Search

Your search keyword '"Çakılkaya, Barış"' showing total 2 results
Start Over Author "Çakılkaya, Barış" Topic sars-cov-2
2 results on '"Çakılkaya, Barış"'

1. Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography

Author

Fatma Betul Ertem, Omur Guven, Cengizhan Buyukdag, Oktay Gocenler, Esra Ayan, Busra Yuksel, Mehmet Gul, Gozde Usta, Barıs Cakılkaya, J. Austin Johnson, E. Han Dao, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Brandon Hayes, Mengning Liang, Mark S. Hunter, Alexander Batyuk, Raymond G. Sierra, Gihan Ketawala, Sabine Botha, Çağdaş Dağ, Hasan DeMirci, Ertem, Fatma Betül, Güven, Ömür, Büyükdağ, Cengizhan, Göçenler, Oktay, Ayan, Esra, Yüksel, Büşra, Gül, Mehmet, Usta, Gözde, Çakılkaya, Barış, Johnson, J. Austin, Demirci, Hasan, Dağ, Çağdaş, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), 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, 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, and Department of Molecular Biology and Genetics

Subjects
Models, Molecular, Science (General), General Immunology and Microbiology, SARS-CoV-2, General Neuroscience, fungi, Crystallography, X-Ray, General Biochemistry, Genetics and Molecular Biology, body regions, Q1-390, X-ray Crystallography, X-Ray laser, Crystallography, Serials, Structural Biology, Protein Biochemistry, Protocol, Protein expression and purification, Humans, skin and connective tissue diseases, Protein biochemistry, Structural biology, X-ray crystallography, Crystallization, Coronavirus 3C Proteases
Abstract

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. For complete details on the use and execution of this protocol, please refer to Durdagi et al. (2021)., Graphical abstract, 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.

Published
2022

2. Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Author

Gozde Usta, Fatma Betul Ertem, Nurettin Tokay, Chun Hong Yoon, Raymond G. Sierra, Christopher Kupitz, Oktay Gocenler, Mehmet Gul, Busra Yuksel, Baris Cakilkaya, Frédéric Poitevin, Zhen Su, Gihan K. Ketawala, Cengizhan Buyukdag, Sabine Botha, Serdar Durdagi, Brandon Hayes, Hasan DeMirci, Omur Guven, Esra Ayan, J. Austin Johnson, Alexander Batyuk, Güven, Ömür, Gül, Mehmet, Ayan, Esra, Johnson, Jerome Austin, Çakılkaya, Barış, Usta, Gözde Karakadıoğlu, Ertem, Fatma Betül, Tokay, Nurettin, Yüksel, Büşra, Göcenler, Oktay, Büyükdağ, Cengizhan, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Botha, Sabine, Ketawala, Gihan, Su, Zhen, Hayes, Brandon, Poitevin, Frederic, Batyuk, Alexander, Yoon, Chun Hong, Kupitz, Christopher, Durdağı, Serdar, Sierra, Raymond G., 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, Department of Molecular Biology and Genetics, and Department of Chemical and Biological Engineering

Subjects
Drug, serial femtosecond crystallography, Data collection, Crystallography, Coronavirus disease 2019 (COVID-19), Computer science, Drug candidate, SARS-CoV-2, media_common.quotation_subject, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), General Chemical Engineering, high-throughput drug screening, Computational biology, Condensed Matter Physics, Main protease, Serial femtosecond crystallography, High-throughput drug screening, Inorganic Chemistry, Drug repositioning, Materials science, main protease, QD901-999, Femtosecond, General Materials Science, Throughput (business), media_common
Abstract

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., National Science Foundation (NSF) Science and Technology Centers Grant; Biology with X-ray Lasers (BioXFEL); Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; 2244 Industrial PhD Fellowship Program; 1001 Scientific and Technological Research Projects Funding Program

Published
2021

Catalog

Books, media, physical & digital resources
See catalog results