Yazar "Uversky, Vladimir N." için listeleme
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Alanine scanning effects on the biochemical and viophysical properties of intrinsically disordered proteins: a case study of the histidine to alanine mutations in amyloid-beta(42)
Weber, Orkide Coşkuner; Uversky, Vladimir N. (Amer Chemical Soc, 2019)Alanine scanning is a tool in molecular biology that is commonly used to evaluate the contribution of a specific amino acid residue to the stability and function of a protein. Additionally, this tool is also used to ... -
BMP-2 and BMP-9 binding specificities with ALK-3 in aqueous solution with dynamics
Weber, Orkide Coşkuner; Uversky, Vladimir N. (Elsevier Science Inc, 2017)Signal ligands of the transforming growth factor-beta (TGF-beta) superfamily include the bone morphogenetic proteins (BMPs). BMPs bind to type I and type II serine-threonine kinase receptors and trigger the transphosphorylation ... -
Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective
Ballı, Öykü İrem; Uversky, Vladimir N.; Durdağı, Serdar; Weber, Orkide Coşkuner (WILEY, 2021)Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and ... -
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 ... -
Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of alpha-synuclein on simulation techniques and force field parameters
Mandacı, Sunay Yağız; Çalışkan, Murat; Sarıaslan, M. Furkan; Uversky, Vladimir N.; Weber, Orkide Coşkuner (Wiley, 2020)Due to fast aggregation processes of many disordered proteins in neurodegenerative diseases, it is difficult to study their epitope regions at the monomeric and oligomeric levels. Computer simulations complement experiments ... -
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 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 ... -
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 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 ... -
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 ... -
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 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, ...
