Yazar "TAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümü" için Araştırma Çıktıları | TR-Dizin | WoS | Scopus | PubMed listeleme
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Identification of food/nonfood visual stimuli from event-related brain potentials
Güney, Selen; Arslan, Sema; Duru, Adil Deniz; Duru, Dilek Göksel (Hindawi Publishing Corporation, 2021)Although food consumption is one of the most basic human behaviors, the factors underlying nutritional preferences are not yet clear. The use of classification algorithms can clarify the understanding of these factors. ... -
Improvement of design of a surgical interface using an eye tracking device
Erol Barkana, Duygun; Açık, Alper; Göksel Duru, Dilek; Duru, Adil Deniz (Springer Nature, 2014)Background: Surgical interfaces are used for helping surgeons in interpretation and quantification of the patient information, and for the presentation of an integrated workflow where all available data are combined to ... -
Insights into the molecular mechanisms of Alzheimer's and Parkinson's diseases with molecular simulations: understanding the roles of artificial and pathological missense mutations in intrinsically disordered proteins related to pathology
Weber, Orkide Coşkuner; Uversky, Vladimir N. (Mdpi, 2018)Amyloid-beta and alpha-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt ... -
Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases
Weber, Orkide Coşkuner; Uversky, Vladimir N. (Elsevier Academic Press Inc, 2019)Amyloid-beta (A beta) and alpha-synuclein (alpha S) are two intrinsically disordered proteins (IDPs) at the centers of the pathogenesis of Alzheimer's and Parkinson's diseases, respectively. Different hypotheses have been ... -
Microbial peptidyl-prolyl cis/trans isomerases (ppIases): virulence factors and potential alternative drug targets
Ünal, Can Murat; Steinert, Michael (Amer Soc Microbiology, 2014)Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline ... -
MIPs and aptamers for recognition of proteins in biomimetic sensing
Menger, Marcus; Yarman, Aysu; Erdossy, Julia; Yıldız, Hüseyin Bekir; Gyurcsanyi, Robert E.; Scheller, Frieder W. (Mdpi, 2016)Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides ... -
Molecular LEGO by domain-imprinting of cytochrome P450 BM3
Jetzschmann, Katharina J.; Yarman, Aysu; Rustam, L.; Kielb, P.; Urlacher, V. B.; Fischer, A.; Scheller, Frieder W. (Elsevier Science Bv, 2018)Hypothesis: Electrosynthesis of the MIP nano-film after binding of the separated domains or holocytochrome BM3 via an engineered anchor should result in domain-specific cavities in the polymer layer. Experiments: Both the ... -
Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions
Fatafta, Hebah; Samantray, Suman; Sayyed-Ahmad, Abdallah; Weber, Orkide Coşkuner; Strodel, Birgit (Academic Press Inc Elsevier Science, 2021)Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are ... -
Molecularly imprinted polymer based sensors for SARS-CoV-2: where are we now?
Yarman, Aysu; Kurbanoğlu, Sevinç (MDPI-Multidisciplinary Digital Publishing Institute, 2022)Since the first reported case of COVID-19 in 2019 in China and the official declaration from the World Health Organization in March 2021 as a pandemic, fast and accurate diagnosis of severe acute respiratory syndrome ... -
NFI transcriptionally represses CDON and is required for SH-SY5Y cell survival
Uluca, Betül; Esen, Cemre Lektemur; Erdoğan, Sinem Sarıtaş; Kumbasar, Aslı (Elsevier, 2022)Nuclear Factor One (NFI) family of transcription factors regulate proliferation and multiple aspects of differentiation, playing analogous roles in embryonic development and various types of cancer. While all NFI family ... -
Novel cycloheximide derivatives targeting the moonlighting protein Mip exhibit specific antimicrobial activity against Legionella pneumophila
Rasch, Janine; Theuerkorn, Martin; Ünal, Can Murat; Heinsohn, Natascha; Tran, Stefan; Fischer, Gunter; Steinert, Michael (Frontiers Media Sa, 2015)Macrophage infectivity potentiator (Mip) and Mip-like proteins are virulence factors in a wide range of pathogens including Legionella pneumophila. These proteins belong to the FK506 binding protein (FKBP) family of ... -
Novel therapeutic strategies for Clostridium difficile infections
Ünal, Can Murat; Steinert, Michael (Taylor & Francis Ltd, 2016)Introduction: In recent years, Clostridium difficile has become the primary cause of antibiotic-associated diarrhea and pseudomembranous colitis, resulting in long and complicated hospital stays that represent a serious ... -
Peptidylprolyl cis-trans isomerases of Legionella pneumophila: virulence, moonlighting and novel therapeutic targets
Rasch, Janine; Ünal, Can Murat; Steinert, Michael (Portland Press Ltd, 2014)Legionella pneumophila, typically a parasite of free-living protozoa, can also replicate in human alveolar macrophages and lung epithelial cells causing Legionnaires' disease in humans, a severe atypical pneumonia. The ... -
The phenotypes of ATG9, ATG16 and ATG9/16 knock-out mutants imply autophagy-dependent and -independent functions
Xiong, Qiuhong; Ünal, Can Murat; Matthias, Jan; Steinert, Michael; Eichinger, Ludwig (Royal Soc, 2015)Macroautophagy is a highly conserved intracellular bulk degradation system of all eukaryotic cells. It is governed by a large number of autophagy proteins (ATGs) and is crucial for many cellular processes. Here, we describe ... -
Pleiotropic clostridioides difficile cyclophilin PpiB controls cysteine-tolerance, toxin production, the central metabolism and multiple stress responses
Ünal, Can Murat; Karagoz, Mustafa Safa; Berges, Mareike; Priebe, Christina; de Acuna, Jose Manuel Borrero; Wissing, Josef; Steinert, Michael (Frontiers Media Sa, 2019)The Gram-positive pathogen Clostridioides difficile is the main bacterial agent of nosocomial antibiotic associated diarrhea. Bacterial peptidyl-prolyl-cis/trans-isomerases (PPlases) are well established modulators of ... -
Polyketide synthase (PKS) reduces fusion of Legionella pneumophila-containing vacuoles with lysosomes and contributes to bacterial competitiveness during infection
Shevchuk, Olga; Paegelow, Dennis; Rasch, Janine; Döhrmann, Simon; Günther, Gabriele; Hoppe, Julia; Steinert, Michael; Ünal, Can Murat; Bronietzki, Marc; Gutierrez, Maximiliano Gabriel (Elsevier Gmbh, Urban & Fischer Verlag, 2014)L. pneumophila-containing vacuoles (LCVs) exclude endocytic and lysosomal markers in human macrophages and protozoa. We screened a L. pneumophila mini-Tn10 transposon library for mutants, which fail to inhibit the fusion ... -
PrsA2 (CD630_35000) of clostridioides difficile Is an Active Parvulin-Type PPlase and a virulence modulator
Ünal, Can Murat; Berges, Mareike; Smit, Nathiana; Schiene-Fischer, Cordelia; Priebe, Christina; Strowig, Till; Steinert, Michael (Frontiers Media Sa, 2018)Clostridioides difficile is the main cause for nosocomial antibiotic associated diarrhea and has become a major burden for the health care systems of industrial countries. Its main virulence factors, the small GTPase ... -
Revisiting cu(II) bound amyloid-?40 and amyloid-?42 peptides: varying coordination chemistries
Weber, Orkide Coşkuner (Turkish Chemical Society, 2018)Metal ions and intrinsically disordered peptides amyloid-?40 and amyloid-?42 are at the center of Alzheimer´s disease pathology. Divalent copper ion binds to amyloid-?40 and amyloid-?42 peptides with varying coordination ... -
Secondary structure dependence of amyloid-beta(1-40) on simulation techniques and force field parameters
Çalışkan, Murat; Mandacı, Sunay Y.; Uversky, Vladimir N.; Weber, Orkide Coşkuner (Wiley, 2021)Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered alpha-synuclein that are ... -
Structures of the Wild-Type and S59L Mutant CHCHD10 ProteinsImportant in Amyotrophic Lateral Sclerosis-FrontotemporalDementia
Alıcı, Hakan; Uversky, Vladimir N.; Kang, David E.; Woo, Junga Alexa; Weber, Orkide Coşkuner (American Chemical Society, 2022)The S59L genetic mutation of the mitochondrial coiled-coil-helix-coiled-coil-helixdomain-containing protein 10 (CHCHD10) is involved in the pathogenesis of amyotrophic lateralsclerosis (ALS) and frontotemporal dementia ...