Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins

Basit Öğe Kaydı
dc.authorid0000-0002-0772-9350
dc.contributor.authorCoşkuner Weber, Orkid
dc.contributor.authorÇaglayan, Şule İrem
dc.date.accessioned2024-12-27T17:07:06Z
dc.date.available2024-12-27T17:07:06Z
dc.date.issued2021
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.description.abstractComputer simulations are used for identifying the secondary structure properties of ordered and disordered proteins. However, our recent studies showed that the chosen computer simulation protocol, simulation technique, and force feld parameter set for a disordered protein impact its predicted secondary structure properties. Here, we compare the outcome from computer simulations utilizing molecular dynamics simulations without parallel tempering techniques using various force feld parameter sets and temperature-replica exchange molecular dynamics simulations both for a model ordered and two model disordered proteins. Specifcally, the model ordered protein is the third IgG-binding domain of Protein G (GB3) and the two model disordered proteins are amyloid-?(1–40) and ?-synuclein in water. Our fndings clearly indicate that temperaturereplica exchange molecular dynamics simulations and molecular dynamics simulations without special sampling techniques yield similar results for the ordered GB3 protein whereas such agreement between simulation techniques using various force feld parameter sets could not be obtained for disordered proteins. These fndings clearly indicate that a consensus has to be reached via further development in computer simulation technique and force feld parameter sets for disordered proteins.
dc.identifier.citationCoşkuner Weber, O., Çaglayan, Şule İ. (2021). Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins. Biophysical Reviews, 13 (6), 1173-1178.
dc.identifier.doi10.1007/s12551-021-00850-5
dc.identifier.endpage1178en_US
dc.identifier.issue6en_US
dc.identifier.scopus2-s2.0-85117029220
dc.identifier.startpage1173en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12846/1505
dc.identifier.volume13en_US
dc.identifier.wosWOS:001074281400053
dc.indekslendigikaynakScopus
dc.language.isoen
dc.relation.ispartofBiophysical Reviews
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectDisordered proteinsen_US
dc.subjectOrdered proteinsen_US
dc.subjectForce feld parametersen_US
dc.subjectSimulation techniquesen_US
dc.subjectSimulation protocolsen_US
dc.titleSecondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins
dc.typeArticle

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
Küçük Resim
İsim:
s12551-021-00850-5.pdf
Boyut:
976.2 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
Scopus İndeksli Yayınlar Koleksiyonu