Transition path sampling QM/MM simulations of lytic transglycosylases

• Grant number: 17/01151-3
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: April 20, 2017
• End date: January 31, 2018
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Munir Salomao Skaf
• Grantee: Caroline Simões Pereira
• Supervisor: Gregg Beckham
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: National Renewable Energy Laboratory (NREL), United States
• Associated to the scholarship: 15/25031-1 - Molecular Dynamics of Carbohydrate Modifying Enzymes for Lignocellulosic Biomass Deconstruction and Valorization, BP.DR

Abstract

Lignocellulosic biomass constitutes the largest source of biopolymers on Earth and offers unmatched potential to produce biofuels, materials and valuable chemicals. These biopolymers exhibit resistance against thermal, chemical and enzymatic degradation (biomass recalcitrance) due to its molecular architecture and chemical nature of the polymeric matrices. Comprehending the mechanisms of action of biomass-active enzymes is, therefore, essential to control and possibly enhance its activity against recalcitrant biomaterials by means of enzyme engineering techniques. While the catalytic mechanisms of many of these enzymes are relatively well understood, a particular group of evolutionarily-related enzymes, including glycoside hydrolases (GH) belonging to family 45, expansins and lytic transglycosylases (LTs), which share common active sites, lacks an expected residue to act as general base and, therefore, may follow a different (yet unknown) catalytic route from other enzymes. Here, we propose to use transition path sampling QM/MM (quantum mechanics/molecular mechanics) computer simulations to study the catalytic mechanism of LTs. The results will contribute to construct a rational basis for development of novel enzymes, and help to understand the mechanism of other carbohydrate-active enzymes of the same group. The project will be carried out at the National Renewable Energy Laboratory, whose computational team has long been working on elucidating mechanisms of lignocellulose-active enzymes, and has all the expertise necessary to apply unbiased transition path sampling simulations to unveil the LTs mechanism. Our group at Unicamp has been collaborating with NREL, and the development of this project will further strengthen the efforts to understanding the mechanisms of enzymes in the ambit of the Center of Computational Engineering & Sciences (CEPID, Proc. 2013/08293-7). (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)

SILVEIRA, RODRIGO L.; KNOTT, BRANDON C.; PEREIRA, CAROLINE S.; CROWLEY, MICHAEL F.; SKAF, MUNIR S.; BECKHAM, GREGG T.. Transition Path Sampling Study of the Feruloyl Esterase Mechanism. Journal of Physical Chemistry B, v. 125, n. 8, p. 2018-2030, MAR 4 2021. (15/25031-1, 17/01151-3, 16/22956-7, 13/08293-7, 14/10448-1)