Yazar "Weber, Orkide Coşkuner" 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 ... -
Current challenges and limitations in the studies of intrinsically disordered proteins in neurodegenerative diseases by computer simulations
Akbayrak, İbrahim Yağız; Çağlayan, Şule İrem; Özcan, Zilan; Uversky, Vladimir; Weber, Orkide Coşkuner (Bentham Science Publishers, 2020)Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely ... -
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 ... -
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 ... -
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 ... -
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 ... -
Transition metal Ion interactions with disordered Amyloid-beta Peptides in the pathogenesis of Alzheimer's disease: insights from computational chemistry studies
Strodel, Birgit; Weber, Orkide Coşkuner (Amer Chemical Soc, 2019)Monomers and oligomers of the amyloid-beta peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition ... -
Tyrosine regulates beta-sheet structure formation in amyloid-beta(42): a new clustering algorithm for disordered proteins
Weber, Orkide Coşkuner; Uversky, Vladimir N. (Amer Chemical Soc, 2017)Our recent studies show that the single Tyr residue in the sequence of amyloid-beta(42) (A beta(42)) is reactive toward various ligands, including metals and adenosine trisphospate (see: Coskuner, O. J. Biol. Inorg. Chem. ...
