Hostname: page-component-78c5997874-lj6df Total loading time: 0 Render date: 2024-11-16T22:24:50.712Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular Simulation of Interaction between Graphene Doped with Iron and Coenzyme A

Published online by Cambridge University Press:  09 December 2019

Ernesto López-Chávez ,
Alberto García-Quiroz ,
Yesica A. Peña-Castañeda ,
José A. I. Díaz-Góngora  and
Fray de Landa Castillo-Alvarado
Ernesto López-Chávez
Affiliation:
Autonomous University of Mexico City. Fray Servando Teresa de Mier 92, Col. Obrera, Cuauhtémoc, México, City, C.P. 06080.
Alberto García-Quiroz
Affiliation:
Autonomous University of Mexico City. Fray Servando Teresa de Mier 92, Col. Obrera, Cuauhtémoc, México, City, C.P. 06080.
Yesica A. Peña-Castañeda*
Affiliation:
Autonomous University of Mexico City. Fray Servando Teresa de Mier 92, Col. Obrera, Cuauhtémoc, México, City, C.P. 06080.
José A. I. Díaz-Góngora
Affiliation:
Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada del Instituto Politécnico Nacional, Unidad Legaria. Calzada Legaria No. 694 Col. Irrigación, Del. Miguel Hidalgo, Mexico City, C.P. 11500.
Fray de Landa Castillo-Alvarado
Affiliation:
Escuela Superior de Física y Matemáticas del Instituto Politécnico Nacional. Edificio 9 de la Unidad Profesional Adolfo López Mateos, Col. Lindavista, Del. Gustavo A. Madero, Mexico City, C.P 07030.
*
*(Email: [email protected])
Get access

Abstract

In recent years, modified graphene has been used in various biomedical applications due to its excellent properties that allow the development of devices capable of detecting macromolecules within the human organism, also for biomolecular analysis, discovery of biomarkers, bioimaging and target delivery. These applications involve interactions between enzymes, proteins, peptides, DNA, RNA, etc. and modified graphene, therefore the study and the theoretical and experimental investigation of these interactions is essential for the development of nanobio-technology. For example, many applications based on using modified graphene to detect macromolecules require studying the changes in the properties of doped graphene when interacting with macromolecules. In this work, DFT and molecular dynamics methods were used to obtain results of the changes in energy density of states of graphene doped with iron when it is made to interact with coenzyme A. Besides, we presented a study of molecular dynamics in order to determine the quantum factors that guide the interaction graphene-coenzyme A. The system was studied in aqueous medium which it was simulated by the dielectric constant of water. The results confirm that the methodology presented in this work can be used to theoretically detect various macromolecules.

Keywords

biomaterialdeviceselectronic structureFegraphene
Type
Articles
Information
MRS Advances , Volume 4 , Issue 64: International Materials Research Congress XXVIII , 2019 , pp. 3523 - 3536
Copyright
Copyright © Materials Research Society 2019 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Pandey, R.B., Heinz, H., Feng, J., Farmer, B.L., Slocik, J.M., Drummy, L.F., Naik, R.R., Phys. Chem. Chem. Phys. 11 (12), 1989–2001 (2009).10.1039/b816187aCrossRefGoogle Scholar
Mogharabi, M., Abdollahi, M., Faramarzi, M.A., J. Pharm. Sci. 22 (23) (2014).Google Scholar
Ou, L., Song, B., Liang, H., Liu, J., Feng, X., Deng, B., Sun, T., Shao, L., Fibre Toxicol. 13 (57) (2016).10.1186/s12989-016-0168-yCrossRefGoogle Scholar
Sarikaya, M., Tamerler, C., Jen, A.K.Y., Schulten, K. and Baneyx, F., Nat.Mater. 2, 577–585 (2003).10.1038/nmat964CrossRefGoogle Scholar
Liao, K.H., Lin, Y.S., Macosko, C.W., Haynes, C.L., ACS Appl. Mater. Interfaces. 3, 2607–2615 (2011).10.1021/am200428vCrossRefGoogle Scholar
Mukherjee, S.P., Gliga, A.R., Lazzaretto, B., Brandner, B., Fielden, M., Vogt, C.. Newman, L., Rodrigues, A.F., Shao, W., Fournier, P.M. et al, Nanoscale. 10, 1180–1188 (2018).10.1039/C7NR03552GCrossRefGoogle Scholar
Luo, N., Ni, D., Yue, H., Wei, W., Ma, G., ACS Appl. Mater. Interfaces. 7, 5239–5247 (2015).10.1021/am5084607CrossRefGoogle Scholar
Bianco, A., Cheng, H.M., Enoki, T., Gogotsi, Y., Hurt, R.H., Koratkar, N., et al, Carbon. 65:1–6 (2013).10.1016/j.carbon.2013.08.038CrossRefGoogle Scholar
Kuilla, T., Bhadra, S., Yao, D., Kim, N.H., Bose, S., Lee, J.H., Prog Polym Sci. 35(11), 1350–75 (2010).10.1016/j.progpolymsci.2010.07.005CrossRefGoogle Scholar
Wu, Z., Cui, Q. and Yethiraj, A., J. Chem. Theory Comput. 7, 3793–3802 (2011).10.1021/ct200593tCrossRefGoogle Scholar
Bitounis, D., Ali-Boucetta, H., Hong, B.H., Min, D.H., Kostarelos, K., Adv. Mater. 25, 2258–2268 (2013).10.1002/adma.201203700CrossRefGoogle Scholar
Kostarelos, K., Novoselov, K.S., Science 344, 261–263 (2014).10.1126/science.1246736CrossRefGoogle ScholarPubMed
Barahuie, F., Saifullah, B., Dorniani, D., Fakurazi, S., Karthivashan, G., Hussein, M.Z., Elfghi, F.M., Mater. Sci. Eng. C 74, 177–185 (2017).10.1016/j.msec.2016.11.114CrossRefGoogle Scholar
Kang, X., Wang, J., Wu, H., Aksay, I.A., Liu, J., Lin, Y., Bioelectron. 25, 901–905 (2009).10.1016/j.bios.2009.09.004CrossRefGoogle Scholar
Gu, Y., Ju, C., Li, Y., Shang, Z., Wu, Y., Jia, Y., et al, Bioelectron. 66, 24–31 (2015).CrossRefGoogle Scholar
Min, S.K., Kim, W.Y., Cho, Y., Kim, K.S., Nat. Nanotechnol. 6, 162–165 (2011).10.1038/nnano.2010.283CrossRefGoogle Scholar
Liu, J., Cui, L., Losic, D., Acta Biomater. 9, 9243–9257 (2013).10.1016/j.actbio.2013.08.016CrossRefGoogle Scholar
Sibon, O.C.M., Strauss, E., Nature Reviews Molecular Cell Biology. 17 (10): 605–606 (2016).10.1038/nrm.2016.110CrossRefGoogle Scholar
Daugherty, M., Polanuyer, B., Farrell, M., Scholle, M., Lykidis, A., Crécy-Lagard, V., Osterman, A., J. of Biological Chemistry. 277 (24), 21431–21439 (2002).10.1074/jbc.M201708200CrossRefGoogle Scholar
Baddiley, J., Thain, E.M., Novelli, G.D., Lipmann, F., Nature. 171 (4341), 76 (1953).CrossRefGoogle Scholar
Tsuchiya, Y., Peak-Chew, S.Y., Newell, C., Miller-Aidoo, S., Mangal, S., Zhyvoloup, A., Bakovic´, J., Malanchuk, O., Pereira, G.C., Biochemical Journal. 474 (14), 2489–2508 (2017).10.1042/BCJ20170129CrossRefGoogle Scholar
Perdew, J.P., Ruzsinszky, A., Tao, J., Staroverov, V.N., Scuseria, G.E., Csonka, G.I., J. Chem. Phys. 123, 062201 (2005).CrossRefGoogle Scholar
Burke, K., Perdew, J.P., Wang, Y., in Electronic Density Functional Theory: Recent Progress and New Directions (Eds.: Dobson, J. F., Vignale, G., Das, M. P., Plenum Press, New York, 1997) p. 81.Google Scholar
Perdew, J.P., Ruzsinszky, A., Csonka, G.I., Vydrov, O.A., Scuseria, G.E., Constantin, L.A., Zhou, X., Burke, K., Phys. Rev. Lett. 100, 136406 (2008).10.1103/PhysRevLett.100.136406CrossRefGoogle Scholar
Frenkel, D., Smit, B., Understanding Molecular Simulations: From Algorithms to Applications, 2nd ed. (Academic Press, Inc. Orlando FL, USA, 2001) p. 63-163.Google Scholar
Nosè, S., Mol. Phys. 52: 255-268 (1984).CrossRefGoogle Scholar
Hoover, W.G, Phys. Rev. A 31:1965-1967 (1985).10.1103/PhysRevA.31.1695CrossRefGoogle Scholar
Dawson, R.M.C., Elliott, D.C., Elliott, H.W. and Jones, K.M., Data for Biochemical Research, 3rd ed. (Clarendon Press, 2002).Google Scholar
Nelson, D.L., Cox, M.C., Lehninger: Principles of Biochemistry 4th ed. (W.H. Freeman & Co, New York).Google Scholar
López-Chávez, E., García-Quiroz, A., Peña-Castañeda, Y.A, Díaz-Góngora, J.A.I., Castillo-Alvarado, F.L, presented at the XXVIII International Materials Research Congress, Cancun, Mexico, 2019 (unpublished).Google Scholar
Kresge, N., Simoni, R.D., Hill, R.L., J of Biol. Chem. 280 (21), (2005).Google Scholar
Murugappa, S., Kunapuli, S.P., Front Biosci . 11, 1977–86 (2006).10.2741/1939CrossRefGoogle Scholar
Besouw, M., Masereeuw, R., van den Heuvel, L., Levtchenko, E., Drug Discovery Today 18 (15–16):785–92 (2013).CrossRefGoogle Scholar
Greenberg, D., Metabolism of Sulfur Compounds, 3rd ed. (Academic Press, New York:), p. 545.Google Scholar
L Zeng, F., Sun, Y., Zhou, Y., Li, Q.K., Modelling Simul. Mater. Sci. Eng. 17 (2009)10.1088/0965-0393/17/7/075002CrossRefGoogle Scholar
Delley, B., Ellis, D. E., Freeman, A. J., Baerends, E. J., and Post, D. Phys. Rev. B 27, (1983).Google Scholar
Ohta, T., Bostwick, A., Seyller, T., Horn, K., Rotenberg, E., Controlling the electronic structure of bilayer graphene, Science 313 (2006).10.1126/science.1130681CrossRefGoogle ScholarPubMed
Son, Y.W., Cohen, M.L., Louie, S.G., Nature 444 (2006).10.1038/nature05180CrossRefGoogle Scholar
Gorbachev, R.V. et al., Science 346 (2014).10.1126/science.1254966CrossRefGoogle Scholar
Foo, M.E., Gopinath, S.C.B., Biomedicine & Pharmacotherapy 94: 354–361 (2017).CrossRefGoogle Scholar