Two important classes of glycosyl hydrolases: functional studies and structural analysis

• Grant number: 11/20505-4
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: March 01, 2012
• End date: August 31, 2015
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Igor Polikarpov
• Grantee: Marco Antonio Seiki Kadowaki
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , 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
• Associated scholarship(s): 14/15887-3 - Construction and optimization of a fungal secretion system suitable for high-yield biomass hydrolytic and oxidation enzyme production for structural and functional studies, BE.EP.PD

Abstract

The ethanol production from vegetal biomass degradation is an alternative to fossil fuels and a good way to reach the energy independence. This cellulose rich material is a renewable and unexhausted source whose degradation products (sugars) can be useful in ethanol production (second generation ethanol) generated by fermentative processes. However the recalcitrance of crystalline cellulose to enzyme treatment is an obstacle to popularize this product and the major biotechnological challenge in 21st century. Therefore the development of new catalysts or enzymes to enhance the ethanol production from vegetal sources becomes the main scientific challenge in this field. This process is based on identification, characterization and enzyme improvement not just individually but also to compose enzymatic cocktail. These enzymes are called cellulases and hydrolyse specifically²-1-4 glycosidic bonds in the middle of the cellulose chains (endoglucanases) or from cellulose chain ends (exoglucanases). The protein engineering methodology is a rational way to improve enzyme activity to reach a complete biomass degradation of insoluble raw material. In this scientific project we intend to study endoglucanases from GHF45 family and enzymes from GHF61 family, recently described as cellulose enhancer factors. Structural information will provide knowledge about enzymatic mechanism and basis for enzyme activity improvement. (AU)

Scientific publications

(19)

(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)

GODOY, ANDRE S.; DE LIMA, MARIANA Z. T.; CAMILO, CESAR M.; POLIKARPOV, IGOR. Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 72, n. 4, p. 288-293, APR 2016. (09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9, 11/05712-3)

NAKAMURA, ALINE M.; SEIKI KADOWAKI, MARCO ANTONIO; GODOY, ANDRE; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Low-resolution envelope, biophysical analysis and biochemical characterization of a short-chain specific and halotolerant carboxylesterase from Bacillus licheniformis. International Journal of Biological Macromolecules, v. 120, n. B, p. 1893-1905, DEC 2018. (11/20505-4)

EVANGELISTA, DANILO ELTON; DE ARAUJO, EVANDRO A.; OLIVEIRA NETO, MARIO; SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS structure of an exopolygalacturonase from Bacillus licheniformis. NEW BIOTECHNOLOGY, v. 40, n. B, p. 268-274, JAN 25 2017. (11/20505-4, 15/13684-0)

EVANGELISTA, DANILO ELTON; SEIKI KADOWAKI, MARCO ANTONIO; MELLO, BRUNO LUAN; POLIKARPOV, IGOR. Biochemical and biophysical characterization of novel GH10 xylanase prospected from a sugar cane bagasse compost-derived microbial consortia. International Journal of Biological Macromolecules, v. 109, p. 560-568, APR 2018. (11/20505-4, 11/21608-1, 10/52362-5, 15/13684-0)

SEIKI KADOWAKI, MARCO ANTONIO; RABELO HIGASI, PAULA MIWA; DE GODOY, MARIANA ORTIZ; DE ARAUJO, EVANDRO ARES; GODOY, ANDRE SCHUTZER; PRADE, ROLF ALEXANDER; POLIKARPOV, IGOR. Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, v. 1864, n. 10, OCT 2020. (15/13684-0, 11/20505-4)

NAKAMURA, ALINE M.; SEIKI KADOWAKI, MARCO ANTONIO; GODOY, ANDRE; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Low-resolution envelope, biophysical analysis and biochemical characterization of a short-chain specific and halotolerant carboxylesterase from Bacillus licheniformis. International Journal of Biological Macromolecules, v. 120, p. 13-pg., 2018-12-01. (11/20505-4)

GODOY, ANDRE S.; DE LIMA, MARIANA Z. T.; CAMILO, CESAR M.; POLIKARPOV, IGOR. Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 72, p. 6-pg., 2016-04-01. (11/05712-3, 09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9)

GODOY, ANDRE SCHUTZER; CAMILO, CESAR MOISES; KADOWAKI, MARCO ANTONIO; MUNIZ, HELOISA DOS S.; SANTO, MELISSA ESPIRITO; MURAKAMI, MARIO TYAGO; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Crystal structure of beta 1 -> 6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by alpha-galactose. FEBS Journal, v. 283, n. 22, p. 4097-4112, NOV 2016. (09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9, 14/06565-2, 11/05712-3)

EVANGELISTA, DANILO ELTON; ARNOLDI PELLEGRIN, VANESSA DE OLIVEIRA; SANTO, MELISSA ESPIRITO; MCQUEEN-MASON, SIMON; BRUCE, NEIL C.; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-beta-xylanase identified in a microbial consortium. Applied Microbiology and Biotechnology, v. 103, n. 19, p. 8035-8049, OCT 2019. (15/13684-0, 11/21608-1, 10/52362-5, 11/20505-4)

CALIFANO, DAVIDE; KADOWAKI, MARCO A. S.; CALABRESE, VINCENZO; PRADE, ROLF ALEXANDER; MATTIA, DAVIDE; EDLER, KAREN J.; POLIKARPOV, IGOR; SCOTT, JANET L.. Multienzyme Cellulose Films as Sustainable and Self-Degradable Hydrogen Peroxide-Producing Material. Biomacromolecules, v. 21, n. 12, p. 5315-5322, DEC 2020. (11/20505-4)

DE ARAUJO, EVANDRO ARES; MANZINE, LIVIA REGINA; PIIADOV, VASSILI; SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Biochemical characterization, low-resolution SAXS structure and an enzymatic cleavage pattern of BlCel48 from Bacillus licheniformis. International Journal of Biological Macromolecules, v. 111, p. 302-310, MAY 2018. (14/00769-5, 11/20505-4, 10/52362-5, 15/13684-0)

KADOWAKI, MARCO A. S.; VARNAI, ANIKO; JAMESON, JOHN-KRISTIAN; LEITE, ANA E. T.; COSTA-FILHO, ANTONIO J.; KUMAGAI, PATRICIA S.; PRADE, ROLF A.; POLIKARPOV, IGOR; EIJSINK, VINCENT G. H.. Functional characterization of a lytic polysaccharide monooxygenase from the thermophilic fungus Myceliophthora thermophila. PLoS One, v. 13, n. 8, AUG 20 2018. (11/20505-4, 15/13684-0)

PUHL, ANA C.; PRATES, ERICA T.; ROSSETO, FLAVIO R.; MANZINE, LIVIA R.; STANKOVIC, IVANA; DE ARAUJO, SIMARA S.; ALVAREZ, THABATA M.; SQUINA, FABIO M.; SKAF, MUNIR S.; POLIKARPOV, IGOR. Crystallographic structure and molecular dynamics simulations of the major endoglucanase from Xanthomonas campestris pv. campestris shed light on its oligosaccharide products release pattern. International Journal of Biological Macromolecules, v. 136, p. 493-502, SEP 1 2019. (11/20505-4, 15/13684-0, 09/52840-7, 10/52362-5, 11/21608-1, 15/50590-4)

SEIKI KADOWAKI, MARCO ANTONIO; DE GODOY, MARIANA ORTIZ; KUMAGAI, PATRICIA SUEMY; DA COSTA-FILHO, ANTONIO JOSE; MORT, ANDREW; PRADE, ROLF ALEXANDER; POLIKARPOV, IGOR. Characterization of a New Glyoxal Oxidase from the Thermophilic Fungus Myceliophthora thermophila M77: Hydrogen Peroxide Production Retained in 5-Hydroxymethylfurfural Oxidation. CATALYSTS, v. 8, n. 10, OCT 2018. (15/13684-0, 11/20505-4)

KADOWAKI, MARCO A. S.; HIGASI, PAULA; DE GODOY, MARIANA O.; PRADE, ROLF A.; POLIKARPOV, IGOR. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS Journal, v. 285, n. 3, p. 559-579, FEB 2018. (09/52840-7, 15/13684-0, 11/20505-4)

GODOY, ANDRE S.; PEREIRA, CAROLINE S.; RAMIA, MARINA PAGLIONE; SILVEIRA, RODRIGO L.; CAMILO, CESAR M.; KADOWAKI, MARCO A.; LANGE, LENE; BUSK, PETER K.; NASCIMENTO, ALESSANDRO S.; SKAF, MUNIR S.; et al. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. SCIENTIFIC REPORTS, v. 8, FEB 27 2018. (15/13684-0, 11/21608-1, 10/52362-5, 11/20505-4)

SEIKI KADOWAKI, MARCO ANTONIO; CAMILO, CESAR MOISES; MUNIZ, AMANDA BERNARDES; POLIKARPOV, IGOR. Functional Characterization and Low-Resolution Structure of an Endoglucanase Cel45A from the Filamentous Fungus Neurospora crassa OR74A: Thermostable Enzyme with High Activity Toward Lichenan and beta-Glucan. MOLECULAR BIOTECHNOLOGY, v. 57, n. 6, p. 574-588, JUN 2015. (10/08680-2, 11/20505-4, 09/11536-3, 09/54035-4, 08/56255-9)

GODOY, ANDRE SCHUTZER; CAMILO, CESAR MOISES; KADOWAKI, MARCO ANTONIO; MUNIZ, HELOISA DOS S.; SANTO, MELISSA ESPIRITO; MURAKAMI, MARIO TYAGO; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Crystal structure of beta 1 -> 6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by alpha-galactose. FEBS Journal, v. 283, n. 22, p. 16-pg., 2016-11-01. (11/05712-3, 09/52840-7, 11/20505-4, 14/06565-2, 08/56255-9, 09/05328-9)

EVANGELISTA, DANILO ELTON; DE ARAUJO, EVANDRO A.; OLIVEIRA NETO, MARIO; SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS structure of an exopolygalacturonase from Bacillus licheniformis. NEW BIOTECHNOLOGY, v. 40, p. 7-pg., 2018-01-25. (15/13684-0, 11/20505-4)