Structures prediction and replica exchange molecular dynamics simulations of ?-synuclein: A case study for intrinsically disordered proteins

Basit Öğe Kaydı
dc.contributor.authorCoşkuner Weber, Orkid
dc.date.accessioned2024-10-02T19:31:53Z
dc.date.available2024-10-02T19:31:53Z
dc.date.issued2024
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.description.abstractIn 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 disordered proteins. However, a comprehensive validation of these tools specifically for intrinsically disordered proteins has yet to be conducted. In this study, we utilize AlphaFold2, AlphaFold3, I-TASSER, C-ITASSER, Phyre2, ESMFold, and RoseTTAFold to predict the structure of a model intrinsically disordered ?-synuclein protein. Additionally, extensive replica exchange molecular dynamics simulations of the intrinsically disordered protein are conducted. The resulting structures from both structure prediction tools and replica exchange molecular dynamics simulations are analyzed for radius of gyration, secondary and tertiary structure properties, as well as C? and H? chemical shift values. A comparison of the obtained results with experimental data reveals that replica exchange molecular dynamics simulations provide results in excellent agreement with experimental observations. However, none of the structure prediction tools utilized in this study can fully capture the structural characteristics of the model intrinsically disordered protein. This study shows that a cluster of ensembles are required for intrinsically disordered proteins. Artificial-intelligence based structure prediction tools such as AlphaFold3 and C-I-TASSER could benefit from stochastic sampling or Monte Carlo simulations for generating an ensemble of structures for intrinsically disordered proteins.
dc.identifier.citationCoşkuner Weber, O. (2024). Structures prediction and replica exchange molecular dynamics simulations of ?-synuclein: A case study for intrinsically disordered proteins. International Journal of Biological Macromolecules, 276.
dc.identifier.doi10.1016/j.ijbiomac.2024.133813
dc.identifier.issn0141-8130
dc.identifier.scopus2-s2.0-85198755231
dc.identifier.urihttps://hdl.handle.net/20.500.12846/1377
dc.identifier.volume276en_US
dc.identifier.wosWOS:001275371300001
dc.indekslendigikaynakWeb of Science
dc.language.isoen
dc.relation.ispartofInternational Journal of Biological Macromolecules
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectAlphaFold3en_US
dc.subjectAlphaFold2en_US
dc.subjectC-I-TASSER I-TASSERen_US
dc.subjectPhyre2en_US
dc.subjectESMFolden_US
dc.subjectRoseTTAFolden_US
dc.subjectREMD simulationsen_US
dc.subjectIntrinsically disordered proteinsen_US
dc.titleStructures prediction and replica exchange molecular dynamics simulations of ?-synuclein: A case study for intrinsically disordered proteins
dc.typeArticle

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
Küçük Resim
İsim:
1-s2.0-S014181302404618X-main.pdf
Boyut:
9.51 MB
Biçim:
Adobe Portable Document Format
Açıklama:
Makale Dosyası
İndir
Lisans paketi
Listeleniyor 1 - 1 / 1
[ X ]
İsim:
license.txt
Boyut:
1.44 KB
Biçim:
Item-specific license agreed upon to submission
Açıklama:
İndir

Koleksiyon

Moleküler Biyoteknoloji
WoS İndeksli Yayınlar Koleksiyonu