Intrinsically disordered proteins by homology modeling and replica exchange molecular dynamics simulations: A case study of amyloid-?42

Basit Öğe Kaydı
dc.authorid0000-0002-0772-9350
dc.contributor.authorCoşkuner Weber, Orkid
dc.date.accessioned2024-10-02T19:44:22Z
dc.date.available2024-10-02T19:44:22Z
dc.date.issued2024
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.description.abstractHomology modeling emerges as a potent tool unveiling the structural enigma of intrinsically disordered proteins (IDPs), with recent advancements such as AlphaFold2 enhancing the precision of these analyses. The process usually involves identifying homologous proteins with known structures and utilizing their templates to predict the three-dimensional architecture of the target IDP. However, IDPs lack a welldefined three-dimensional structure, and their flexibility makes it difficult to predict their conformations accurately. On the other hand, special sampling molecular dynamics simulations have been shown to be useful in defining the distinct structural properties of IDPs. Here, the structural properties of the disordered amyloid-?42 peptide were predicted using various homology modeling tools, including C-I-TASSER, ITASSER, Phyre2, SwissModel, and AlphaFold2. In parallel, extensive replica exchange molecular dynamics simulations of A?42 were conducted. Results from homology modeling were compared to our replica exchange molecular dynamics simulations and experiments to gain insights into the accuracy of homology modeling tools for IDPs used in this work. Based on our findings, none of the homology modeling tools used in this work can fully capture the structural properties of A?42. However, C-I-TASSER yields a radius of gyration and tertiary structure properties that are more in accord with the simulations and experimental data rather than I-TASSER, Phyre2, SwissModel, and AlphaFold2.
dc.identifier.citationCoskuner Weber O. (2024). Intrinsically disordered proteins by homology modeling and replica exchange molecular dynamics simulations: A case study of amyloid-?42. Journal of the Turkish Chemical Society.11(3):1151-1164.
dc.identifier.doi10.18596/jotcsa.1457169
dc.identifier.endpage1164en_US
dc.identifier.issue3en_US
dc.identifier.scopus2-s2.0-85203160285
dc.identifier.startpage1151en_US
dc.identifier.trdizinid1260834
dc.identifier.urihttps://hdl.handle.net/20.500.12846/1379
dc.identifier.volume11en_US
dc.indekslendigikaynakTR-Dizin
dc.language.isoen
dc.relation.ispartofJournal of the Turkish Chemical Society
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectIntrinsically disordered proteinsen_US
dc.subjectAmyloid-β42en_US
dc.subjectHomology modelingen_US
dc.subjectReplica exchange molecular dynamics simulationsen_US
dc.titleIntrinsically disordered proteins by homology modeling and replica exchange molecular dynamics simulations: A case study of amyloid-?42
dc.typeArticle

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
Küçük Resim
İsim:
10.18596-jotcsa.1457169-3814232.pdf
Boyut:
796.67 KB
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
TR-Dizin İndeksli Yayınlar Koleksiyonu