Study of two bioactive peptides in vacuum and solvent by molecular modeling

The thermodynamic and structural properties of Tyrosine-Glycine-Leusine- Phenylalanine (YGLP, in a one letter code) and Lysine-Valine-Leusine-Proline- Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of ß-turn, ?-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of ?-turns and low level of ß-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model. © World Scientific Publishing Company.

Dergi Adı International Journal of Modern Physics C
Dergi Cilt Bilgisi 17
Dergi Sayısı 6
Sayfalar 825 - 839
Yayın Yılı 2006
Eser Adı
[dc.title]
Study of two bioactive peptides in vacuum and solvent by molecular modeling
Yazar
[dc.contributor.author]
Yaşar F.
Yazar
[dc.contributor.author]
Demir K.
Yayın Yılı
[dc.date.issued]
2006
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
The thermodynamic and structural properties of Tyrosine-Glycine-Leusine- Phenylalanine (YGLP, in a one letter code) and Lysine-Valine-Leusine-Proline- Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of ß-turn, ?-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of ?-turns and low level of ß-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model. © World Scientific Publishing Company.
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Konu Başlıkları
[dc.subject]
Bioactive peptides
Konu Başlıkları
[dc.subject]
Molecular modeling
Konu Başlıkları
[dc.subject]
Multicanonical simulation
Konu Başlıkları
[dc.subject]
Solvation models
Haklar
[dc.rights]
info:eu-repo/semantics/closedAccess
ISSN
[dc.identifier.issn]
0129-1831
İlk Sayfa Sayısı
[dc.identifier.startpage]
825
Son Sayfa Sayısı
[dc.identifier.endpage]
839
Dergi Adı
[dc.relation.journal]
International Journal of Modern Physics C
Dergi Sayısı
[dc.identifier.issue]
6
Dergi Cilt Bilgisi
[dc.identifier.volume]
17
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1142/S0129183106009382
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/7677
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
15
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
23 Şubat 2024 06:20
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Tıklayınız
sequences vacuum peptide simulation solvent three-dimensional probabilities structural advantage occurrence relative predict distance analysed prepared ß-turn protein Ramachandran function technique temperature ?-turn Company Publishing Scientific higher observed helical ß-turns ?-turns presence cumulant indicate predictions Although
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