Researcher:
Göcenler, Oktay

Profile Picture
ORCID

Job Title

Undergraduate Student

First Name

Oktay

Last Name

Göcenler

Name

Name Variants

Göcenler, Oktay

Email Address

Birth Date

Filters

2021 - 20224

Advanced Search

Filter by

Settings

Researcher Of Publications: search.filters.isAuthorOfPublication.d8f3e510-7e16-4ef0-822a-5a6f8f5a9a89

Search Results

Now showing 1 - 4 of 4
  • Placeholder
    PublicationMetadata only
    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.
  • Thumbnail Image
    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.
  • Thumbnail Image
    PublicationOpen Access
    Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography
    (Multidisciplinary Digital Publishing Institute (MDPI), 2021) Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdağı, Serdar; Sierra, Raymond G.; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Güven, Ömür; Gül, Mehmet; Ayan, Esra; Johnson, Jerome Austin; Çakılkaya, Barış; Karakadıoğlu, Gözde Usta; Ertem, Fatma Betül; Tokay, Nurettin; Yüksel, Büşra; Göcenler, Oktay; Büyükdağ, Cengizhan; Demirci, Hasan; PhD Student; Master Student; Undergraduate Student; Undergraduate Student; Faculty Member; 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); 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; 307350
    Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.
  • Thumbnail Image
    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.