Yazar "Coşkuner Weber, Orkid" için listeleme
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Chapter 33 - Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins
Alıcı, Hakan; Uversky, Vladimir N.; Coşkuner Weber, Orkid; Hasekioğlu, Orkun (Elsevier Academic Press, 2022)[Özet yok] -
Current stage and future perspectives for homology modeling, molecular dynamics simulations, machine learning with molecular dynamics, and quantum computing for intrinsically disordered proteins and proteins with intrinsically disordered regions
The structural ensembles of intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) cannot be easily characterized using conventional experimental techniques. Computational ... -
Effects of the Jokela type of spinal muscular atrophy-relatedG66V mutation on the structural ensemble characteristics ofCHCHD10
The G66V pathological variant of the coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), mitochondrial, plays a role in Jokela type spinalmuscular atrophy. The wild-type and G66V mutant-type CHCHD10 ... -
From quantum mechanics, classical mechanics, and bioinformatics to artificial intelligence studies in neurodegenerative diseases
Habiboğlu, Mehmet Gökhan; Coşkuner Weber, Orkid; Uversky, Vladimir N.; Teplow, David (Springer, 2022)The amyloid β-protein is an intrinsically disordered protein that has the potential to assemble into myriad structures, including oligomers and fibrils. These structures are neurotoxic and are thought to initiate a cascade ... -
Frontotemporal dementia-related V57E mutation impairs mitochondrial function and alters the structural properties of CHCHD10
Alıcı, Hakan; Uversky, Vladimir N.; Liu, Tian; Kang, David E.; Woo, Junga Alexa; Coşkuner Weber, Orkid (2023)The V57E pathological variant of the mitochondrial coiled-coil-helix–coiled-coil-helix domain-containing protein 10 (CHCHD10) plays a role in frontotemporal dementia. The wild-type and V57E mutant CHCHD10 proteins contain ... -
The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10
The mitochondria are responsible for producing energy within the cell, and in mitochondrial myop-athy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein calledcoiled-coil-helix-coil ... -
Insights into the structural properties of SARS-CoV-2 main protease
Akbayrak, İbrahim Yağız; Çağlayan, Şule İrem; Kurgan, Lukasz; Uversky, Vladimir N.; Coşkuner Weber, Orkid (Elsevier BV, 2022)SARS-CoV-2 is the infectious agent responsible for the coronavirus disease since 2019, which is the viral pneumonia pandemic worldwide. The structural knowledge on SARS-CoV-2 is rather limited. These limitations are ... -
Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases
Mirzanlı, Ozan; Coşkuner Weber, Orkid; Uversky, Vladimir N. (Elsevier BV., 2022)Many diferent intrinsically disordered proteins and proteins with intrinsically disordered regions are associated with neurodegenerative diseases. These types of proteins including amyloid-β, tau, α-synuclein, CHCHD2, ... -
Intrinsically disordered proteins by homology modeling and replica exchange molecular dynamics simulations: A case study of amyloid-β42
Coşkuner Weber, Orkid (2024)Homology modeling emerges as a potent tool unveiling the structural enigma of intrinsically disordered proteins (IDPs), with recent advancements such as AlphaFold2 enhancing the precision of these analyses. The process ... -
Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer’xxs and Parkinson’xxs diseases
Uversky, Vladimir N.; Coşkuner Weber, Orkid (Academic Press, 2019)"Dancing protein clouds: Intrinsically disordered proteins in the norm and pathology" represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this update ... -
Intrinsically disordered synthetic polymers in biomedical applications
Yüce-Erarslan, Elif; Kasem, Haytam; Uversky, Vladimir N.; Coşkuner Weber, Orkid; Domb, Abraham (Avi) J. (Polymers, 2023)In biology and medicine, intrinsically disordered synthetic polymers bio-mimicking intrinsically disordered proteins, which lack stable three-dimensional structures, possess high structural/conformational flexibility. They ... -
Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools
The phenomenon of Liquid-Liquid Phase Separation (LLPS) serves as a vital mechanism for the spatial organization of biomolecules, significantly influencing the elementary processes within the cellular milieu. Intrinsically ... -
Paving the way for synthetic intrinsically disordered polymers for soft robotics
Nature is full of examples of processes that, through evolution, have been perfected over the ages to effectively use matter and sustain life. Here, we present our strategies for designing intrinsically disordered smart ... -
Quantum chemistry meets deep learning for complex carbohydrate and glycopeptide species I
Carbohydrate complexes are crucial in many various biological and medicinal processes. The impacts of N-acetyl on the glycosidic linkage flexibility of methyl β-D-glucopyranose, and of the glycoamino acid β-D-glucopyrano ... -
Structural properties of rat intestinal fatty acid-binding protein with its dynamics: Insights into intrinsic disorder
Background: The rat intestinal fatty acid-binding protein (I-FABP) is expressed in the small intestine and is involved in the absorption and transport of dietary fatty acids. It is used as a marker for intestinal injury ... -
Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and\n CHARMM36m\n and\n AMBER99SB\n force field parameters
Akbayrak, İbrahim Yağız; Çağlayan, Şule İrem; Durdağı, Serdar; Kurgan, Lukasz; Uversky, Vladimir N.; Ulver, Burak; Dervişoğlu, Havvanur; Haklıdır, Mehmet; Hasekioğlu, Orkun; Coşkuner Weber, Orkid (Wiley, 2021)A novel virus, severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) worldwide appeared in 2019. Detailed scientific knowledge of the members of the Coronaviridae family, ... -
Structures prediction and replica exchange molecular dynamics simulations of α-synuclein: A case study for intrinsically disordered proteins
Coşkuner Weber, Orkid (2024)In recent years, a variety of three-dimensional structure prediction tools, including AlphaFold2, AlphaFold3, ITASSER, C-I-TASSER, Phyre2, ESMFold, and RoseTTAFold, have been employed in the investigation of intrinsically ...
