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1. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

Author: Gul, Mehmet, Ayan, Esra, Destan, Ebru, Johnson, J. Austin, Shafiei, Alaleh, Kepceoğlu, Abdullah, Yilmaz, Merve, Ertem, Fatma Betül, Yapici, İlkin, Tosun, Bilge, Baldir, Nilüfer, Tokay, Nurettin, Nergiz, Zeliş, Karakadioğlu, Gözde, Paydos, Seyide Seda, Kulakman, Cahine, Ferah, Cengiz Kaan, Güven, Ömür, Atalay, Necati, Akcan, Enver Kamil, Cetinok, Haluk, Arslan, Nazlı Eylül, Şabanoğlu, Kardelen, Aşci, Bengisu, Tavli, Serra, Gümüsboğa, Helin, Altuntaş, Sevde, Otsuka, Masami, Fujita, Mikako, Teki̇n, Şaban, Çi̇ftçi̇, Halilibrahim, Durdaği, Serdar, Karaca, Ezgi, Kaplan Türköz, Burcu, Kabasakal, Burak Veli, Kati, Ahmet, and DeMi̇rci̇, Hasan
Published: 2023
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2. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

Author: Atalay, Necati; Akcan, Enver Kamil; Gül, Mehmet; Ayan, Esra; Destan, Ebru; Ertem, Fatma Betül; Tokay, Nurettin; Çakılkaya, Barış; Nergiz, Zeliş; Karakadıoğlu, Gözde; Kepçeoğlu, Abdullah; Yapıcı, İlkin; Tosun, Bilge; Baldır, Nilüfer; Yıldırım, Günseli; Johnson, Jerome Austin; Güven, Ömür; Shafiei, Alaleh; Arslan, Nazlı Eylül; Yılmaz, Merve; Kulakman, Cahine; Paydos, Seyide Seda; Çinal, Zeynep Sena; Şabanoğlu, Kardelen; Pazarçeviren, Ayşegül; Yılmaz, Ayşenur; Canbay, Başak; Aşcı, Bengisu; Kartal, Esra; Tavlı, Serra; Çiftçi, Halil İbrahim; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Caliseki, Mehmet; Goc, Gunce; Mermer, Arif; Yesilay, Gamze; Altuntas, Sevde; Tateishi, Hiroshi; Otsuka, Masami; Fujita, Mikako; Tekin, Saban; Durdagi, Serdar; Doganay, Gizem Dinler; Karaca, Ezgi; Turkoz, Burcu Kaplan; Kabasakal, Burak Veli; Kati, Ahmet, 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; Department of Chemical and Biological Engineering, Atalay, Necati; Akcan, Enver Kamil; Gül, Mehmet; Ayan, Esra; Destan, Ebru; Ertem, Fatma Betül; Tokay, Nurettin; Çakılkaya, Barış; Nergiz, Zeliş; Karakadıoğlu, Gözde; Kepçeoğlu, Abdullah; Yapıcı, İlkin; Tosun, Bilge; Baldır, Nilüfer; Yıldırım, Günseli; Johnson, Jerome Austin; Güven, Ömür; Shafiei, Alaleh; Arslan, Nazlı Eylül; Yılmaz, Merve; Kulakman, Cahine; Paydos, Seyide Seda; Çinal, Zeynep Sena; Şabanoğlu, Kardelen; Pazarçeviren, Ayşegül; Yılmaz, Ayşenur; Canbay, Başak; Aşcı, Bengisu; Kartal, Esra; Tavlı, Serra; Çiftçi, Halil İbrahim; Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Caliseki, Mehmet; Goc, Gunce; Mermer, Arif; Yesilay, Gamze; Altuntas, Sevde; Tateishi, Hiroshi; Otsuka, Masami; Fujita, Mikako; Tekin, Saban; Durdagi, Serdar; Doganay, Gizem Dinler; Karaca, Ezgi; Turkoz, Burcu Kaplan; Kabasakal, Burak Veli; Kati, Ahmet, 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; Department of Chemical and Biological Engineering
Abstract: X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis., NSF Science and Technology Center Grant; Biology with X-ray Lasers, BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); TÜBİTAK 2218 - National Postdoctoral Research Fellowship Program; TÜBİTAK 2232 International Outstanding Researchers Program; 2232 International Fellowship for Outstanding Researchers Program; European Union (EU); Horizon 2020; 2236 CoCirculation2 Program; TÜBİTAK 1001 Scientific and Technological Research Projects Funding Program
Published: 2023

3. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish DeLight"

Author: ATALAY, NECATİ, primary, AKCAN, ENVER KAMİL, additional, GÜL, MEHMET, additional, AYAN, ESRA, additional, DESTAN, EBRU, additional, KUZUCU, FATMA BETÜL ERTEM, additional, TOKAY, NURETTİN, additional, ÇAKILKAYA, BARIŞ, additional, NERGİZ, ZELİŞ, additional, USTA, GÖZDE KARAKADIOĞLU, additional, KEPCEOĞLU, ABDULLAH, additional, YAPICI, İLKİN, additional, TOSUN, BİLGE, additional, BALDIR, NİLÜFER, additional, YILDIRIM, GÜNSELİ, additional, JOHNSON, J AUSTIN, additional, GÜVEN, ÖMÜR, additional, SHAFIEI, ALALEH, additional, ARSLAN, NAZLI EYLÜL, additional, YILMAZ, MERVE, additional, KULAKMAN, CAHİNE, additional, PAYDOS, SEYİDE SEDA, additional, ÇİNAL, SEYNEP SENA, additional, ŞABANOĞLU, KARDELEN, additional, PAZARÇEVİREN, AYŞEGÜL, additional, YILMAZ, AYŞENUR, additional, CANBAY, BAŞAK, additional, AŞÇI, BENGİSU, additional, KARTAL, ESRA, additional, TAVLI, SERRA, additional, ÇALISEKİ, MEHMET, additional, GÖÇ, GÜNCE, additional, MERMER, ARİF, additional, YEŞİLAY, GAMZE, additional, ALTUNTAŞ, SEVDE, additional, TATEISHI, HIROSHI, additional, OTSUKA, MASAMI, additional, FUJITA, MIKAKO, additional, TEKİN, ŞABAN, additional, ÇİFTÇİ, HALİLİBRAHİM, additional, DURDAĞI, SERDAR, additional, DOĞANAY, GİZEM DİNLER, additional, KARACA, EZGİ, additional, TÜRKÖZ, BURCU KAPLAN, additional, KABASAKAL, BURAK VELİ, additional, KATI, AHMET, additional, and DEMİRCİ, HASAN, additional
Published: 2023
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4. Rapid and High Resolution Ambient Temperature Structure Determination at Turkish Light Source

Author: Gul, Mehmet, primary, Ayan, Esra, additional, Destan, Ebru, additional, Johnson, J Austin, additional, Shafiei, Alaleh, additional, Kepceoğlu, Abdullah, additional, Yilmaz, Merve, additional, Ertem, Fatma Betül, additional, Yapici, İlkin, additional, Tosun, Bilge, additional, Baldir, Nilüfer, additional, Tokay, Nurettin, additional, Nergiz, Zeliş, additional, Karakadioğlu, Gözde, additional, Paydos, Seyide Seda, additional, Kulakman, Cahine, additional, Ferah, Cengiz Kaan, additional, Güven, Ömür, additional, Atalay, Necati, additional, Akcan, Enver Kamil, additional, Cetinok, Haluk, additional, Arslan, Nazlı Eylül, additional, Şabanoğlu, Kardelen, additional, Aşci, Bengisu, additional, Tavli, Serra, additional, Gümüsboğa, Helin, additional, Altuntaş, Sevde, additional, Otsuka, Masami, additional, Fujita, Mikako, additional, Tekin, Şaban, additional, Çiftçi, Halilibrahim, additional, Durdaği, Serdar, additional, Karaca, Ezgi, additional, Kaplan Türköz, Burcu, additional, Kabasakal, Burak Veli, additional, Kati, Ahmet, additional, and DeMirci, Hasan, additional
Published: 2022
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5. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

Author: Atalay, Necati, primary, Akcan, Enver Kamil, additional, Gül, Mehmet, additional, Ayan, Esra, additional, Destan, Ebru, additional, Ertem, Fatma Betül, additional, Tokay, Nurettin, additional, Çakilkaya, Barış, additional, Nergiz, Zeliş, additional, Karakadioğlu, Gözde, additional, Kepceoğlu, Abdullah, additional, Yapici, İlkin, additional, Tosun, Bilge, additional, Baldir, Nilüfer, additional, Yildirim, Günseli, additional, Johnson, J Austin, additional, Güven, Ömür, additional, Shafiei, Alaleh, additional, Arslan, Nazlı Eylül, additional, Yilmaz, Merve, additional, Kulakman, Cahine, additional, Paydos, Seyide Seda, additional, Çinal, Zeynep Sena, additional, Şabanoğlu, Kardelen, additional, Pazarçeviren, Ayşegül, additional, Yilmaz, Ayşenur, additional, Canbay, Başak, additional, Aşci, Bengisu, additional, Kartal, Esra, additional, Tavli, Serra, additional, Çaliseki, Mehmet, additional, Göç, Günce, additional, Mermer, Arif, additional, Yeşilay, Gamze, additional, Altuntaş, Sevde, additional, Tateishi, Hiroshi, additional, Otsuka, Masami, additional, Fujita, Mikako, additional, Tekin, Şaban, additional, Çiftçi, Halilibrahim, additional, Durdaği, Serdar, additional, Dinler Doğanay, Gizem, additional, Karaca, Ezgi, additional, Kaplan Türköz, Burcu, additional, Kabasakal, Burak Veli, additional, Kati, Ahmet, additional, and Demirci, Hasan, additional
Published: 2022
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6. Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography

Author: 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, Department of Molecular Biology and Genetics, 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
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., National Science Foundation (NSF) Science and Technology Centers; BioXFEL; National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program of TÜBİTAK; 2244 Industrial PhD Program of TÜBİTAK; 1001 TÜBİTAK Supporting Scientific and Technological Research Projects Program; Linac Coherent Light Source (LCLS); Stanford Synchrotron Light Source (SSRL); SLAC National Accelerator Laboratory; U.S. Department of Energy, Office of Science, Basic Energy Sciences
Published: 2022

7. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

Author: Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Materials Science and Engineering, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Yığın, Merve; Büyükdağ, Cengizhan; Ertem, Fatma Betül; Yıldırım, Günseli; Destan, Ebru; Güven, Ömür; Ayan, Esra; Yüksel, Büşra; Pekşen, Ayşe Buket; Göçenler, Oktay; Yücel, Ali Doğa; Can, Özgür; Ozabrahamyan, Serena; Shafiei, Alaleh; Akşit, Fulya; Tanısalı, Gökhan; Besler, Sabri Özkan, 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; Department of Materials Science and Engineering, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Yığın, Merve; Büyükdağ, Cengizhan; Ertem, Fatma Betül; Yıldırım, Günseli; Destan, Ebru; Güven, Ömür; Ayan, Esra; Yüksel, Büşra; Pekşen, Ayşe Buket; Göçenler, Oktay; Yücel, Ali Doğa; Can, Özgür; Ozabrahamyan, Serena; Shafiei, Alaleh; Akşit, Fulya; Tanısalı, Gökhan; Besler, Sabri Özkan, and 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.
Abstract: 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.
Published: 2021

8. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Author: Department of Molecular Biology and Genetics, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Shafiei, Alaleh; Güven, Ömür; Besler, Sabri Özkan; Ertem, Fatma Betül, 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 (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Shafiei, Alaleh; Güven, Ömür; Besler, Sabri Özkan; Ertem, Fatma Betül, and 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
Abstract: 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.
Published: 2021

9. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

Author: Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Yığın, Merve; Büyükdağ, Cengizhan; Ertem, Fatma Betül; Yıldırım, Günseli; Destan, Ebru; Güven, Ömür; Ayan, Esra; Yüksel, Büşra; Pekşen, Ayşe Buket; Göçenler, Oktay; Yücel, Ali Doğa; Can, Özgür; Ozabrahamyan, Serena; Shafiei, Alaleh; Akşit, Fulya; Tanısalı, Gökhan; Besler, Sabri Özkan, 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., 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, Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Materials Science and Engineering, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Yığın, Merve; Büyükdağ, Cengizhan; Ertem, Fatma Betül; Yıldırım, Günseli; Destan, Ebru; Güven, Ömür; Ayan, Esra; Yüksel, Büşra; Pekşen, Ayşe Buket; Göçenler, Oktay; Yücel, Ali Doğa; Can, Özgür; Ozabrahamyan, Serena; Shafiei, Alaleh; Akşit, Fulya; Tanısalı, Gökhan; Besler, Sabri Özkan, 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., 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, and Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Materials Science and Engineering
Abstract: 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., National Science Foundation (NSF) Science and Technology Centers; BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); Bahçeşehir University (BAU) Scientific Research Projects (BAP)
Published: 2021

10. 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: 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; Department of Chemical and Biological Engineering, 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, and Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering
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

11. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Author: Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Shafiei, Alaleh; Güven, Ömür; Besler, Sabri Özkan; Ertem, Fatma Betül, 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, 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, Department of Molecular Biology and Genetics, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350); Dağ, Çağdaş; Shafiei, Alaleh; Güven, Ömür; Besler, Sabri Özkan; Ertem, Fatma Betül, 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, 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, and Department of Molecular Biology and Genetics
Abstract: 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., National Science Foundation (NSF) Science and Technology Centers Grant; BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; Grant-in-Aid for Scientific Research; Grant-in-Aid for Research Activity Start-up; Japanese Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research; Grant-in and Aid for JSPS Research Fellow; Japan Agency for Medical Research and Development Basis for Supporting Innovative Drug Discovery and Life Science Research; Platform for Drug Discovery, Informatics, and Structural Life Science (MEXT); Japan Agency for Medical Research and Development (AMED)
Published: 2021

12. 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

13. Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein

Author: Zhen Su, Halil I. Ciftci, Busra Yuksel, Masami Otsuka, Kensaku Anraku, Mikako Fujita, Kotaro Koiwai, Chun Hong Yoon, Çağdaş Dağ, Alaleh Shafiei, Mengling Liang, Gunseli Yildirim, Kazuaki Monde, Toshiya Senda, Hasan DeMirci, Burcin Acar, Hiroshi Tateishi, Ryoko Koga, Raymond G. Sierra, Omur Guven, Fumiaki Yumoto, F. Betul Ertem, Turkan Haliloglu, Merve Yigin, Ebru Destan, Esra Ayan, Sabri O. Besler, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Dağ, Çağdaş, Shafiei, Alaleh, Güven, Ömür, Besler, Sabri Özkan, Ertem, Fatma Betül, 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, 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, and Department of Molecular Biology and Genetics
Subjects: Models, Molecular, Cyclitol, Protein Conformation, Science, Association (object-oriented programming), Human immunodeficiency virus (HIV), HIV Infections, Crystal structure, Crystallography, X-Ray, medicine.disease_cause, Article, World health, chemistry.chemical_compound, Protein Domains, medicine, Molecule, Humans, Protein Precursors, Binding site, X-ray crystallography, Budding, Multidisciplinary, Binding Sites, Viral matrix protein, Chemistry, Virus Assembly, Cell Membrane, Binding sites, Cell membrane, HIV infections, HIV-1, Models molecular, Phosphoric monoester hydrolases, Protein conformation, Protein domains, Protein precursors, Virus assembly, Phosphoric Monoester Hydrolases, Multidisciplinary sciences, Science and technology, Membrane, Virion assembly, Biophysics, Medicine, Structural biology
Abstract: 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., National Science Foundation (NSF) Science and Technology Centers Grant; BioXFEL; Scientific and Technological Research Council of Turkey (TÜBİTAK); 2232 International Fellowship for Outstanding Researchers Program; Grant-in-Aid for Scientific Research; Grant-in-Aid for Research Activity Start-up; Japanese Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research; Grant-in and Aid for JSPS Research Fellow; Japan Agency for Medical Research and Development Basis for Supporting Innovative Drug Discovery and Life Science Research; Platform for Drug Discovery, Informatics, and Structural Life Science (MEXT); Japan Agency for Medical Research and Development (AMED)
Published: 2021

14. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

Author: Gunseli Yildirim, Alaleh Shafiei, Oleksandr Yefanov, Hasan DeMirci, Frédéric Poitevin, Timucin Avsar, Chun Hong Yoon, Muge Didem Orhan, Merve Yigin, Lalehan Oktay, Fulya Aksit, Çağdaş Dağ, Serdar Durdagi, Christopher Kupitz, Omur Guven, Valerio Mariani, Ece Erdemoglu, Ebru Destan, Edward H. Snell, Ismail Erol, Mark S. Hunter, Esra Ayan, Berna Dogan, Mengning Liang, Busecan Aksoydan, A. Batyuk, Ozgur Can, Cengizhan Buyukdag, Sabri O. Besler, Seyma Calis, Brandon Hayes, Matthew Seaberg, Serena Ozabrahamyan, Ilayda Tolu, Gihan K. Ketawala, Anton Barty, Raymond G. Sierra, Kader Sahin, Gokhan Tanisali, Oktay Gocenler, Ali D. Yucel, E. Han Dao, Alpsu Olkan, Ayse B. Peksen, Zhen Su, A. Tolstikova, Sabine Botha, Busra Yuksel, Fatma Betul Ertem, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Dağ, Çağdaş, Yığın, Merve, Büyükdağ, Cengizhan, Ertem, Fatma Betül, Yıldırım, Günseli, Destan, Ebru, Güven, Ömür, Ayan, Esra, Yüksel, Büşra, Pekşen, Ayşe Buket, Göçenler, Oktay, Yücel, Ali Doğa, Can, Özgür, Ozabrahamyan, Serena, Shafiei, Alaleh, Akşit, Fulya, Tanısalı, Gökhan, Besler, Sabri Özkan, 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., 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, Department of Molecular Biology and Genetics, Department of Chemical and Biological Engineering, and Department of Materials Science and Engineering
Subjects: Drug, Molecular model, Protein Conformation, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, medicine.medical_treatment, ambient temperature, Molecular Conformation, Crystallography, X-Ray, Article, Structural Biology, Catalytic Domain, medicine, SFX, Computer Simulation, Molecular Biology, Coronavirus 3C Proteases, media_common, Principal Component Analysis, Protease, Biochemistry and molecular biology, Biophysics, Cell biology, biology, drug repurposing, Drug discovery, SARS-CoV-2, Drug Repositioning, Temperature, Active site, Small molecule, Recombinant Proteins, COVID-19 Drug Treatment, Molecular Docking Simulation, Drug repositioning, Crystallography, main protease, Drug Design, ddc:540, biology.protein, Dimerization, Ambient temperature, Drug repurposing, Main protease
Abstract: 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., Graphical abstract, Durdağı et al. represent radiation damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological temperature and performed MD simulation of apo-form proteins and three known main protease inhibitors. The structures reveal alternate conformation, while MD simulation indicates asymmetric behavior of the protein, which is invaluable information for immediate drug-repurposing studies.
Published: 2021

15. 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

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15 results on '"Güven, Ömür"'

1. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

2. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

3. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish DeLight"

4. Rapid and High Resolution Ambient Temperature Structure Determination at Turkish Light Source

5. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

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

7. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

8. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

9. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

10. Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography

11. Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

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

13. Structural insight into host plasma membrane association and assembly of HIV-1 Matrix protein

14. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

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

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