Multiscale molecular dynamics of glycoside hydrolases and lignocellulosic substrates

• Grant number: 13/15582-5
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): September 01, 2013
• Effective date (End): December 06, 2017
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal researcher: Munir Salomao Skaf
• Grantee: Érica Teixeira Prates
• Home Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID
• Associated scholarship(s): 16/04775-5 - Multiscale simulations of enzymes and enzymatic complexes to lignocellulosic biomass degradation, BE.EP.PD

Abstract

The lignocellulosic biomass from sugar cane bagasse and from other raw materials is a highly promising material for the generation of renewable and environmentally positive fuels. In terms of performance and environmental advantages, the best option for converting this biomass into soluble sugars to produce ethanol is the enzymatic catalysis. However, this is also the most expensive step of the second-generation ethanol production due to the low efficiency and high cost of the currently available enzyme cocktails. In order to make the process more efficient and economically viable, it is necessary to deepen the understanding of the cellulolytic hydrolysis mechanisms. Great investment in research has been employed for this purpose, and as part of these efforts, this work consists on the application of modern molecular dynamics tools in the study of the activity of glycoside hydrolases from GH5 family in a cellulosic matrix. We will use atomistic and coarse-grained models of enzyme-cellulose complexes in order to comprehend better the role of structural elements typically found on cellulases. The coarse-grained model, particularly, will allow global modifications to be done, such as the removal of a cellulose binding module or the shortening of a polypeptide linker, in order to perform the subsequent analysis of their effects on the anchoring of the enzyme on the polymeric matrix. Motivated in part by the Thematic Project Fapesp/BIOEN (Proc. 2008/56255-9), that our group participates in, and by the recently approved Research Center CEPID (Proc. 2013/08293-7), under the direction of Prof. Munir Skaf, we propose the computational study of these enzymes in close collaboration with biophysicist and molecular biologist groups that also participate on the Thematic Project. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

LIBERATO, MARCELO V.; SILVEIRA, RODRIGO L.; PRATES, ERICA T.; DE ARAUJO, EVANDRO A.; PELLEGRINI, VANESSA O. A.; CAMILO, CESAR M.; KADOWAKI, MARCO A.; NETO, MARIO DE O.; POPOV, ALEXANDER; SKAF, MUNIR S.; et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. SCIENTIFIC REPORTS, v. 6, APR 1 2016. (10/18773-8, 13/08293-7, 13/15582-5, 09/52840-7, 14/10448-1, 08/56255-9)

LIBERATO, MARCELO VIZONA; PRATES, ERICA TEIXEIRA; GONCALVES, THIAGO AUGUSTO; BERNARDES, AMANDA; VILELA, NATHALIA; FATTORI, JULIANA; EMATSU, GABRIELA CRISTINA; CHINAGLIA, MARIANA; MACHI GOMES, EMERSON RODRIGO; MIGLIORINI FIGUEIRA, ANA CAROLINA; et al. Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds. Journal of Biological Chemistry, v. 296, JAN-JUN 2021. (17/08166-6, 14/04105-4, 15/50612-8, 17/16089-1, 17/22669-0, 13/15582-5, 13/08293-7)