Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics
© 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...
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th-cmuir.6653943832-569212018-09-05T03:54:38Z Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics Wasinee Khuntawee Manaschai Kunaseth Chompoonut Rungnim Suradej Intagorn Peter Wolschann Nawee Kungwan Thanyada Rungrotmongkol Supot Hannongbua Chemical Engineering Chemistry Computer Science Social Sciences © 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. 2018-09-05T03:31:57Z 2018-09-05T03:31:57Z 2017-04-24 Journal 15205142 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/6653943832/56921 |
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Chemical Engineering Chemistry Computer Science Social Sciences Wasinee Khuntawee Manaschai Kunaseth Chompoonut Rungnim Suradej Intagorn Peter Wolschann Nawee Kungwan Thanyada Rungrotmongkol Supot Hannongbua Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
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© 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. |
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Journal |
author |
Wasinee Khuntawee Manaschai Kunaseth Chompoonut Rungnim Suradej Intagorn Peter Wolschann Nawee Kungwan Thanyada Rungrotmongkol Supot Hannongbua |
author_facet |
Wasinee Khuntawee Manaschai Kunaseth Chompoonut Rungnim Suradej Intagorn Peter Wolschann Nawee Kungwan Thanyada Rungrotmongkol Supot Hannongbua |
author_sort |
Wasinee Khuntawee |
title |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
title_short |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
title_full |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
title_fullStr |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
title_full_unstemmed |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics |
title_sort |
comparison of implicit and explicit solvation models for iota-cyclodextrin conformation analysis from replica exchange molecular dynamics |
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2018 |
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https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85018565544&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/56921 |
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1681424782420082688 |