DEVELOPMENT OF NANOBISENSORS USING ADVANCED COMPUTATIONAL TECHNIQUES

• Grant number: 13/09746-5
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): September 01, 2013
• Effective date (End): August 31, 2017
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal researcher: Fabio de Lima Leite
• Grantee: Gued Souza
• Home Institution: Centro de Ciências e Tecnologias para a Sustentabilidade (CCTS). Universidade Federal de São Carlos (UFSCAR). Sorocaba , SP, Brazil
• Associated scholarship(s): 14/26369-3 - Electrostatic potential of biomolecules immobilized on nanosurfaces, BE.EP.PD

Abstract

The main goal of this project is to ensure, at the molecular level, the experiments of developing "nanobiosensors" using advanced computer simulation techniques. Nanobiosensors are made by functionalizing tips of the atomic force microscopes (AFM) with organic monolayers. The nanoprototypes currently developed at Nanoneurobiophysic Research Group (GNN) are able to detect the presence of contaminants, and allows to understand the physical and chemical processes involved in studies of autoimmune diseases and neurodegenerative diseases. The computational studies will be responsible for quantify interaction energies between the immobilization surface and enzymes as well as the enzyme and inhibitors. The steps in this molecular study will be: i) study of the electronic structure of the enzyme and exact location of the active site; II) study of the effect of specific interactions on the electronic structure of the enzyme; III) parameterization of inhibitors molecules; IV) simulation of the system enzyme monomer/dimer + inhibitor, in order to obtain information about the mechanical stability of the system and the behavior of the active site in the presence of the herbicide; and V) binding free energy calculation of the following solvated systems: enzyme-inhibitor and enzyme-surface. Some of the enzymes studied by the GNN are: Acetyl-CoA Carboxylase (ACCase), shikimate 5-enol-piruvil-shiquimato-3-fosfato sintase (EPSPs) and AcetolactatoSintase (ALS). A combination of molecular docking calculations, electrostatic potential, molecular dynamics simulations and hybrid calculations using quantum mechanics and molecular mechanics QM/MM will delineate the specific interactions of the system.

Scientific publications

(8)

(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)

MAGALHAES IERICH, JESSICA CRISTIANE; BRUM, DORALINA GUIMARAES; MORAES, ARIANA DE SOUZA; HIGA, AKEMI MARTINS; GARCIA, PAMELA SOTO; MIYAZAKI, CELINA MASSUMI; FERREIRA, MARYSTELA; PERONI, LUIS ANTONIO; DE OLIVEIRA, GUEDMILLER SOUZA; FRANCA, EDUARDO DE FARIA; GOMIDE FREITAS, LUIZ CARLOS; LEITE, FABIO LIMA. Antibody-mediated biorecognition of myelin oligodendrocyte glycoprotein: computational evidence of demyelination-related epitopes. SCIENTIFIC REPORTS, v. 9, FEB 14 2019. Web of Science Citations: 1.

FARIA, ROBERTO R.; DE SOUSA NETO, LOURIVAL R.; GUERRA, RENAN F.; FERREIRA JUNIOR, MOACIR F.; OLIVEIRA, GUEDMILLER S.; FRANCA, EDUARDO F. Parameters for glyphosate in OPLS-AA force field. MOLECULAR SIMULATION, v. 45, n. 1, p. 80-85, JAN 2 2019. Web of Science Citations: 0.

OLIVEIRA, GUEDMILLER S.; IERICH, JESSICA C. M.; MORAES, ARIANA S.; SILVA, GISELA B. R. F.; LIU, YANYUN; NETO, LOURIVAL R. DE S.; FARIA, ROBERTO R.; FRANCA, EDUARDO F.; FREITAS, LUIZ C. G.; BRIGGS, JAMES M.; LEITE, FABIO L. Immobilization and unbinding investigation of the antigen -antibody complex using theoretical and experimental techniques. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v. 86, p. 219-227, JAN 2019. Web of Science Citations: 0.

IERICH, JESSICA C. M.; OLIVEIRA, GUEDMILLER S.; VIG, ANA C. A.; AMARANTE, ADRIANO M.; FRANCA, EDUARDO F.; LEITE, FABIO L.; MASCARENHAS, YVONNE P. A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase. Journal of the Brazilian Chemical Society, v. 26, n. 8, p. 1702-1709, AUG 2015. Web of Science Citations: 2.

GARCIA, PAMELA SOTO; DARIO MOREAU, ALBERTO LUIS; MAGALHAES IERICH, JESSICA CRISTIANE; ARAUJO VIG, ANA CAROLINA; HIGA, AKEMI MARTINS; OLIVEIRA, GUEDMILLER S.; ABDALLA, FABIO CAMARGO; HAUSEN, MOEMA; LEITE, FABIO L. A Nanobiosensor Based on 4-Hydroxyphenylpyruvate Dioxygenase Enzyme for Mesotrione Detection. IEEE SENSORS JOURNAL, v. 15, n. 4, p. 2106-2113, APR 2015. Web of Science Citations: 11.

T.O. REIS; E.C. ZIEMATH; G.S. OLIVEIRA; F.L. LEITE. Construção de uma balança simples para determinação da tensão superficial de líquidos. Revista Brasileira de Ensino de Física, v. 37, n. 1, p. -, Mar. 2015.

AMARANTE, ADRIANO M.; OLIVEIRA, GUEDMILLER S.; BUENO, CAROLINA C.; CUNHA, RICHARD A.; IERICH, JESSICA C. M.; FREITAS, LUIZ C. G.; FRANCA, EDUARDO F.; OLIVEIRA, JR., OSVALDO N.; LEITE, FABIO L. Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors. JOURNAL OF MOLECULAR GRAPHICS & MODELLING, v. 53, p. 100-104, SEP 2014. Web of Science Citations: 13.

BUENO, CAROLINA CASTRO; AMARANTE, ADRIANO MORAES; OLIVEIRA, GUEDMILLER S.; DEDA, DAIANA KOTRA; TESCHKE, OMAR; FRANCA, EDUARDO DE FARIA; LEITE, FABIO L. Nanobiosensor for Diclofop Detection Based on Chemically Modified AFM Probes. IEEE SENSORS JOURNAL, v. 14, n. 5, p. 1467-1475, MAY 2014. Web of Science Citations: 11.