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Multiscale simulations of enzymes and enzymatic complexes to lignocellulosic biomass degradation

Grant number: 16/04775-5
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): May 01, 2016
Effective date (End): April 30, 2017
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
Principal Investigator:Munir Salomao Skaf
Grantee:Érica Teixeira Prates
Supervisor: Gregg Beckham
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Research place: National Renewable Energy Laboratory (NREL), United States  
Associated to the scholarship:13/15582-5 - Multiscale molecular dynamics of glycoside hydrolases and lignocellulosic substrates, BP.PD


Enzymatic catalysis is considered the best strategy to saccharification of biomass to ethanol production in an environmentally friendly way. As so, great efforts are being invested in the optimization of the biocatalytical processes. Computational methods represents a valuable tool to make progress in this area. In this project, we propose making use of multiscale simulations to explore two topics of major importance on the field, that are: i) Biodegradation of lignin. The complex matrix of lignin entangling the cellulose microfibrils and hemicellulose chains represents a critical barrier in the lignocellulosic digestion. The enzymatic degradation arises as a promising alternative to thermo-chemical pretreatment that enables to selectively generate valuable coproducts from lignin. In this part of the project, we propose to apply molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations to study the structural basis of substrate affinity and the mechanisms of reaction in bacterial enzymatic degradation of lignin. ii) Cellulosomes as an alternative to enzymatic cocktails. Some evidences suggest that the proximity of catalytic modules of the multiple enzymes forming the cellulosomes favors their synergistic action, conferring superior performance to these enzymatic complexes compared to mixtures of individual enzymes. Despite the considerable body of experimental studies, a mechanistic understanding of cellulosome action remains elusive. In this project, we propose to use muliscale computational approaches to study the inter-modular motions of the cellulosome from C. thermocellum that are important to cooperative catalytic action. This project was prepared to be accomplished during a one year internship in the National Renewable Energy Laboratory (NREL, Colorado, U.S.A), under the supervision of Prof. Dr. Gregg Beckham, one of the leaders of computational research at NREL. Prof. Beckham and his team form of one of the most prominent centers in the computational research of biomass. We believe this internship will be extremely valuable to the related post-doctorate project in progress in Brazil.

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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)
PRATES, ERICA T.; GUAN, XIAOYANG; LI, YAOHAO; WANG, XINFENG; CHAFFEY, PATRICK K.; SKAF, MUNIR S.; CROWLEY, MICHAEL F.; TAN, ZHONGPING; BECKHAM, GREGG T.. The impact of O-glycan chemistry on the stability of intrinsically disordered proteins. CHEMICAL SCIENCE, v. 9, n. 15, p. 3710-3715, . (16/04775-5, 13/08293-7)
PRATES, ERICA TEIXEIRA; CROWLEY, MICHAEL F.; SKAF, MUNIR S.; BECKHAM, GREGG T.. Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG. Journal of Physical Chemistry B, v. 123, n. 48, p. 10142-10151, . (13/08293-7, 16/04775-5)

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