QM/MM Best Practice Workshop webinar: Modeling catalytic mechanisms in carbohydrate-active enzymes with QM/MM MD methods (2021-01-12)

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This is the seventh webinar in the BioExcel Virtual Workshop on Best Practices in QM/MM Simulation of Biomolecular Systems.

Title: Modeling catalytic mechanisms in carbohydrate-active enzymes with QM/MM MD methods

Speaker: Prof. Carme Rovira

Date:
Tuesday 12 January, 2021
Time:
15:00 CET

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Abstract

Carbohydrate-active enzymes (CAZymes) are the focus of enormous interest due to the critically important roles that complex glycans play in health and disease. Nature has devised several mechanisms to form and break glycosidic bonds in carbohydrates, via the action efficient enzymes named glycoside hydrolases (GHs) and glycosyltransferases [1,2,3].

In this webinar I will show two examples of applications of the QM/MM MD approach to the modeling of CAZymes. I will focus on two GHs that catalyze the hydrolysis of carbohydrates via unconventional sugar conformations: endo-β-1,4-mannanase [4] and β-galactocerebrosidase [5]. Tips and tricks related to QM/MM simulations of CAZymes will be discussed [6].

Presenter

Prof. Carme Rovira
University of Barcelona and Catalan Institute for Research and Advanced Studies

Carme Rovira is an ICREA Research Professor at the Department of Chemistry of the University of Barcelona (UB). She obtained her PhD degree in Chemistry from the UB in 1995, and part of her PhD research was carried out in USA (NCSU and SIU) for one year. She was Marie-Curie postdoctoral fellow at the Max-Planck-Institute für Festkörperforschung (Stuttgart, Germany, 1996-1998), working with M. Parrinello. After a postdoc at UB (1999 to 2001, with JJ Novoa), she obtained a Ramón y Cajal position (2002-2006) and started her research group at the Barcelona Science Park. Carme was appointed ICREA Research Professor in 2007 and moved to the Department of Chemistry of the UB in 2012. She has been visiting Professor at the University of York (UK, 2019).

Carme has received research awards from the Catalan Government (Distinció de la Generalitat, 2003), the Barcelona City Council (Barcelona City Prize, 2016) and the European Carbohydrate Organisation (Emil Fischer Award, 2019). She received an ERC SyG grant in 2020. She is the author of about 170 publications in peer-reviewed journals as well as book chapters, mainly in the fields of theoretical chemical physics and computational biology.

The research at Carme’s lab is focused on the simulation of molecular mechanisms underlying ligand-protein interactions and enzymatic reactions, contributing to the design of more efficient enzymes and new drugs. In the last few years,her research has focused on elucidating catalytic mechanisms in heme enzymes (peroxidases and catalases) and carbohydrate-active enzymes (glycosidases, glycosyltransferases and lytic polysaccharide monooxygenases).


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References

[1] A. Ardèvol, C. Rovira, J. Am. Chem. Soc. 2015, 137, 7528-7547
[2] G. J. Davies, A. Planas, C. Rovira, Acc. Chem. Res. 2012, 45, 308-316
[3] J. Coines, L. Raich, C. Rovira. Curr. Opin. Chem. Biol. 2019, 53, 183-191
[4] Y. Jin, M. Petricevic, A. John, L. Raich, H. Jenkins, L. Portela De Souza, F. Cuskin, H. J. Gilbert, C. Rovira, E. D. Goddard-Borger, S. J. Williams, G. J. Davies. ACS Cent. Sci. 2016, 2, 896-903
[5] A. Nin-Hill, C. Rovira. ACS Catal. 2020, 10, 12091-12097
[6] L. Raich, A. Nin-Hill, A. Ardèvol, C. Rovira. Meth. Enzymol. 2016, 577, 159-183