Kinetic characteristics of conformational changes in the hexopyranose rings

Carbohydrate Research
Wojciech Plazinski, Mateusz Drach

Abstract

The shape of the hexopyranose ring is an important factor which can influence the properties of carbohydrate molecules and affect their biological activity. Due to a limited availability of the experimental data, the conformational rearrangements (puckering) which occur within the pyranose rings are studied extensively by using various computational approaches. Contrary to the basic structural and energetic features characterizing the process of ring flexing, the kinetic and dynamics properties of puckering remain less recognized. We performed the first, molecular dynamics-based, systematic calculations aimed at description of the kinetic characteristics of the conformational changes in the rings of α-d- and β-d-glucopyranose molecules. The rate constants representing particular molecular events which comprise the chair-chair inversion are determined and analyzed in the context of the available experimental data. Furthermore, several various variables (e.g. transmission coefficients) and issues (e.g. memorylessness of the puckering process) are investigated and discussed. As several different parameter sets were used during the study (GROMOS 56A6CARBO, GLYCAM, GROMOS 53A6GLYC), the results provide the conclusion on the capabili...Continue Reading

References

Jan 1, 1986·Annals of the New York Academy of Sciences·H J BerendsenR G Geurtsen
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Jul 23, 2004·The Journal of Chemical Physics·R Hagen, U Kaatze
Jun 10, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Ralph Behrends, Udo Kaatze
Apr 4, 2006·Biophysical Journal·Cristina S PereiraPhilippe H Hünenberger
Oct 13, 2006·Journal of the American Chemical Society·Giovanni BussiMichele Parrinello
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Sep 13, 2007·Journal of Computational Chemistry·Karl N KirschnerRobert J Woods
Feb 1, 2008·Physical Review Letters·Alessandro BarducciMichele Parrinello
Jun 18, 2009·The Journal of Chemical Physics·M SegaF Pederiva
Jun 24, 2010·Methods : a Companion to Methods in Enzymology·Vijay S PandeGregory R Bowman
Sep 3, 2010·Journal of the American Chemical Society·Benedict M SattelleAndrew Almond
Aug 3, 2011·Glycobiology·Benedict M Sattelle, Andrew Almond
Feb 27, 2013·Biomacromolecules·Benedict M SattelleAndrew Almond
Dec 3, 2014·Carbohydrate Research·Xiuming XiongJiye Shi
Nov 18, 2015·Journal of Chemical Theory and Computation·Jörg Sauter, Andrea Grafmüller
Feb 11, 2014·Journal of Chemical Theory and Computation·Zack Jarin, Jim Pfaendtner

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Citations

Jun 2, 2017·Physical Chemistry Chemical Physics : PCCP·Katsufumi TomobeKenji Yasuoka
Jun 23, 2020·Physical Chemistry Chemical Physics : PCCP·Wojciech PlazinskiAgnieszka Brzyska
Oct 15, 2019·Journal of Chemical Information and Modeling·Irfan Alibay, Richard A Bryce

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