PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 5Citation - Scopus: 6Sequence Identification and in Silico Characterization of Novel Thermophilic Lipases From Geobacillus Species(WILEY, 2023) Şanlı Mohamed, Gülşah; Tekedar, Hasan Cihad; Sanli-Mohamed, Gulsah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of TechnologyMicrobial lipases are utilized in various biotechnological areas, including pharmaceuticals, food, biodiesel, and detergents. In this study, we cloned and sequenced Lip21 and Lip33 genes from Geobacillus sp. GS21 and Geobacillus sp. GS33, then we in silico and experimentally analyzed the encoded lipases. For this purpose, Lip21 and Lip33 were cloned, sequenced, and their amino acid sequences were investigated for determination of biophysicochemical characteristics, evolutionary relationships, and sequence similarities. 3D models were built and computationally affirmed by various bioinformatics tools, and enzyme-ligand interactions were investigated by docking analysis using six ligands. Biophysicochemical property of Lip21 and Lip33 was also determined experimentally and the results demonstrated that they had similar isoelectric point (pI) (6.21) and T-m (75.5(degrees)C) values as T-m was revealed by denatured protein analysis of the circular dichroism spectrum and pI was obtained by isoelectric focusing. Phylogeny analysis indicated that Lip21 and Lip33 were the closest to lipases from Geobacillus sp. SBS-4S and Geobacillus thermoleovorans, respectively. Alignment analysis demonstrated that S144-D348-H389 was catalytic triad residues in Lip21 and Lip33, and enzymes possessed a conserved Gly-X-Ser-X-Gly motif containing catalytic serine. 3D structure analysis indicated that Lip21 and Lip33 highly resembled each other and they were alpha/beta hydrolase-fold enzymes with large lid domains. BAN Delta IT analysis results showed that Lip21 and Lip33 had higher thermal stability, compared to other thermostable Geobacillus lipases. Docking results revealed that Lip21- and Lip33-docked complexes possessed common residues (H112, K115, Q162, E163, and S141) that interacted with the substrates, except paranitrophenyl (pNP)-C10 and pNP-C12, indicating that these residues might have a significant action on medium and short-chain fatty acid esters. Thus, Lip21 and Lip33 can be potential candidates for different industrial applications.Article Citation - WoS: 13Citation - Scopus: 14Nanotubular Structures Developed From Whey-Based ?-Lactalbumin Fractions for Food Applications(John Wiley and Sons Inc., 2014) Tarhan, Özgür; Harsa, Şebnem; Harsa, Hayriye Şebnem; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyWhey proteins have high nutritional value providing use in dietary purposes and improvement of technological properties in processed foods. Functionality of the whey-based α-lactalbumin (α-La) may be increased when assembled in the form of nanotubes, promising novel potential applications subject to investigation. The purpose of this study was to extract highly pure α-La from whey protein isolate (WPI) and whey powder (WP) and to construct protein nanotubes from them for industrial applications. For protein fractionation, WPI was directly fed to chromatography, however, WP was first subjected to membrane filtration and the retentate fraction, whey protein concentrate (WPC), was obtained and then used for chromatographic separation. α-La and, additionally β-Lg, were purified at the same batches with the purities in the range of 95%-99%. After enzymatic hydrolysis, WPI-based α-La produced chain-like and long nanotubules with ∼20 nm width while WPC-based α-La produced thinner, miscellaneous, and fibril-like nanostructures by self-assembly. Raman and FT-IR spectroscopies revealed that α-La fractions, obtained from both sources and the nanostructures, developed using both fractions have some structural differences due to conformation of secondary structure elements. Nanotube formation induced gelation and nanotubular gel network entrapped a colorant uniformly with a transparent appearance. Dairy-based α-La protein nanotubules could be served as alternative gelling agents and the carriers of natural colorants in various food processes.Article Citation - WoS: 21Citation - Scopus: 24Consistency of Polyphenol Oxidase (ppo) Thermostability in Ripening Apricots (prunus Armeniaca L.): Evidence for the Presence of Thermostable Ppo Forming and Destabilizing Mechanisms in Apricots(American Chemical Society, 2003) Yemenicioğlu, Ahmet; Yemenicioğlu, Ahmet; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyDestabilization of thermostable polyphenol oxidase (TS-PPO) during the ripening of peaches has been previously shown (Yemenicioǧlu, A; Cemeroǧlu, B. Tr. J. Agric. For. 1998, 22, 261-265). This work studied the effect of ripening on thermal stability of apricot PPO for three different cultivars. Kabaaşi cultivar contained thermolabile PPO, whereas TS-PPO appeared in Hacihaliloǧlu and Çataloǧlu cultivars. The TS-PPO showed biphasic inactivation curves, and its D and z values between 60 and 90 °C varied in the ranges of 357-1.12 min and 11.9-12.7 °C, respectively. In Hacihaliloǧlu cultivar the TS-PPO was very consistent and existed at all stages of ripening, whereas in Çataloǧlu cultivar it appeared only at the half-ripe stage. The loss of consistent TS-PPO in Hacihaliloǧlu apricots after partial purification by acetone precipitation and DEAE-cellulose chromatography suggested the non-covalent nature of its stabilization. The main purified fractions (F1 and F2) showed monophasic inactivation curves with similar thermal inactivation parameters (ZF1 = 10.4 °C, ZF2 = 10.1 °C). However, their kinetic properties against catechol (KmF1 = 61 mM, KmF2 = 122.7 mM) and substrate specificities were considerably different. The results of this study showed the presence of TS-PPO forming and destabilizing mechanisms in apricots. Further studies are needed for the solution of these mechanisms and to develop some new strategies that may be utilized by molecular techniques for a planned production of apricot cultivars provided with heat labile but normal PPO activity.