Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - Scopus: 4Quasi-Supervised Strategies for Compound-Protein Interaction Prediction(John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.Review Citation - WoS: 116Citation - Scopus: 125Salivary Biomarkers: Novel Noninvasive Tools To Diagnose Chronic Inflammation(Springer, 2023) Dongiovanni, Paola; Meroni, Marica; Casati, Sara; Goldoni, Riccardo; Thomaz, Douglas Vieira; Kehr, Nermin Seda; Galimberti, DanielaSeveral chronic disorders including type 2 diabetes (T2D), obesity, heart disease and cancer are preceded by a state of chronic low-grade inflammation. Biomarkers for the early assessment of chronic disorders encompass acute phase proteins (APP), cytokines and chemokines, pro-inflammatory enzymes, lipids and oxidative stress mediators. These substances enter saliva through the blood flow and, in some cases, there is a close relation between their salivary and serum concentration. Saliva can be easily collected and stored with non-invasive and cost-saving procedures, and it is emerging the concept to use it for the detection of inflammatory biomarkers. To this purpose, the present review aims to discuss the advantages and challenges of using standard and cutting-edge techniques to discover salivary biomarkers which may be used in diagnosis/therapy of several chronic diseases with inflammatory consequences with the pursuit to possibly replace conventional paths with detectable soluble mediators in saliva. Specifically, the review describes the procedures used for saliva collection, the standard approaches for the measurement of salivary biomarkers and the novel methodological strategies such as biosensors to improve the quality of care for chronically affected patients.Article Citation - WoS: 8Citation - Scopus: 8Invariants of Bonded Knotoids and Applications To Protein Folding(MDPI, 2022) Güğümcü, Neslihan; Gabrovsek, Bostjan; Kauffman, Louis H.In this paper, we study knotoids with extra graphical structure (bonded knotoids) in the settings of rigid vertex and topological vertex graphs. We construct bonded knotoid invariants by applying tangle insertion and unplugging at bonding sites of a bonded knotoid. We demonstrate that our invariants can be used for the analysis of the topological structure of proteins.Article Citation - WoS: 7Citation - Scopus: 7Novel Regulation Mechanism of Adrenal Cortisol and Dhea Biosynthesis Via the Endogen Erad Inhibitor Small Vcp-Interacting Protein(Nature Publishing Group, 2022) İlhan, Recep; Üner, Göklem; Yılmaz, Sinem; Atalay Sahar, Esra; Çaylı, Sevil; Erzurumlu, Yalçın; Gözen, Oğuz; Ballar Kırmızıbayrak, PetekEndoplasmic reticulum-associated degradation (ERAD) is a well-characterized mechanism of protein quality control by removal of misfolded or unfolded proteins. The tight regulation of ERAD is critical for protein homeostasis as well as lipid metabolism. Although the mechanism is complex, all ERAD branches converge on p97/VCP, a key protein in the retrotranslocation step. The multifunctionality of p97/VCP relies on its multiple binding partners, one of which is the endogenous ERAD inhibitor, SVIP (small VCP-interacting protein). As SVIP is a promising target for the regulation of ERAD, we aimed to assess its novel physiological roles. We revealed that SVIP is highly expressed in the rat adrenal gland, especially in the cortex region, at a consistently high level during postnatal development, unlike the gradual increase in expression seen in developing nerves. Steroidogenic stimulators caused a decrease in SVIP mRNA expression and increase in SVIP protein degradation in human adrenocortical H295R cells. Interestingly, silencing of SVIP diminished cortisol secretion along with downregulation of steroidogenic enzymes and proteins involved in cholesterol uptake and cholesterol biosynthesis. A certain degree of SVIP overexpression mainly increased the biosynthesis of cortisol as well as DHEA by enhancing the expression of key steroidogenic proteins, whereas exaggerated overexpression led to apoptosis, phosphorylation of eIF2α, and diminished adrenal steroid hormone biosynthesis. In conclusion, SVIP is a novel regulator of adrenal cortisol and DHEA biosynthesis, suggesting that alterations in SVIP expression levels may be involved in the deregulation of steroidogenic stimulator signaling and abnormal adrenal hormone secretion.Article Citation - WoS: 49Citation - Scopus: 66Bioactive, Functional and Edible Film-Forming Properties of Isolated Hazelnut (corylus Avellana L.) Meal Proteins(Elsevier Ltd., 2014) Aydemir, Levent Yurdaer; Adan Gökbulut, Aysun; Baran, Yusuf; Yemenicioğlu, AhmetThis study aimed characterization of bioactive, functional and edible film making properties of isolated proteins from untreated (HPI), hot extracted (HPI-H), acetone washed (HPI-AW), and acetone washed and hot extracted (HPC-AW-H) hazelnut meals. The most bioactive protein extract was HPC-AW-H, followed by HPI-AW, HPI-H and HPI, based on antioxidant activity (TEAC and ORAC: 158-461mmolTrolox/kg), iron chelation (60.7-126.7mmolEDTA/kg), angiotensin-converting enzyme inhibition (IC50: 0.57-1.0mg/mL) and antiproliferative activity on colon cancer cells (IC50: 3.0-4.6mg/ml). Protein contents of HPI, HPI-H and HPI-AW (93.3-94.5%) were higher than that of HPC-AW-H (86.0%), but HPC-AW-H showed the best pH-solubility profile. The extracts showed good oil absorption (7.4-9.4g/g) and foaming, but limited water holding and gelling capacities, and emulsion stability. The protein extracts gave transparent, yellowish to brownish and reddish colored and water soluble edible films. The HPI gave the lightest colored films with acceptable mechanical properties (elongation up to 144% and tensile strength up to 4.9MPa). 1-D and 2-D electrophoresis clearly showed the molecular and isoelectric profiles of hazelnut proteins. The overall results of this study showed that the bioactive, solubility and gelation properties of hazelnut proteins could be improved by simple processes like acetone washing and/or heat treatment. The hazelnut proteins are valuable as multipurpose food ingredients.Article Citation - WoS: 58Citation - Scopus: 86Intrinsic Surface-Drying Properties of Bioadhesive Proteins(John Wiley and Sons Inc., 2014) Akdoğan, Yaşar; Wei, Wei; Huang, Kuo-Ying; Kageyama, Yoshiyuki; Danner, Eric W.; Miller, Dusty R.; Martinez Rodriguez, Nadine R.; Waite, J. Herbert; Han, SongiSessile marine mussels must "dry" underwater surfaces before adhering to them. Synthetic adhesives have yet to overcome this fundamental challenge. Previous studies of bioinspired adhesion have largely been performed under applied compressive forces, but such studies are poor predictors of the ability of an adhesive to spontaneously penetrate surface hydration layers. In a force-free approach to measuring molecular-level interaction through surface-water diffusivity, different mussel foot proteins were found to have different abilities to evict hydration layers from surfaces - a necessary step for adsorption and adhesion. It was anticipated that DOPA would mediate dehydration owing to its efficacy in bioinspired wet adhesion. Instead, hydrophobic side chains were found to be a critical component for protein-surface intimacy. This direct measurement of interfacial water dynamics during force-free adsorptive interactions at solid surfaces offers guidance for the engineering of wet adhesives and coatings. Home and dry underwater: Repulsive hydration forces hinder wet adhesion in the absence of applied external forces. The direct measurement of hydration-water dynamics by NMR relaxometry at 10 GHz revealed that the most hydrophobic mussel adhesive protein, and not the most enriched with 3,4-dihydroxyphenylalanine, effectively dries the surface and overcomes repulsive hydration forces to adsorb spontaneously to surfaces in preparation for adhesion.Article Citation - WoS: 9Citation - Scopus: 9Rapid Identification of Phosphorus Containing Proteins in Electrophoresis Gel Spots by Laser-Induced Breakdown Spectroscopy, Libs(Royal Society of Chemistry, 2014) Aras, Nadir; Yalçın, ŞerifeA novel method for the rapid in-gel identification of phosphorus containing proteins, specifically casein and ovalbumin, prior to mass spectrometric analysis for the elucidation of phosphorylation sites was developed. After polyacrylamide gel-electrophoretic separation, staining and drying, protein bands were subjected to focused laser pulses at the center or the vicinity of the protein band. Phosphorus containing proteins were recognized from their prominent phosphorus lines in the luminous plasma formed by energetic laser pulses. The LIBS emission intensity of phosphorus lines at 253.5 nm and 255.3 nm has been optimized with respect to laser energy and detector timing parameters by using pure casein in the pellet form. The method was applied to casein, ovalbumin, two commercially available standard protein mixtures and proteins extracted from the canola plant. It was shown that LIBS was capable of identifying phosphorus containing proteins directly in the gel matrix in nanogram amounts. Mass spectrometric analysis of the ovalbumin spot after the in-gel digestion procedure has proved the accuracy of the technique. With the speed and spatial resolution that LIBS offers, this technique shows promise in the micro-local spotting of phosphorus containing proteins in the polyacrylamide gel matrix prior to MS analysis for the determination of the phosphorylation sites. © 2014 The Royal Society of Chemistry.Article Citation - WoS: 104Citation - Scopus: 123Potential of Turkish Kabuli Type Chickpea and Green and Red Lentil Cultivars as Source of Soy and Animal Origin Functional Protein Alternatives(Academic Press Inc., 2013) Aydemir, Levent Yurdaer; Yemenicioğlu, AhmetIn this study, functional properties of proteins from Turkish Kabuli type chickpea (CPEs) and green and red lentil cultivars (LPEs) were characterized and compared with those of soy and animal proteins. The LPEs and whey protein isolate (WPI) showed higher soluble and total protein content than the other proteins. CPEs showed the highest oil absorption capacity (10.9-14.59 g/g), followed by LPEs (6.90 -10.44 g/g), soy protein extract (8.23 g/g), and egg white proteins (6.37 g/g). The highest water absorption capacities were obtained for bovine gelatin (BGEL) (8.84 g/g), CPEs (4.90-7.94 g/g) and soy protein isolate (7.94 g/g). The foaming capacities of BGEL and fish gelatin (FGEL), and emulsifying capacity of WPI were slightly higher than those of CPEs and LPEs, but most stable emulsions and foams were formed by chickpea and lentil proteins. The least gelling concentration of CPEs (5-7 g/100 g) came second after BGEL (3 g/100 g). The 2-D electrophoresis revealed the detailed isoelectric point (between 4.5 and 5.9) and molecular weight patterns of chickpea and lentil proteins. This study clearly showed that the functional properties of Kabuli chickpea proteins are superior than those of lentil proteins and most of the studied soy and animal proteins.Article Citation - WoS: 7Citation - Scopus: 10Biotechnology for Enhanced Nutritional Quality in Plants(Taylor and Francis Ltd., 2013) Uncu, Ayşe Özgür; Doğanlar, Sami; Frary, AnneWith almost 870 million people estimated to suffer from chronic hunger worldwide, undernourishment represents a major problem that severely affects people in developing countries. In addition to undernourishment, micronutrient deficiency alone can be a cause of serious illness and death. Large portions of the world population rely on a single, starch-rich crop as their primary energy source and these staple crops are generally not rich sources of micronutrients. As a result, physical and mental health problems related to micronutrient deficiencies are estimated to affect around two billion people worldwide. The situation is expected to get worse in parallel with the expanding world population. Improving the nutritional quality of staple crops seems to be an effective and straightforward solution to the problem. Conventional breeding has long been employed for this purpose but success has been limited to the existing diversity in the gene pool. However, biotechnology enables addition or improvement of any nutrient, even those that are scarce or totally absent in a crop species. In addition, biotechnology introduces speed to the biofortification process compared to conventional breeding. Genetic engineering was successfully employed to improve a wide variety of nutritional traits over the last decade. In the present review, progress toward engineering various types of major and minor constituents for the improvement of plant nutritional quality is discussed. © 2013 Copyright Taylor and Francis Group, LLC.Article Citation - WoS: 7Citation - Scopus: 9Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences(Public Library of Science, 2013) Doğan, Tunca; Karaçalı, BilgeIdentifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.