| ชื่อเรื่อง | : | Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
| นักวิจัย | : | Khuntawee W. , Kunaseth M. , Rungnim C. , Intagorn S. , Wolschann P. , Kungwan N. , Rungrotmongkol T. , Hannongbua S. |
| คำค้น | : | - |
| หน่วยงาน | : | มหาวิทยาลัยเชียงใหม่ |
| ผู้ร่วมงาน | : | - |
| ปีพิมพ์ | : | 2560 |
| อ้างอิง | : | 15499596 , 2-s2.0-85018565544 , 10.1021/acs.jcim.6b00595 , https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85018565544&origin=inward , http://cmuir.cmu.ac.th/jspui/handle/6653943832/40541 |
| ที่มา | : | - |
| ความเชี่ยวชาญ | : | - |
| ความสัมพันธ์ | : | - |
| ขอบเขตของเนื้อหา | : | - |
| บทคัดย่อ/คำอธิบาย | : | © 2017 American Chemical Society. Large ring cyclodextrins have become increasingly important for drug delivery applications. In this work, we have performed replica-exchange molecular dynamics simulations using both implicit and explicit water solvation models to study the conformational diversity of iota-cyclodextrin containing 14 α-1,4 glycosidic linked d-glucopyranose units (CD14). The new quantifiable calculation methods are proposed to analyze the openness, bending, and twisted conformation of CD14 in terms of circularity, biplanar angle, and one-directional conformation (ODC). CD14 in GB implicit water model (Igb5) was found mostly in an opened conformation with average circularity of 0.39 ± 0.16 and a slight bend with average biplanar angle of 145.5 ± 16.0°. In contrast, CD14 in TIP3P explicit water solvation is significantly twisted with average circularity of 0.16 ± 0.10, while 29.1% are ODCs. In addition, classification of CD14 conformations using a Gaussian mixture model (GMM) shows that 85.0% of all CD14 in implicit water at 300 K correspond to the elliptical conformation, in contrast to 82.3% in twisted form in explicit water. GMM clustering also reveals minority conformations of CD14 such as the 8-shape, boat-form, and twisted conformations. This work provides fundamental insights into CD14 conformation, influence of solvation models, and also proposes new quantifiable analysis techniques for molecular conformation studies in the future. |
| บรรณานุกรม | : |
Khuntawee W. , Kunaseth M. , Rungnim C. , Intagorn S. , Wolschann P. , Kungwan N. , Rungrotmongkol T. , Hannongbua S. . (2560). Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics.
เชียงใหม่ : มหาวิทยาลัยเชียงใหม่ . Khuntawee W. , Kunaseth M. , Rungnim C. , Intagorn S. , Wolschann P. , Kungwan N. , Rungrotmongkol T. , Hannongbua S. . 2560. "Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics".
เชียงใหม่ : มหาวิทยาลัยเชียงใหม่ . Khuntawee W. , Kunaseth M. , Rungnim C. , Intagorn S. , Wolschann P. , Kungwan N. , Rungrotmongkol T. , Hannongbua S. . "Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics."
เชียงใหม่ : มหาวิทยาลัยเชียงใหม่ , 2560. Print. Khuntawee W. , Kunaseth M. , Rungnim C. , Intagorn S. , Wolschann P. , Kungwan N. , Rungrotmongkol T. , Hannongbua S. . Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. เชียงใหม่ : มหาวิทยาลัยเชียงใหม่ ; 2560.
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