Structural networks and functional properties in enzymes

• Grant number: 14/19439-5
• Support Opportunities: Regular Research Grants
• Start date: November 01, 2014
• End date: October 31, 2016
• Field of knowledge: Biological Sciences - Biochemistry - Enzymology
• Principal Investigator: Sandro Roberto Marana
• Grantee: Sandro Roberto Marana
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

The functional properties of enzymes may be traced to groups of aminoacid residues forming chains based on covalent and non-covalent contacts. Based on that, this project aims to map these "chains of residues" on protein structures and characterize their role on the determination of functional properties as catalytic activity, substrate specificity and thermal stability. Beta-glucosidases from family GH1 and the lisozyme MdL1 from family GH23 will be used as experimental models in this project. The mapping of the "chains of residues" potentially related to functional properties will rely on the representation of the protein structures as networks (graphs). Additionally, the evaluation of the functional properties will be based on quantitative parameters as kinetic constants for the hydrolysis of different substrates (kcat and Km), rate constants for thermal denaturation, transition temperature for protein desnaturation (Tm) and dynamics evaluated in NMR experiments. (AU)

Scientific publications

(9)

(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)

SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; ARANTES, GUILHERME M.; MARANA, SANDRO R.. Protein thermal denaturation is modulated by central residues in the protein structure network. FEBS Journal, v. 283, n. 6, p. 1124-1138, MAR 2016. (14/21900-2, 08/55914-9, 14/19439-5)

SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; ARANTES, GUILHERME M.; MARANA, SANDRO R.. Mutations close to a hub residue affect the distant active site of a GH1 beta-glucosidase. PLoS One, v. 13, n. 6, JUN 6 2018. (14/19439-5, 16/22365-9)

FLORINDO, RENATA N.; SOUZA, VALQUIRIA P.; MANZINE, LIVIA R.; CAMILO, CESAR M.; MARANA, SANDRO R.; POLIKARPOV, IGOR; NASCIMENTO, ALESSANDRO S.. Structural and biochemical characterization of a GH3 beta-glucosidase from the probiotic bacteria Bifidobacterium adolescentis. Biochimie, v. 148, p. 107-115, MAY 2018. (14/19439-5, 08/56255-9, 14/06565-2)

SAYEGH, RAPHAEL S. R.; TAMAKI, FABIO K.; MARANA, SANDRO R.; SALINAS, ROBERTO K.; ARANTES, GUILHERME M.. Conformational flexibility of the complete catalytic domain of Cdc25B phosphatases. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 84, n. 11, p. 1567-1575, NOV 2016. (14/19439-5, 08/55914-9, 13/17883-2, 14/21900-2, 12/00543-1)

SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; ARANTES, GUILHERME M.; MARANA, SANDRO R.. Protein thermal denaturation is modulated by central residues in the protein structure network. FEBS Journal, v. 283, n. 6, p. 15-pg., 2016-03-01. (08/55914-9, 14/21900-2, 14/19439-5)

FLORINDO, RENATA N.; SOUZA, VALQUIRIA P.; MUTTI, HEMILY S.; CAMILO, CESAR; MANZINE, LIVIA REGINA; MARANA, SANDRO R.; POLIKARPOV, IGOR; NASCIMENTO, ALESSANDRO S.. Structural insights into beta-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum. NEW BIOTECHNOLOGY, v. 40, n. B, p. 218-227, JAN 25 2017. (14/19439-5, 08/56255-9, 14/06565-2)

ALMEIDA, VITOR M.; FRUTUOSO, MAIRA A.; MARANA, SANDRO R.. Search for independent (beta/alpha)(4) subdomains in a (beta/alpha)(8) barrel beta-glucosidase. PLoS One, v. 13, n. 1, JAN 16 2018. (14/19439-5, 16/22365-9)

TAMAKI, FABIO K.; SOUZA, DIORGE P.; SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; FARAH, CHUCK S.; MARANA, SANDRO R.. Using the Amino Acid Network to Modulate the Hydrolytic Activity of beta-Glycosidases. PLoS One, v. 11, n. 12, DEC 9 2016. (08/55914-9, 14/19439-5)

FLORINDO, RENATA N.; SOUZA, VALQUIRIA P.; MUTTI, HEMILY S.; CAMILO, CESAR; MANZINE, LIVIA REGINA; MARANA, SANDRO R.; POLIKARPOV, IGOR; NASCIMENTO, ALESSANDRO S.. Structural insights into beta-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum. NEW BIOTECHNOLOGY, v. 40, p. 10-pg., 2018-01-25. (14/19439-5, 08/56255-9, 14/06565-2)