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Dağ, Çağdaş

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Çağdaş

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Dağ

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Dağ, Çağdaş

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2021 - 20228

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    TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates
    (Springer, 2021) Robson, Scott A.; Wu, Hongwei; Ziarek, Joshua J.; N/A; Dağ, Çağdaş; Faculty Member; N/A; N/A
    Accurate rotational correlation times (tau(c)) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of tau(c) using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipole-dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S-2 approximate to 0.9 to further improve the accuracy of tau(c) estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H-N internuclear distance (r), difference of the two principal components of the axially-symmetric N-15 CSA tensor (Delta delta(N)), and angle of the CSA tensor relative to the N-H bond vector (theta). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.
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    Biomolecular solution X-ray scattering at n2STAR beamline
    (Muğla Sıtkı Koçman Üniversitesi Fen Bilimleri Enstitüsü, 2022) Department of Molecular Biology and Genetics; N/A; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Göcenler, Oktay; Yenici, Cansu Müşerref; Kahraman, Kerem; Büyükdağ, Cengizhan; Dağ, Çağdaş; Undergraduate Student; Master Student; Undergraduate Student; Undergraduate Student; Faculty Member; Department of Molecular Biology and Genetics; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; N/A
    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 of biomolecules faster than any other conventional experimental structural biology tool. SAXS data is mostly collected in synchrotron facilities to obtain the best scattering data possible however home source SAXS devices can also generate valuable data when properly optimized. Here, we examined sample data collection and optimization at home source SAXS beamline in terms of the concentration, purity, and duration of data acquisition. We validated that high concentration, monodisperse and ultra pure protein samples obtained by size exclusion chromatography are necessary for generating viable SAXS data using a home source beamline. At least one hour is required to generate a feasible model from SAXS data, although longer data collection times do not always translate to higher resolutions. We show that with small optimizations during data collection and analysis SAXS can characterize properties such as oligomerization, molecular mass, and overall shape of particles in solution under physiological conditions. / Öz: Küçük açılı X-ışını Saçılımı (SAXS), parçacıkların boyutu, şekli ve yüzeyi gibi temel yapısal özellikleri belirlemek için kullanılan bir yöntemdir. SAXS verisi ile diğer geleneksel deneysel yapısal biyoloji araçlarından daha hızlı düşük çözünürlüklü biyomolekül modelleri hesaplanabilir. SAXS verileri, mümkün olan en iyi saçılma verilerini elde etmek için çoğunlukla senkrotron tesislerinde toplanır, ancak yerel kaynaklı SAXS cihazları da uygun şekilde optimize edildiğinde değerli veriler üretebilir. Burada, yerel kaynaklı SAXS ışın hattında numune veri toplama ve optimizasyonunu konsantrasyon, saflık ve veri toplama süresi açısından inceledik. Boyut dışlama kromatografisiyle elde edilen yüksek konsantrasyonlu, monodispers ve ultra saf protein numunelerinin, ev kaynaklı laboratuvar tipi ışın hattı kullanılarak uygulanabilir SAXS verilerinin üretilmesi için gerekli olduğunu doğruladık. Daha uzun veri toplama süresi her zaman daha yüksek çözünürlükler üretmez, ancak SAXS verilerinden uygun bir model oluşturmak için en az bir saat gereklidir. Ayrıca, hem veri toplama sırasında hem de daha sonra veri analizi sırasında küçük optimizasyonlarla SAXS, fizyolojik koşullar altında oligomerizasyon, moleküler kütle ve çözeltideki parçacıkların genel şekli gibi özellikleri belirleyebilir.
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    An ultra-compact and wireless tag for battery-free sweat glucose monitoring
    (Elsevier Advanced Technology, 2022) N/A; Department of Mechanical Engineering; N/A; N/A; Department of Mechanical Engineering; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Mirzajani, Hadi; Abbasiasl, Taher; Mirlou, Fariborz; İstif, Emin; Bathaei, Mohammad Javad; Dağ, Çağdaş; Deyneli, Oğuzhan; Dereli, Dilek Yazıcı; Beker, Levent; Researcher; PhD Student; PhD Student; Other; PhD Student; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced Research; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; School of Medicine; School of Medicine; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 171914; 179659; 308798
    Glucose monitoring before, during, and after exercise is essential for people with diabetes as exercise increases the risk of activity-induced hyper- and hypo-glycemic events. The situation is even more challenging for athletes with diabetes as they have impaired metabolic control compared to sedentary individuals. In this regard, a compact and noninvasive wearable glucose monitoring device that can be easily worn is critical to enabling glucose monitoring. This report presents an ultra-compact glucose tag with a footprint and weight of 1.2 cm(2) and 0.13 g, respectively, for sweat analysis. The device comprises a near field communication (NFC) chip, antenna, electrochemical sensor, and microfluidic channels implemented in different material layers. The device has a flexible and conformal structure and can be easily attached to different body parts. The battery-less operation of the device was enabled by NFC-based wireless power transmission and the compact antenna. Femtosecond laser ablation was employed to fabricate a highly compact and flexible NFC antenna. The proposed device demonstrated excellent operating characteristics with a limit of detection (LOD), limit of quantification (LOQ), and sensitivity of 24 mu M, 74 mu M, and 1.27 mu A cm(-2) mM(-1), respectively. The response of the proposed sensor in sweat glucose detection and quantification was validated by nuclear magnetic resonance spectroscopy (NMR). Also, the device's capability in attachment to the body, sweat collection, and glucose measurement was demonstrated through in vitro and in vivo experiments, and satisfactory results were obtained.
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    PublicationOpen Access
    Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography
    (Cell Press, 2022) Dao, E. Han; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Hayes, Brandon; Liang, Mengning; Hunter, Mark S.; Batyuk, Alexander; Sierra, Raymond G.; Ketawala, Gihan; Botha, Sabine; Department of Molecular Biology and Genetics; Ertem, Fatma Betül; Güven, Ömür; Büyükdağ, Cengizhan; Göcenler, Oktay; Ayan, Esra; Yüksel, Büşra; Gül, Mehmet; Karakadıoğlu, Gözde Usta; Çakılkaya, Barış; Johnson, Jerome Austin; Demirci, Hasan; Dağ, Çağdaş; Undergraduate Student; PhD Student; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 307350
    The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography.
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    PublicationOpen Access
    Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein
    (Nature Publishing Group (NPG), 2021) Çiftçi, Halilibrahim; Tateishi, Hiroshi; Koiwai, Kotaro; Koga, Ryoko; Anraku, Kensaku; Monde, Kazuaki; Destan, Ebru; Yüksel, Büşra; Ayan, Esra; Yıldırım, Günseli; Yığın, Merve; Sierra, Raymond G.; Yoon, Chun Hong; Su, Zhen; Liang, Mengling; Acar, Burçin; Haliloğlu, Türkan; Otsuka, Masami; Yumoto, Fumiaki; Fujita, Mikako; Senda, Toshiya; Department of Molecular Biology and Genetics; Demirci, Hasan; Dağ, Çağdaş; Güven, Ömür; Ertem, Fatma Betül; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); College of Sciences; Graduate School of Sciences and Engineering; 307350; N/A; N/A; N/A; N/A; N/A
    Oligomerization of Pr55(Gag) is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55(Gag). However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55(Gag) to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18-33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles' membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain's 2D layers during assembly and budding.
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    PublicationOpen Access
    Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature
    (Springer Nature, 2022) Yefanov, Oleksandr M.; Barty, Anton; Tolstikova, Alexandra; Ketawala, Gihan K.; Botha, Sabine; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alexander; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Cohen, Aina; Doukov, Tzanko; Sierra, Raymond G.; Department of Molecular Biology and Genetics; Dağ, Çağdaş; Ayan, Esra; Yüksel, Büşra; Destan, Ebru; Ertem, Fatma Betül; Yıldırım, Günseli; Eren, Meryem; Demirci, Hasan; Faculty Member; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 307350
    Ayan et al. report two structures of the protein streptavidin - one at ambient temperature determined using serial femtosecond crystallography and a second one determined at cryogenic temperature. These results provide insights into the structural dynamics of apo streptavidin and reveal a cooperative allostery between monomers for binding to biotin, and the findings are supported by GNM analysis. Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 angstrom resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 angstrom resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
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    PublicationOpen Access
    Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing
    (Elsevier, 2021) Durdağı, Serdar; Doğan, Berna; Avşar, Timuçin; Erol, İsmail; Çalış, Şeyma; Orhan, Müge D.; Aksoydan, Busecan; Şahin, Kader; Oktay, Lalehan; Tolu, İlayda; Olkan, Alpsu; Erdemoğlu, Ece; Yefanov, Oleksandr M.; Dao, E. Han; Hayes, Brandon; Liang, Mengning; Seaberg, Matthew H.; Hunter, Mark S.; Batyuk, Alex; Mariani, Valerio; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Sierra, Raymond G.; Snell, Edward H.; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; N/A; Demirci, Hasan; Dağ, Çağdaş; Büyükdağ, Cengizhan; Ertem, Fatma Betül; Yıldırım, Günseli; Destan, Ebru; Güven, Ömür; Ayan, Esra; Yüksel, Büşra; Göcenler, Oktay; Can, Özgür; Özabrahamyan, Serena; Tanısalı, Gökhan; Faculty Member; Faculty Member; Undergraduate Student; PhD Student; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); College of Sciences; Graduate School of Sciences and Engineering; School of Nursing; 307350; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A
    The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.
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    PublicationOpen Access
    Effectiveness of different types of masks in aerosol dispersion in SARS-CoV-2 infection
    (Elsevier, 2021) Sözak, A.; Bulut, A. S.; Sander, T. Z.; Department of Molecular Biology and Genetics; Department of Industrial Engineering; N/A; Tanısalı, Gökhan; Doğan, Özlem; Dağ, Çağdaş; Gönen, Mehmet; Can, Füsun; Demirci, Hasan; Ergönül, Önder; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Industrial Engineering; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; School of Medicine; N/A; 170418; N/A; 237468; 103165; 307350; 110398
    Objective: to compare the effectiveness of different mask types in limiting the dispersal of coughed air. Method: the Schlieren method with a single curved mirror was used in this study. Coughed air has a slightly higher temperature than ambient air, which generates a refractive index gradient. A curved mirror with a radius of curvature of 10 m and a diameter of 60 cm was used. The spread of the cough wavefront was investigated among five subjects wearing: (1) no mask; (2) a single surgical mask; (3) a double surgical mask; (4) a cloth mask; (5) a valveless N95 mask; and (6) a valved N95 mask. Results: all mask types reduced the size of the contaminated region significantly. The percentage reduction in the cross-sectional area of the contaminated region for the same mask types on different subjects revealed by normalized data suggests that the fit of a mask plays an important role. Conclusions: no significant difference in the spread of coughed air was found between the use of a single surgical mask or a double surgical mask. Cloth masks may be effective, depending on the quality of the cloth. Valved N95 masks exclusively protect the user. The fit of a mask is an important factor to minimize the contaminated region.