A5051647305- Protein Structure and Dynamics
- Edible Oils Quality and Analysis
- Enzyme Structure and Function
- NMR spectroscopy and applications
- Computational Drug Discovery Methods
- Advanced NMR Techniques and Applications
- Molecular spectroscopy and chirality
- HIV/AIDS drug development and treatment
- Insect and Pesticide Research
- Metabolomics and Mass Spectrometry Studies
- Spectroscopy and Chemometric Analyses
- HIV Research and Treatment
- Essential Oils and Antimicrobial Activity
- Bee Products Chemical Analysis
- SARS-CoV-2 and COVID-19 Research
- Metalloenzymes and iron-sulfur proteins
- Viral Infections and Vectors
- Biochemical and Molecular Research
- Glycosylation and Glycoproteins Research
- Ubiquitin and proteasome pathways
- Biosensors and Analytical Detection
- Advanced Chemical Sensor Technologies
- Sesame and Sesamin Research
- Mosquito-borne diseases and control
- Organometallic Complex Synthesis and Catalysis
Koç University
2020-2025
Indiana University Bloomington
2021
SLAC National Accelerator Laboratory
2021
Muğla University
2012-2018
TÜBİTAK Marmara Research Center
2015-2018
Scientific and Technological Research Council of Turkey
2018
Abstract Continuous monitoring of protein biomarkers in interstitial fluid (ISF) is essential for improving patient care and outcomes. This study presents a novel electrochemical impedance spectroscopy (EIS) sensor utilizing microneedles (MNs) patterned with interdigitated electrodes the detection vascular endothelial growth factor (VEGF). The MNs, are fabricated from flexible polylactide (PLA) using simple molding technique, followed by metal deposition an pattern to serve as platform EIS...
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for includes: (1) designing a vaccine future protection; (2) de novo drug discovery; (3) identifying existing drugs repurpose them immediate treatments. To assist repurposing design, we determine two apo structures severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial...
The SARS-CoV-2 main protease of (Mpro) is an important target for related drug repurposing and development studies. Here, we describe the steps structural characterization Mpro, starting from plasmid preparation protein purification. We detail crystallization using sitting drop, microbatch (under oil) approach. Finally, cover data collection structure determination serial femtosecond crystallography. For complete details on use execution this protocol, please refer to Durdagi et al. (2021).
Introduction: Ubiquitin and ubiquitin-like systems play crucial roles across a wide range of organisms, from simple to complex. Among the three enzyme-mediated post-translational modification (PTM) steps, ligation step is most critical. HERC5, member HECT ligase family, one enzymes involved in ISGylation system. However, precise start points lengths domains ligases are still under debate. Method: Some studies suggest inclusion an additional N-terminal alpha helix region within domain. To...
The use of Escherichia coli for recombinant protein production is a cornerstone in structural biology, particularly nuclear magnetic resonance (NMR) spectroscopy studies. Understanding the metabolic behavior E. under different carbon sources critical optimizing isotope labeling strategies, which are essential structure determination by NMR. Recent advancements, such as mixed pyruvate labeling, have enabled improved backbone assignment large proteins, making selective isotopic strategies more...
HERC5 is an interferon-induced E3 ubiquitin ligase involved in ISGylation, a crucial post-translational modification regulating antiviral responses. The HECT domain of plays key role substrate recognition and transfer. In this study, we employed small-angle X-ray scattering (SAXS) to investigate the molecular organization oligomeric state solution. protein was expressed purified using affinity size-exclusion chromatography, followed by SAXS measurements at 2.0 mg/ml 10 C. Data analysis...
Abstract Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric complexes. Also, it offers versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, first one ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution second cryogenic (Apo-Cryo) 1.1 resolution. These structures mostly...
In this study the Fourier transform-near infrared (FT-NIR) spectroscopy technique was used to predict fatty acid and sterol content of sesame. For purpose, partial least square regression (PLS-R)-based prediction models were developed, which relate FT-NIR spectra reference GC measurements. total, 39 sesame samples collected from local producers around Muğla Province. Sesame oil extracted seeds by using a screw press analyzed without any refining. The results showed that among different acids...
Abstract Extra virgin olive oils were extracted from six different major cultivars (Gemlik, Ayvalik, Domat, Akhisar, Memecik, Arbequina) cultivated in the Aegean region of Turkey. Fatty acid, sterol and tocopherol compositions analyzed results compared by multivariate statistical analysis. Olive samples collected same orchard order to limit contribution parameters such as climate, soil quality agricultural practices total variance chemical composition oils. Principal component analysis (PCA)...
Oligomerization of Pr55
Abstract Upper limb amputation severely impairs tactile perception, limiting daily activities. Developing a near‐natural replacement with prosthetic devices requires improving user sensory experiences during object interactions. The ideal upper prosthesis should provide real‐time feedback, mirroring natural experiences. Current prostheses struggle providing adequate feedback due to limitations. Inspired by the properties of skin, we present micro‐fabricated, multiplexed electronic skin...
Milk is one of the primary animal-based foods in a healthy diet which provides vitamins, fats and particularly calcium to meet daily requirements. Currently, there are limited number metabolomics studies on milk more required establish reliable international standards databases for metabolite profiles. In this study, analysis three types UHT whole-milk, semi-skimmed lactose-free from Türkiye was investigated by NMR, with emphasis differences concentrations related lactose energy metabolism....
Abstract The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for includes: i) designing a vaccine as future protection; ii) structure-based drug design; iii) identifying existing drugs repurpose them immediate treatments. To assist repurposing design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray...
Abstract The covalent attachment of ubiquitin (Ub) and ubiquitin‐like (Ubl) proteins to various eukaryotic targets plays critical roles in regulating numerous cellular processes. E1‐activating enzymes are critical, because they catalyze activation their cognate Ub/Ubl protein responsible for its transfer the correct E2‐conjugating enzyme(s). activating enzyme neural‐precursor‐cell‐expressed developmentally downregulated 8 (NEDD8) is a heterodimer composed APPBP1 Uba3 subunits. carboxyl...
Small angle X-ray Scattering (SAXS) is a method for determining basic structural characteristics such as the size, shape, and surface of particles. SAXS data can be used to generate low resolution models biomolecules faster than any other conventional experimental biology tool. mostly collected in synchrotron facilities obtain best scattering possible however home source devices also valuable when properly optimized. Here, we examined sample collection optimization at beamline terms...
SUMMARY Crimean-Congo Hemorrhagic Fever (CCHF) is a severe tick-borne viral disease with high mortality rates and significant public health implications. Despite its global prevalence, the mechanisms underlying pathogenesis remain poorly understood, effective diagnostic therapeutic tools are limited. Metabolomics, as powerful tool for exploring host-pathogen interactions, offers promising avenue identifying biomarkers elucidating mechanisms. In this study, we investigated metabolic...
Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain and conjugated of the ISGylation system. Similar to ubiquitin other Ubls, ISG15 ligated its target proteins through series E1, E2, E3 enzymes known as Uba7, Ube2L6/UbcH8, HERC5, respectively. Ube2L6/UbcH8 plays central role in ISGylation, underscoring it important drug for boosting innate antiviral immunity. Depending on type ultimate protein, E2 have...