Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations

Wasinee Khuntawee; Thanyada Rungrotmongkol; Peter Wolschann; Piamsook Pongsawasdi; Nawee Kungwan; Hisashi Okumura; Supot Hannongbua

doi:10.1016/j.carbpol.2015.10.018

Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations

Carbohydr Polym. 2016 May 5:141:99-105. doi: 10.1016/j.carbpol.2015.10.018. Epub 2015 Oct 13.

Authors

Wasinee Khuntawee¹, Thanyada Rungrotmongkol², Peter Wolschann³, Piamsook Pongsawasdi⁴, Nawee Kungwan⁵, Hisashi Okumura⁶, Supot Hannongbua⁷

Affiliations

¹ Nanoscience and Technology Program, Graduate School, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand. Electronic address: w.khutawee@gmail.com.
² Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand. Electronic address: t.rungrotmongkol@gmail.com.
³ Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna 1090, Austria; Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria. Electronic address: karl.peter.wolschann@univie.ac.at.
⁴ Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand. Electronic address: piamsook.p@chula.ac.th.
⁵ Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai 50200, Thailand. Electronic address: naweekung@gmail.com.
⁶ Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan. Electronic address: hokumura@ims.ac.jp.
⁷ Computational Chemistry Unit Cell, Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand. Electronic address: supot.h@chula.ac.th.

PMID: 26877001
DOI: 10.1016/j.carbpol.2015.10.018

Abstract

There is growing interest in large-ring cyclodextrins (LR-CDs) which are known to be good host molecules for larger ligands. The isolation of a defined size LR-CD is an essential prerequisite for studying their structural properties. Unfortunately the purification procedure of these substances turned out to be very laborious. Finally the problem could be circumvented by a theoretical consideration: the highly advantageous replica exchange molecular dynamics (REMD) simulation (particularly suitable for studies of conformational changes) offers an ideal approach for studying the conformational change of ɛ-cyclodextrin (CD10), a smaller representative of LR-CDs. Three carbohydrate force fields and three solvent models were tested. The conformational behavior of CD10 was analyzed in terms of the flip (turn) of the glucose subunits within the macrocyclic ring. In addition a ranking of conformations with various numbers of turns was preformed. Our findings might be also helpful in the temperature controlled synthesis of LR-CDs as well as other experimental conditions, in particular for the host-guest reaction.

Keywords: Conformational changes; Large-ring cyclodextrin; Replica exchange molecular dynamics; ɛ-Cyclodextrin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cyclodextrins / chemistry*
Glucose / chemistry
Molecular Dynamics Simulation*

Substances

Cyclodextrins
Glucose