Study of the binding interactions of carbohydrate binding modules and carbohydrates

• Grant number: 15/14009-5
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Effective date (Start): September 08, 2015
• Effective date (End): December 07, 2015
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Ana Carolina de Mattos Zeri
• Grantee: Bruna Medéia de Campos
• Supervisor: Isaac Cann
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovações (Brasil). Campinas , SP, Brazil
• Research place: University of Illinois at Urbana-Champaign, United States
• Associated to the scholarship: 13/06336-0 - Study of the Molecular Basis of Carbohydrate Binding Modules (CBMs) from Metagenomic Screenings, BP.PD

Abstract

In recent years, due to the growing global demand for energy, the dependence on fossil fuels, limited natural resources, and environmental pollution, biofuels have attracted great interest as source of renewable energy. However, production of biofuels from plant biomass is still considered an expensive technology with low efficiency. In this context, the study of carbohydrate binding modules (CBMs) is attracting attention. CBMs are protein modules involved in guiding catalytic modules in polysaccharidases (enzymes that breakdown polysaccharides) to the substrate. The study of these protein modules is critical for future engineering of enzyme chimeras, aimed at the development of more efficient and inexpensive process for biomass conversion onto biofuels. The study of metagenomics has also been extremely important for the identification of new biocatalysts. Currently, 99% of the microorganisms found in these studies cannot be cultured in the laboratory. Thus researchers resort to large-scale DNA extraction from samples (or an environment of interest) without cultivation and apply bioinformatics to either determine or predict the functions of genes encoded within extracted environmental DNA. During this Post-doc, we have studied six different CBMs, three derived from a functional screening of sugarcane soil metagenomics, and three from a CAZy database analysis. So far the three-dimensional structure of three of these CBMs have been solved. All of them show a typical CBM fold, although none shows high similarity with any CBM structure in the PDB. CBM_E1 has not been assigned to any family of CBM already described in the CAZy database, suggesting that it belongs to a new CBM family. CBM64 apparently forms a dimer, shown in dynamic light scattering (DLS) and in NMR experiments. The three dimensional structure of CBM08 has also been solved, and its binding site is composed of tryptophan, phenylalanine and tyrosine residues, different from the other CBMs that usually have only tryptophan residues interacting with the ligand. The functional characterization of all these CBMs, with structure solved or not, is of importance to understanding which carbohydrate they bind preferably and how their interactions impact the catalytic modules linked to these families of CBMs. The aim of this BEPE project is to understand the function of the novel carbohydrate binding modules, discovered through my postdoc research, in carbohydrate degradation. A deeper understanding of the function of these CBMs will allow development of new biocatalysts with robust activities for biomass degradation and therefore aiding in the production of low-cost biofuels from lignocellulosic feedstock.

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 VIZONA; CAMPOS, BRUNA MEDEIA; TOMAZETTO, GEIZECLER; CROUCH, LUCY ISOBEL; GARCIA, WANIUS; DE MATTOS ZERI, ANA CAROLINA; BOLAM, DAVID NICHOL; SQUINA, FABIO MARCIO.

Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions

. Journal of Biological Chemistry, v. 298, n. 5, p. 10-pg., 2022-05-02. (15/50590-4, 13/06336-0, 15/23279-6, 20/15595-3, 14/04105-4, 20/05784-3, 15/14009-5, 17/17275-3)