Researcher:
Köroğlu, Yunus Emre

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Master Student

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Yunus Emre

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Köroğlu

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Köroğlu, Yunus Emre

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20212

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Researcher Of Publications: search.filters.isAuthorOfPublication.4e5c1e2a-25ff-41d7-b99f-d92e2bb6e9b5

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    PublicationOpen Access
    Neuropsychiatric symptoms of COVID-19 explained by SARS-CoV-2 proteins' mimicry of human protein interactions
    (Frontiers, 2021) Department of Chemical and Biological Engineering; N/A; Eser, Hale Yapıcı; Keskin, Özlem; Gürsoy, Attila; Köroğlu, Yunus Emre; Çakmak, Özgür Öztop; Özdemir, Yasemin Gürsoy; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; College of Engineering; Graduate School of Sciences and Engineering; 134359; 26605; 8745; N/A; 299358; 170592
    The first clinical symptoms focused on the presentation of coronavirus disease 2019 (COVID-19) have been respiratory failure, however, accumulating evidence also points to its presentation with neuropsychiatric symptoms, the exact mechanisms of which are not well known. By using a computational methodology, we aimed to explain the molecular paths of COVID-19 associated neuropsychiatric symptoms, based on the mimicry of the human protein interactions with SARS-CoV-2 proteins. Methods: available 11 of the 29 SARS-CoV-2 proteins’ structures have been extracted from Protein Data Bank. HMI-PRED (Host-Microbe Interaction PREDiction), a recently developed web server for structural PREDiction of protein-protein interactions (PPIs) between host and any microbial species, was used to find the “interface mimicry” through which the microbial proteins hijack host binding surfaces. Classification of the found interactions was conducted using the PANTHER Classification System. Results: predicted Human-SARS-CoV-2 protein interactions have been extensively compared with the literature. Based on the analysis of the molecular functions, cellular localizations and pathways related to human proteins, SARS-CoV-2 proteins are found to possibly interact with human proteins linked to synaptic vesicle trafficking, endocytosis, axonal transport, neurotransmission, growth factors, mitochondrial and blood-brain barrier elements, in addition to its peripheral interactions with proteins linked to thrombosis, inflammation and metabolic control. Conclusion: SARS-CoV-2-human protein interactions may lead to the development of delirium, psychosis, seizures, encephalitis, stroke, sensory impairments, peripheral nerve diseases, and autoimmune disorders. Our findings are also supported by the previous in vivo and in vitro studies from other viruses. Further in vivo and in vitro studies using the proteins that are pointed here, could pave new targets both for avoiding and reversing neuropsychiatric presentations.
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    PublicationOpen Access
    Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions
    (Oxford University Press (OUP), 2021) Tsai, Chung-Jung; Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Övek, Damla; Taweel, Ameer; Abalı, Zeynep; Tezsezen, Ece; Köroğlu, Yunus Emre; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26605; 8745; N/A; N/A; N/A; N/A; N/A
    Summary: we present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein-protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy.