydrogels at pH 7.4 with 1 wt% concentration in deionized water (DIW). AFM results of these hydrogels indicated that KLKV1 and KLKV2 had fibrous morphology with a width of 5-20 nm and 7-18 nm respectively. KLDV and KLKV3 peptide hydrogels, on the other hand, exhibited globular structures, having sizes with 15-50 nm and 8-15 nm, respectively. Storage moduli (G’) of these hydrogels in DIW were obtained as ~860 ± 150 Pa, ~260 ± 60 Pa, ~210 ± 30 Pa and ~1850 ± 200 Pa for KLDV, KLKV1, KLKV2 and KLKV3 respectively. Of these peptides, only HCl salt of KLDV and KLKV1 peptides more readily formed hydrogels in PBS but at 1.5 wt% concentration. G’ values of these KLDV and KLKV1 hydrogels were determined as ~1810 ± 850 Pa and ~700 ± 230 Pa, respectively. Cell proliferation tests (CCK-8 assay) of KLDV and KLKV1 hydrogels were performed by using L929 mouse fibroblast cells. Empty wells (TCPS) were used as a control group. Cell proliferation was observed to be comparable for both select hydrogels and empty wells, suggesting possible applications of these hydrogels in tissue engineering.Master Thesis Development of Peg-Peptide Conjugate Based Curcumin Delivery Systems(01. Izmir Institute of Technology, 2022) Aydoğan, Gamze; Top, AybenIn this study, a drug delivery system based on Pluronic F127 and a peptide conjugate was proposed. The F127-peptide conjugate was prepared by the reaction between succinimidyl functionalized F127 (SC-F127) and peptide. SC-F127 was synthesized using disuccinimidyl carbonate and DMAP. Folic acid-functionalized F127 (FA-F127) was also prepared to obtain active targeting copolymers. Four peptides containing pH-responsive multiple histidines and endosome disruptive GFWFG domain were synthesized using the Fmoc procedure. H-Gly-2-ClTrt resin and Rink amide MBHA resin were used to synthesize side-chain-protected and deprotected peptides, respectively. 2-chlorotrityl resin failed in synthesizing the high-purity peptides with adjacent histidines in their sequences. Peptide-4 having a sequence of GGH6GFWFG, was prepared with acceptable purity using rink amide MBHA resin and was conjugated to SC-F127. Curcumin was loaded to F127 and F127-peptide using the thin film method with DCM solvent. Almost all curcumin was encapsulated into F127 micelles. However, the entrapment efficiency % of the F127-peptide micelles was ~86% due to the lower solubility of F127-peptide conjugate in DCM. Dynamic light scattering experiments were used to determine the stability and size distribution of the micelles. Number-based size distributions of both micelles indicated that a single peak between 10 and 30 nm was independent of pH. The peak position did not change upon incubating the micelles at 37oC up to a few days. Initially, intensity-based results of both samples indicate bidisperse populations at pH 5.0 and 7.4. Curcumin-loaded F127 micelles aggregated in the three days, as revealed by the formation of the third peak above 1000 nm independent of pH. Curcumin-loaded F127-peptide micelles, on the other hand, retain their stability for up to five days at neutral pH. For this sample, the third peak was observed only at pH 5.0 on days 2 and 5.Master Thesis Cation Exchange (ag+, Zn2+, Cu2+) Behavior of Natural Zeolites(01. Izmir Institute of Technology, 2001) Top, Ayben; Ülkü, SemraIn this study, clinoptilolite, most abundant zeolite present in nature, was proposed as a low cost antibacterial material. As a preliminary work, antibacterial activities of the original, Ag, and Zn forms of the clinoptilolite were investigated against several strains and compared to the commercial antibiotics. No antibacterial action was observed for the original clinoptilolite. Ag loaded clinoptilolite was found to be superior to the Zn-form against Proteus spp. and Pseudomonas aeruginosa.The original, Na, Ag, Zn, and Cu forms of the clinoptilolite samples were characterized by FTIR spectroscopy, thermal analyses (TGA, DTA, and DSC), and N2 physisorption studies. Specific attention was given in to the chemical analysis of the clinoptilolite by ICP-AES. Using the standard addition method, the respective idealized formulas of the original and Na-clinoptilolite based on 72 oxygen atoms in the unit cell were calculated as:(Na0.816 K2.070) (Ca1.060 Mg0.264) (Al5.653 Fe0.390) (Si30.084) O72. 20.023 H2O, and (Na4.763 K1.057) (Ca0.076 Mg0.094) (Al5.843 Fe0.221) (Si29.911) O72.17.049 H2O.In the FTIR spectra of the original and exchanged forms of the clinoptilolite, considerable shifts (from 3460 to 3494.8 cm-1) were observed in the band, which is formed due to the interactions of water molecules with the framework via hydrogen bonds. The positions of the other bands were not affected by cation exchange significantly. From the TGA curves, the water contents ranged between 14.31 and 11.00 % for the original and the cation-exchanged forms of the clinoptilolite. Mainly, two endotherms and one exotherm were obtained in the DTA curves. The first endotherm occurred up to about 150 oC, the second endotherm lied between 200 and 700 oC, and the exotherm was obtained at about 850 oC. Significant differences observed between the shapes of the DSC curves indicated that the cations control the dehydration behavior of the samples. N2 physisorption isotherms of five samples were all, Type IV with BET surface areas ranging between 34.97 and 46.76 m2/g.Ag, Zn and Cu ion exchange equilibria were investigated at 25 oC for both the original clinoptilolite and Na-clinoptilolite. In the former case, from the plateau of the isotherms cation exchange capacities were determined as 1.184, 0.439, 0.539 meq/g clinoptilolite for Ag+, Zn2+, and Cu2+ respectively. The major portion of the exchanges was contributed by Na+ and Ca2+. Distribution coefficient values indicated that at Ag, Zn and Cu ion exchange equilibria were investigated at 25 oC for both the original clinoptilolite and Na-clinoptilolite. In the former case, from the plateau of the isotherms cation exchange capacities were determined as 1.184, 0.439, 0.539 meq/g clinoptilolite for Ag+, Zn2+, and Cu2+ respectively. The major portion of the exchanges was contributed by Na+ and Ca2+. Distribution coefficient values indicated that at relatively low initial concentrations, the preference of the clinoptilolite for Zn2+ and Cu2+ was significant. At higher concentrations, higher distribution coefficients were obtained for Ag+ compared to Zn2+ and Cu2+. Langmuir and Freundlich models were applied for each equilibrium data. For Zn2+ and Cu2+ exchanges, Langmuir model gave better correlation and Freundlich model fitted experimental data slightly better in the case of Ag+ exchange.Equilibrium isotherms for Ag+-Na+, Zn2+-Na+, and Cu2+-Na+ pairs were investigated. Silver exchange isotherm lied above the diagonal over the whole composition range. For zinc and copper exchanges, the isotherms were above the diagonal up to equivalent fractions of exchanging ion in solution phase (As) at about 0.2. While full exchange was attained for silver, partial exchanges were obtained in the case of zinc and copper. The standard free energy of exchange values were found as .6.0, 2.03 and 3.09 kj/equiv for Ag+-Na+, Zn2+-Na+, and Cu2+-Na+ pairs respectively. From these values selectivity sequence was obtained as Ag+ > Na+ > Zn2+ > Cu2+.Consequently, by considering the preliminary antibacterial activity results, specific cation exchange capacities, and selectivity sequence of the clinoptilolite, Ag-clinoptilolite seemed to be promising antibacterial material. The results of the current study compared to the literature data pointed out that cation exchange behavior of the clinoptilolite is dependent on its original cationic composition. Therefore, it is necessary to carry out specific studies on representative samples from the deposit before any practical application.
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