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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 ...
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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 ...
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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 ...
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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 ...

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 ...

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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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Weber, Orkide Coşkuner (13)
Uversky, Vladimir N. (9)Strodel, Birgit (2)Çalışkan, Murat (2)Akbayrak, İbrahim Yağız (1)Alıcı, Hakan (1)Ballı, Öykü İrem (1)Durdağı, Serdar (1)Fatafta, Hebah (1)Kang, David E. (1)... View MoreSubjectAlzheimer's Disease (2)Amyloid-? (2)Copper (2)Epitope Region (2)Molecular Dynamics Simulations (2)?-synuclein (1)Ab Initio Molecular Dynamics Simulations (1)Activin Receptor-Like Kinases (1)Alpha-Synuclein (1)Alzheimer´s disease (1)... View MoreDate Issued2019 (3)2021 (3)2017 (2)2018 (2)2020 (2)2022 (1)Has File(s)Yes (8)No (5)

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