Adsorption of cytochrome c on graphene oxide: a molecular dynamic study

doi:10.7523/j.issn.2095-6134.2016.01.011

Abstract

Abstract:

Through molecular dynamic simulations, we have investigated the adsorption behavior of cytochrome c on graphene oxide. Results indicate that graphene oxide has a great binding affinity towards cytochrome c. Analyses of root mean square deviation and gyration radius show that there is a large structural damage occurring in system P3 among all the systems. Our study shows that graphene oxide has the ability to deteriorate the native structure of cytochrome c.

Key words: cytochrome c, graphene oxide, adsorption, molecular dynamics

CLC Number:

O642

ZHANG Chi, HUANG Xuqi, LI Xiaoyi. Adsorption of cytochrome c on graphene oxide: a molecular dynamic study[J]. , 2016, 33(1): 70-74.

References

[1] Stevens J M. Cytochrome c as an experimental model protein[J]. Metallomics, 2011, 3(4): 319-322.
[2] Weinkam P, Zimmermann J, Romesberg F E, et al. The folding energy landscape and free energy excitations of cytochrome c[J]. Accounts of Chemical Research, 2010, 43(5): 652-660.
[3] Winkler J R. Cytochrome c folding dynamics[J]. Current Opinion in Chemical Biology, 2004, 8(2): 169-174.
[4] Stevens J M, Uchida T, Daltrop O, et al. Covalent cofactor attachment to proteins: cytochrome c biogenesis[J]. Biochemical Society Transactions, 2005, 33(Pt 4): 792-795.
[5] Allen J W, Daltrop O, Stevens JM, et al. C-type cytochromes: diverse structures and biogenesis systems pose evolutionary problems[J]. Philos Trans R Soc Lond B Biol Sci, 2003, 358(1429): 255-266.
[6] Diekert K, de Kroon A I, Ahting U, et al. Apocytochrome c requires the TOM complex for translocation across the mitochondrial outer membrane[J]. EMBO Journal, 2001, 20(20): 5 626-5 635.
[7] Bashir Q, Volkov A N, Ullmann G M, et al. Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase[J]. Journal of the American Chemical Society, 2010, 132(1): 241-247.
[8] Feng L, Chen Y, Ren J, et al. A graphene functionalized electrochemical aptasensor for selective label-free detection of cancer cells[J]. Biomaterials, 2011, 32(11): 2 930-2 937.
[9] Peng C, Hu W, Zhou Y, et al. Intracellular imaging with a graphene-based fluorescent probe[J]. Small, 2010, 6(15): 1 686-1 692.
[10] Wei T, Carignano M A, Szleifer I. Lysozyme adsorption on polyethylene surfaces: why are long simulations needed?[J]. Langmuir, 2011, 27(19): 12 074-12 081.
[11] Heinz H, Farmer B L, Pandey R B, et al. Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution[J]. Journal of the American Chemical Society, 2009, 131(28): 9 704-9 714.
[12] Yang W, Xue H, Li W, et al. Pursuing "zero" protein adsorption of poly(carboxybetaine) from undiluted blood serum and plasma[J]. Langmuir, 2009, 25(19): 11 911-11 916.
[13] Dringen R, Koehler Y, Derr L, et al. Adsorption and reduction of glutathione disulfide on alpha-Al₂O₃ nanoparticles: experiments and modeling[J]. Langmuir, 2011, 27(15): 9 449-9 457.
[14] Nel AE, Madler L, Velegol D, et al. Understanding biophysicochemical interactions at the nano-bio interface[J]. Nature Materials, 2009, 8(7): 543-557.
[15] Benesch J, Hungerford G, Suhling K, et al. Fluorescence probe techniques to monitor protein adsorption-induced conformation changes on biodegradable polymers[J]. Journal of Colloid and Interface Science, 2007, 312(2): 193-200.
[16] Lu JR, Su TJ, Thirtle PN, et al. The denaturation of lysozyme layers adsorbed at the hydrophobic solid/Liquid surface studied by neutron reflection[J]. Journal of Colloid and Interface Science, 1998, 206(1): 212-223.
[17] Billsten P, Wahlgren M, Arnebrant T, et al. Structural changes of T4 lysozyme upon adsorption to silica nanoparticles measured by circular dichroism[J]. Journal of Colloid and Interface Science, 1995, 175(1): 77-82.
[18] Wei T, Kaewtathip S, Shing K. Buffer effect on protein adsorption at liquid solid interface[J]. The Journal of Physical Chemistry C, 2009, 113(6): 2 053-2 062.
[19] Li G, Xue H, Gao C, et al. Nonfouling Polyampholytes from an lon-pair comonomer with biomimetic adhesive groups[J]. Macromolecules, 2010, 43(1): 14-16.
[20] Kim D T, Blanch H W, Radke C J. Direct imaging of lysozyme adsorption onto mica by atomic force microscopy[J]. Langmuir, 2002, 18(15): 5 841-5 850.
[21] Zhong J, Song L, Meng J, et al. Bio-nano interaction of proteins adsorbed on single-walled carbon nanotubes[J]. Carbon, 2009, 47(4): 967-973.
[22] Bushnell G W, Louie G V, Brayer G D. High-resolution three-dimensional structure of horse heart cytochrome c[J]. Journal of Molecular Biology, 1990, 214(2): 585-595.
[23] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics[J]. Journal of Molecular Graphics, 1996, 14(1): 33-38.
[24] Lerf A, He H, Forster M, et al. Structure of graphite oxide revisited[J]. The Journal of Physical Chemistry B, 1998, 102(23): 4 477-4 482.
[25] Hu B, Ge Z, Li X. Interface adsorption taking the most advantageous conformation for electron transfer between graphene and cytochrome c[J]. Journal of Nanoscience and Nanotechnology, 2015, 15(7): 4 863-4 869.
[26] Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water[J]. Journal of Chemical Physics, 1983, 79(2): 926-935.
[27] Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD[J]. J Comput Chem, 2005, 26(16): 1 781-1 802.
[28] Berendsen H J C, Postma J P M, van Gunsteren WF, et al. Molecular dynamics with coupling to an external bath[J]. Journal of Chemical Physics, 1984, 81(8): 3 684-3 690.
[29] MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins[J]. J Phys Chem B, 1998, 102(18): 3 586-3 616.
[30] Autenrieth F, Tajkhorshid E, Baudry J, et al. Classical force field parameters for the heme prosthetic group of cytochrome c[J]. J Comput Chem, 2004, 25(13): 1613-1622.
[31] Darden T, York D, Pedersen L. Particle mesh ewald: an NlogN method for ewald sums in large systems[J]. Journal of Chemical Physics, 1993, 98(12): 10 089-10 092.