Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of alpha-synuclein on simulation techniques and force field parameters

Basit Öğe Kaydı
dc.contributor.authorMandacı, Sunay Yağız
dc.contributor.authorÇalışkan, Murat
dc.contributor.authorSarıaslan, M. Furkan
dc.contributor.authorUversky, Vladimir N.
dc.contributor.authorWeber, Orkide Coşkuner
dc.date.accessioned2021-01-08T21:51:21Z
dc.date.available2021-01-08T21:51:21Z
dc.date.issued2020
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.descriptionUversky, Vladimir N./0000-0002-4037-5857; Coskuner, Orkid/0000-0002-0772-9350;en_US
dc.descriptionWOS:000508167000001en_US
dc.descriptionPubMed: 31903719en_US
dc.description.abstractDue 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 and have been used to identify the epitope regions of proteins. Residues that adopt beta-sheet conformation play a central role in the oligomerization and aggregation mechanisms of such proteins, including alpha-synuclein, which is at the center of Parkinson's and Alzheimer's diseases. In this study, we simulated the monomeric alpha-synuclein protein in an aqueous environment to evaluate its secondary structure properties, including beta-sheet propensity, and radius of gyration by replica exchange molecular dynamics simulations. We also obtained the molecular dynamics simulation trajectories of alpha-synuclein that were conducted using various force field parameters by the David E. Shaw group. Using these trajectories, we calculated the impacts of force field parameters on alpha-synuclein secondary structure properties and radius of gyration values and obtained results are compared with our data from REMD simulations. This study shows that the chosen force field parameters and computer simulation techniques effect the predicted secondary structure properties and radius of gyration values of alpha-synuclein in water. Herewith, we illustrate the challenges in epitope region identification of intrinsically disordered proteins in neurodegenerative diseases by current computer simulations.
dc.identifier.doi10.1111/cbdd.13662
dc.identifier.endpage667en_US
dc.identifier.issn1747-0277
dc.identifier.issn1747-0285
dc.identifier.issue1en_US
dc.identifier.scopus2-s2.0-85078655322
dc.identifier.scopusqualityQ2
dc.identifier.startpage659en_US
dc.identifier.urihttp://doi.org/10.1111/cbdd.13662
dc.identifier.urihttps://hdl.handle.net/20.500.12846/163
dc.identifier.volume96en_US
dc.identifier.wosWOS:000508167000001
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorMandacı, Sunay Yağız
dc.institutionauthorÇalışkan, Murat
dc.institutionauthorSarıaslan, M. Furkan
dc.institutionauthorWeber, Orkide Coşkuner
dc.language.isoen
dc.publisherWiley
dc.relation.ispartofChemical Biology & Drug Design
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectComputer Simulationsen_US
dc.subjectEpitope Regionen_US
dc.subjectForce Field Parametersen_US
dc.subjectSimulation Techniquesen_US
dc.subjectAlpha-Synucleinen_US
dc.titleEpitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of alpha-synuclein on simulation techniques and force field parameters
dc.typeArticle

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
[ X ]
İsim:
00163.pdf
Boyut:
1.18 MB
Biçim:
Adobe Portable Document Format
Açıklama:
Tam Metin / Full Text
İndir

Koleksiyon

WoS İndeksli Yayınlar Koleksiyonu
Moleküler Biyoteknoloji
PubMed İndeksli Yayın Koleksiyonu
Scopus İndeksli Yayınlar Koleksiyonu

We collect and process your personal information for the following purposes: Authentication, Preferences, Acknowledgement and Statistics.
To learn more, please read our privacy policy.

Customize