| Full text | |
| Author(s): Show less - |
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 Opportunities: | Regular Research Grants |
| FAPESP's process: | 15/05283-6 - Nanoimmunosensors development to neuromyelitis optica survey and detection |
| Grantee: | Ariana de Souza Moraes dos Santos |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| FAPESP's process: | 13/09746-5 - DEVELOPMENT OF NANOBISENSORS USING ADVANCED COMPUTATIONAL TECHNIQUES |
| Grantee: | Guedmiller Souza de Oliveira |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| FAPESP's process: | 14/21530-0 - Imnunonanosensors based on atomic force microscopy for multiple sclerosis studies |
| Grantee: | Pâmela Soto Garcia |
| Support Opportunities: | 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 Opportunities: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 14/26369-3 - Electrostatic potential of biomolecules immobilized on nanosurfaces |
| Grantee: | Guedmiller Souza de Oliveira |
| Support Opportunities: | 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 Opportunities: | Scholarships in Brazil - Master |