GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins

Carbohydrate Research
C L FernandesH Verli

Abstract

In previous work [Pol-Fachin, L.; Fernandes, C. L.; Verli, H.; Carbohydr. Res.2009, 344, 491-500], we had demonstrated that GROMOS96 43a1 force field and Löwdin HF/6-31G * *-derived atomic charges, adequately represent a glycoprotein's conformational ensemble in aqueous solutions, taking as the starting geometries NMR-determined structures. Based on such data, the present work intends to evaluate the use of the main solution conformations of isolated disaccharides, to build the carbohydrate moiety of glycoproteins, for which no previous experimental information is available. The observed results suggested that the entire glycoprotein scaffold appears unable to promote major modifications in the conformational behavior of glycosidic linkages. Additionally, when compared to energy contour plots, the results support the use of solution ensembles, to refine vacuum conformations of carbohydrate databases in the assembling of glycoproteins 3D structures. Finally, such approach is applied to build a full glycosylated model for COX-1 and COX-2 enzymes.

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Citations

Apr 13, 2013·Carbohydrate Research·Carla G Chiodi, Hugo Verli
Oct 18, 2012·Chemical Reviews·Hashem A TahaTodd L Lowary
Nov 20, 2012·The Journal of Biological Chemistry·Paula V FernándezMarina Ciancia
Jun 18, 2011·Science·Silvia M VelasquezJose M Estevez
Mar 26, 2014·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Conrado PedebosHugo Verli
Jul 1, 2012·Wiley Interdisciplinary Reviews. Computational Molecular Science·B Lachele FoleyRobert J Woods
Mar 30, 2016·Glycoconjugate Journal·Laercio Pol-FachinMaria Luiza Saraiva-Pereira
Apr 16, 2013·Journal of Biomolecular Structure & Dynamics·Madza Yasodara Farias VirgensMaria Luiza Saraiva-Pereira
Jul 3, 2013·Journal of Biomolecular Structure & Dynamics·Cláudia L FernandesHugo Verli
Jan 14, 2018·Journal of Computational Chemistry·Chuancai SunHenry F Schaefer
Jun 6, 2020·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Liang-Yin KeChu-Huang Chen
Oct 3, 2018·Journal of Molecular Modeling·Ranga Srinath JayakodyShehani Perera
Jul 14, 2019·Journal of Computer-aided Molecular Design·Wen-Shan LiuRun-Ling Wang
Oct 22, 2020·International Journal of Molecular Sciences·Sofya I Scherbinina, Philip V Toukach
Oct 9, 2020·The Biochemical Journal·Balasubramani GlAbhinav Grover
Jan 22, 2020·Journal of Chemical Information and Modeling·João L de MeirellesHugo Verli
Aug 18, 2020·Journal of Molecular Graphics & Modelling·Rajalakshmi KumarAdithan Chandrasekaran
Aug 18, 2017·Journal of Chemical Information and Modeling·Aysegül Turupcu, Chris Oostenbrink

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