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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Immobilization and unbinding investigation of the antigen -antibody complex using theoretical and experimental techniques

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Author(s):
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Oliveira, Guedmiller S. [1] ; Ierich, Jessica C. M. [2] ; Moraes, Ariana S. [2] ; Silva, Gisela B. R. F. [2] ; Liu, Yanyun [3] ; Neto, Lourival R. de S. [1] ; Faria, Roberto R. [1] ; Franca, Eduardo F. [1] ; Freitas, Luiz C. G. [4] ; Briggs, James M. [3] ; Leite, Fabio L. [2]
Total Authors: 11
Affiliation:
[1] Univ Fed Uberlandia, Inst Quim, BR-38400902 Uberlandia, MG - Brazil
[2] Univ Fed Sao Carlos, Dept Fis Quim & Matemat, Grp Nanoneurobiofis, BR-18052780 Sorocaba, SP - Brazil
[3] Univ Houston, Dept Biol & Biochem, Houston, TX 77204 - USA
[4] Univ Fed Sao Carlos, Dept Quim, BR-13565905 Sao Carlos, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: JOURNAL OF MOLECULAR GRAPHICS & MODELLING; v. 86, p. 219-227, JAN 2019.
Web of Science Citations: 0
Abstract

Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found. Although, only three of them (P1, P2, P5) maintained the Fragment antigen binding available for antigen interaction. Therefore, these configurations were equilibrated after reaching 100 ns molecular dynamics trajectory. The average interaction energy between the surface and the immunoglobulin G - IgG antibody in the P1, P2 and P5 configurations were -62.4 +/- 2.4 kcal/mol; -54.3 +/- 5.7 kcal/mol, and -360.9 +/- 4.2 kcal/mol respectively. Phenobarbital was docked within the Fab domain of P1, P2, and P5 immobilized configurations and equilibrated with molecular dynamics for binding energy estimation. Then, steered molecular dynamics was performed to evaluate unbinding energy pathway between phenobarbital and IgG in each of the three-oriented IgG configurations. No significant differences were observed in the rupture force values (EPI =591 +/- 13 pN, EP2 = 605 +/- 18 pN, and EP5 = 610 +/- 45 pN). In comparison, the average AFM experimental results were (641.6 +/- 363.3 pN). Therefore, it is worth noting that P5 is the configuration with highest protein-surface interaction. Therefore, the force value calculated for the P5 orientation is statistically more favorable and it is the one to be compared to the experimental data. The agreement between experimental and theoretical results indicates a favorable presented for this study opening new perspectives for antigen-antibody evaluation. (C) 2018 Published by Elsevier Inc. (AU)

FAPESP's process: 12/50839-4 - Development of new method for detection of anti-aquaporin-4 for the study of neuromyelitis optica
Grantee:Doralina Guimarães Brum Souza
Support type: Regular Research Grants
FAPESP's process: 15/05283-6 - Nanoimmunosensors development to neuromyelitis optica survey and detection
Grantee:Ariana de Souza Moraes
Support type: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 13/09746-5 - DEVELOPMENT OF NANOBISENSORS USING ADVANCED COMPUTATIONAL TECHNIQUES
Grantee:Gued Souza
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 14/21530-0 - Imnunonanosensors based on atomic force microscopy for multiple sclerosis studies
Grantee:Pâmela Soto Garcia
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 14/12082-4 - Molecular modeling of the antigen-antibody complex to the investigations of autoimmune demyelinating diseases
Grantee:Jéssica Cristiane Magalhães Ierich
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 14/26369-3 - Electrostatic potential of biomolecules immobilized on nanosurfaces
Grantee:Gued Souza
Support type: Scholarships abroad - Research Internship - Post-doctor
FAPESP's process: 15/06847-0 - Synthesis and characterization of silver nanoparticles applied to immunoglobulins G detection
Grantee:Akemi Martins Higa
Support type: Scholarships in Brazil - Master