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Yıldırım, Günseli

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PhD Student

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Günseli

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Yıldırım

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Yıldırım, Günseli

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2021 - 20222

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Researcher Of Publications: search.filters.isAuthorOfPublication.49a1ecb7-a6d1-4805-8135-583bb27aafff

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Now showing 1 - 2 of 2
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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; 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; 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; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; 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; 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.