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Electrostatic potential of biomolecules immobilized on nanosurfaces

Grant number: 14/26369-3
Support type:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): May 01, 2015
Effective date (End): April 30, 2016
Field of knowledge:Biological Sciences - Biophysics
Principal Investigator:Fabio de Lima Leite
Grantee:Gued Souza
Supervisor abroad: James M. Briggs
Home Institution: Centro de Ciências e Tecnologias para a Sustentabilidade (CCTS). Universidade Federal de São Carlos (UFSCAR). Sorocaba , SP, Brazil
Local de pesquisa : University of Houston (UH), United States  
Associated to the scholarship:13/09746-5 - Development of NANOBISENSORS using advanced computational techniques, BP.PD

Abstract

Atomic Force Microscope molecular recognition measurements are based on the interaction between two molecules: one attached to the AFM tip and the other bound to the surface of interest. The experimental immobilization of this system on AFM nanocomponents is a tough challenge for researchers worldwide. However, the experimental procedure can be assisted by computer simulations which provide an insight of a target molecular interaction. The main goal of this project is to investigate reaction mechanisms involved in humoral responses of neurodegenerative diseases such as multiple sclerosis and neuromyelitis optica. Hypothesis from the literature report a relevant role of antibodies autoreactive on the development of neurodegenerative diseases. In this context, the immobilization of antibodies on the AFM nanocomponents can reveal the chemical mechanisms involved in the disease propagation. Advanced computer simulations will be performed to estimate the orientation of antigens and antibodies on the surface and its interaction energies. Above all, electrostatic interactions play an important role in bimolecular immobilization (adsorption), it will be calculated by solving Poisson Boltzmann equation numerically. In cooperation with Prof. Dr. James M. Briggs from the Biology and Biochemistry Department of the University of Houston, Houston, TX, USA; the University of Houston Brownian Dynamics (UHBD) program will be used to solve the linear and non-linear Poisson-Boltzmann equation using a finite-difference method. Moreover, Brownian dynamics simulations will be performed to investigate molecular association and the internal dynamics of antigen-antibody interactions. (AU)

Scientific publications (4)
(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: 0.
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: 3.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.