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Molecular dynamics simulations of hydrolases for saccharification of cellulose and related proteins

Grant number: 09/14107-6
Support Opportunities:Scholarships in Brazil - Doctorate
Effective date (Start): November 01, 2009
Effective date (End): January 31, 2013
Field of knowledge:Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
Principal Investigator:Munir Salomao Skaf
Grantee:Érica Teixeira Prates
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated research grant:08/56255-9 - Structure and function of enzymes and auxiliary proteins from Trichoderma, active in cell-wall hydrolysis, AP.BIOEN.TEM


The lignocellulosic biomass, such as sugar cane bagass, holds a promise of renewable and environmentally positive fuel. The best option to the conversion of this biomass to soluble fermentable sugars and, then, to ethanol, is the enzymatic catalysis. Because of the low efficiency and high cost of the available enzymatic cocktails, this is also the most expensive step on the second generation ethanol production. To make this technology sustainable and cost effective, our comprehension of cellulose enzymatic hydrolysis should be significantly improved. With these concerns, our group has been applying molecular dynamics computer simulations to study cellulosic substrates and cellulases, coordinating the molecular modeling work of the Bioen Thematic Project (Proc. 08/56255-9) and of the INCT of the bioethanol, both recently approved. Here we propose to employ modern molecular dynamics techniques to conduct structural-dynamical-functional studies of proteins that are relevant to cellulosic biomass saccharification. The main focus are the Trichoderma cellulases and, eventually, auxiliary proteins, like swollenins, which plays an important role in the cristaline cellulosic degradation. We plan to explore the interactions between the enzymes and cellulosic substrates in an atomistic level and, also, to investigate the molecular mechanisms involved on the enzymatic hydrolysis of cellulose. The computational studies will be conducted in strict collaboration with the structural biophysicists and molecular biologists integrating the BioEn Thematic Project and the INCT of the bioethanol.

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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)
BLEICHER, LUCAS; PRATES, ERICA T.; GOMES, THIAGO C. F.; SILVEIRA, RODRIGO L.; NASCIMENTO, ALESSANDRO S.; ROJAS, ADRIANA L.; GOLUBEV, ALEXANDER; MARTINEZ, LEANDRO; SKAF, MUNIR S.; POLIKARPOV, IGOR. Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations. Journal of Physical Chemistry B, v. 115, n. 24, p. 7940-7949, . (10/08680-2, 09/14107-6, 10/18849-4, 10/16947-9)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
PRATES, Érica Teixeira. Molecular dynamics study of hydrolases for saccharification of cellulose and related proteins. 2013. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Instituto de Química Campinas, SP.

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