The role of basic residues in the adsorption of blood proteins onto the graphene surface

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Gu, Zonglin ^a   Yang, Zaixing ^a   Wang, Lingle ^a   Zhou, Hong ^a   Jimenez Cruz, Camilo A ^b   Zhou, Ruhong ^a,b,c  

^a SOOCHOW UNIVERSITY   (China)

^b IBM T J WATSON RESEARCH CENTER   (United States)

^c Department of Chemistry Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPHITE; NANOMATERIAL; PLASMA PROTEIN;

ADSORPTION; ANIMAL; BOVINE; CHEMISTRY; MOLECULAR MODEL; PROTEIN CONFORMATION; SURFACE PROPERTY; TIME FACTOR;

ADSORPTION; ANIMALS; BLOOD PROTEINS; CATTLE; GRAPHITE; MODELS, MOLECULAR; NANOSTRUCTURES; PROTEIN CONFORMATION; SURFACE PROPERTIES; TIME FACTORS;

EID: 84934881013     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10873     Document Type: Article

References (75)

1. Kroto, H. W., Heath, J. R., Obrien, S. C., Curl, R. F. & Smalley, R. E. C60: Buckminsterfullerene. Nature 318, 162-163 (1985).
2. Iijima, S. Helical microtubules of graphitic carbon. Nature 354, 56-58 (1991).
3. Wu, J. et al. Structure-dependent hydrostatic deformation potentials of individual single-walled carbon nanotubes. Phys. Rev. Lett. 93, 4 (2004).
4. Lee, J. S., Joung, H. A., Kim, M. G. & Park, C. B. Graphene-based chemiluminescence resonance energy transfer for homogeneous immunoassay. ACS Nano 6, 2978-2983 (2012).
5. Ocsoy, I. et al. Nanotechnology in plant disease management: DNA-directed silver nanoparticles on graphene oxide as an antibacterial against xanthomonas perforans. ACS Nano 7, 8972-8980 (2013).
6. Singh, N. et al. Cicer alpha-galactosidase immobilization onto functionalized graphene nanosheets using response surface method and its applications. Food Chem. 142, 430-438 (2014).
7. Cha, C. Y., Shin, S. R., Annabi, N., Dokmeci, M. R. & Khademhosseini, A. Carbon-based nanomaterials: multifunctional materials for biomedical engineering. ACS Nano 7, 2891-2897 (2013).
8. Wang, C. et al. A novel hydrazine electrochemical sensor based on the high specific surface area graphene. Microchim. Acta 169, 1-6 (2010).
9. Katsnelson, M. I. Graphene: carbon in two dimensions. Mater. Today 10, 20-27 (2007).
10. Ajayan, P. M. Nanotubes from carbon. Chem. Rev. 99, 1787-1799 (1999).
11. Dresselhaus, M., Dresselhaus, G., Eklund, P. & Saito, R. Carbon nanotubes. Phys. World 11, 33-38 (1998).
12. Zhang, M. X. et al. Graphene oxide based theranostic platform for T-1-weighted magnetic resonance imaging and drug delivery. ACS Appl. Mater. Interfaces 5, 13325-13332 (2013).
13. Wang, C. Y. et al. Multifunctional chitosan magnetic-graphene (CMG) nanoparticles: a theranostic platform for tumor-targeted co-delivery of drugs, genes and MRI contrast agents. J. Mat. Chem. B 1, 4396-4405 (2013).
14. Sun, X. M. et al. Nano-graphene oxide for cellular imaging and drug delivery. Nano Res. 1, 203-212 (2008).
15. Sanchez, V. C., Jachak, A., Hurt, R. H. & Kane, A. B. Biological interactions of graphene-family nanomaterials: an interdisciplinary review. Chem. Res. Toxicol. 25, 15-34 (2012).
16. Tu, Y. S. et al. Destructive extraction of phospholipids from Escherichia coli membranes by graphene nanosheets. Nat. Nanotechnol. 8, 594-601 (2013).
17. Hu, W. B. et al. Graphene-Based Antibacterial Paper. ACS Nano 4, 4317-4323 (2010).
18. Akhavan, O. & Ghaderi, E. Toxicity of graphene and graphene oxide nanowalls against bacteria. ACS Nano 4, 5731-5736 (2010).
19. Li, Y. F. et al. Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites. Proc. Natl. Acad. Sci. U. S. A. 110, 12295-12300 (2013).
20. Yang, K. & Ma, Y. Q. Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. Nat. Nanotechnol. 5, 579-583 (2010).
21. Wang, S. et al. Magnetic graphene-based nanotheranostic agent for dual-modality mapping guided photothermal therapy in regional lymph nodal metastasis of pancreatic cancer. Biomaterials 35, 9473-9483 (2014).
22. Kang, S. G. et al. Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine. Proc. Natl. Acad. Sci. U. S. A. 109, 15431-15436 (2012).
23. Zhou, R. H. & Gao, H. J. Cytotoxicity of graphene: recent advances and future perspective. Wiley Interdiscip. Rev.-Nanomed. Nanobiotechnol. 6, 452-474 (2014).
24. Zuo, G. H., Kang, S. G., Xiu, P., Zhao, Y. L. & Zhou, R. H. Interactions between proteins and carbon-based nanoparticles: exploring the origin of nanotoxicity at the molecular level. Small 9, 1546-1556 (2013).
25. Zuo, G. H., Huang, Q., Wei, G. H., Zhou, R. H. & Fang, H. P. Plugging into proteins: poisoning protein function by a hydrophobic nanoparticle. ACS Nano 4, 7508-7514 (2010).
26. Zuo, G. H., Gu, W., Fang, H. P. & Zhou, R. H. Carbon nanotube wins the competitive binding over proline-rich motif ligand on SH3 domain. J. Phys. Chem. C 115, 12322-12328 (2011).
27. Zhang, J. L. et al. Pressure-induced superconductivity in topological parent compound Bi2Te3. Proc. Natl. Acad. Sci. U. S. A. 108, 24-28 (2011).
28. Zhang, Y. B. et al. Cytotoxicity effects of graphene and single-wall carbon nanotubes in neural phaeochromocytoma-derived PC12 cells. ACS Nano 4, 3181-3186 (2010).
29. Jacobsen, N. R. et al. Genotoxicity, cytotoxicity, and reactive oxygen species induced by single-walled carbon nanotubes and C-60 fullerenes in the FE1-Muta (TM) mouse lung epithelial cells. Environ. Mol. Mutagen. 49, 476-487 (2008).
30. Ge, C. C. et al. Binding of blood proteins to carbon nanotubes reduces cytotoxicity. Proc. Natl. Acad. Sci. U. S. A. 108, 16968-16973 (2011).
31. Hu, W. B. et al. Protein corona-mediated mitigation of cytotoxicity of graphene oxide. ACS Nano 5, 3693-3700 (2011).
32. De Paoli, S. H. et al. The effect of protein corona composition on the interaction of carbon nanotubes with human blood platelets. Biomaterials 35, 6182-6194 (2014).
33. Huang, Y. X. et al. Graphene oxide nanoribbons greatly enhance extracellular electron transfer in bio-electrochemical systems. Chem. Commun. 47, 5795-5797 (2011).
34. Wang, Y., Li, Z. H., Wang, J., Li, J. H. & Lin, Y. H. Graphene and graphene oxide: biofunctionalization and applications in biotechnology. Trends Biotechnol. 29, 205-212 (2011).
35. Wang, Y. et al. Aptamer/Graphene oxide nanocomplex for in situ molecular probing in living cells. J. Am. Chem. Soc. 132, 9274-9276 (2010).
36. Altieri, D. C. Coagulation assembly on leukocytes in transmembrane signaling and cell adhesion. Blood 81, 569-579 (1993).
37. Page, R. C. & Schroeder, H. E. Pathogenesis of inflammatory periodontal disease. A summary of current work. Lab. Invest. 34, 235-249 (1976).
38. Humphrey, W., Dalke, A. & Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996).
39. Tu, Y. S. et al. Water-mediated signal multiplication with Y-shaped carbon nanotubes. Proc. Natl. Acad. Sci. U. S. A. 106, 18120-18124 (2009).
40. Brown, J. H., Volkmann, N., Jun, G., Henschen-Edman, A. H. & Cohen, C. The crystal structure of modified bovine fibrinogen. Proc. Natl. Acad. Sci. U. S. A. 97, 85-90 (2000).
41. Zhou, R. H., Huang, X. H., Margulis, C. J. & Berne, B. J. Hydrophobic collapse in multidomain protein folding. Science 305, 1605-1609 (2004).
42. Liu, P., Huang, X. H., Zhou, R. H. & Berne, B. J. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 437, 159-162 (2005).
43. Eleftheriou, M., Germain, R. S., Royyuru, A. K. & Zhou, R. Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields. J. Am. Chem. Soc. 128, 13388-13395 (2006).
44. Fitch, B. G. et al. Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. 846-854 (Springe rBerlin Heidelberg, 2006).
45. Zhou, R., Das, P. & Royyuru, A. K. Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study. J. Phys. Chem. B 112, 15813-15820 (2008).
46. Das, P., King, J. A. & Zhou, R. Aggregation of gamma-crystallins associated with human cataracts via domain swapping at the C-terminal beta-strands. Proc. Natl. Acad. Sci. U. S. A. 108, 10514-10519 (2011).
47. Das, P., Li, J., Royyuru, A. K. & Zhou, R. Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. J. Comput. Chem. 30, 1654-1663 (2009).
48. Li, J. Y. et al. Electrostatic gating of a nanometer water channel. Proc. Natl. Acad. Sci. U. S. A. 104, 3687-3692 (2007).
49. Das, P. & Zhou, R. Urea-induced drying of carbon nanotubes suggests existence of a dry globule-like transient state during chemical denaturation of proteins. J. Phys. Chem. B 114, 5427-5430 (2010).
50. Guo, C., Luo, Y., Zhou, R. & Wei, G. Probing the self-assembly mechanism of diphenylalanine-based Peptide nanovesicles and nanotubes. ACS Nano 6, 3907-3918 (2012).
51. Xiu, P. et al. Urea-induced drying of hydrophobic nanotubes: comparison of different urea models. J. Phys. Chem. B 115, 2988-2994 (2011).
52. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435-447 (2008).
53. Mackerell, A. D., Feig, M. & Brooks, C. L. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25, 1400-1415 (2004).
54. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935 (1983).
55. Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 7 (2007).
56. Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690 (1984).
57. Selkoe, D. J. Alzheimer's disease: Genes, proteins, and therapy. Physiol. Rev. 81, 741-766 (2001).
58. Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463-1472 (1997).
59. Miyamoto, S. & Kollman, P. A. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13, 952-962 (1992).
60. Stauffer, D. et al. An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water. J. Chem. Phys. 141, 8 (2014).
61. He, Z. & Zhou, J. Probing carbon nanotube-amino acid interactions in aqueous solution with molecular dynamics simulations. Carbon 78, 500-509 (2014).
62. Zuo, G., Zhou, X., Huang, Q., Fang, H. P. & Zhou, R. H. Adsorption of villin headpiece onto graphene, carbon nanotube, and C60: effect of contacting surface curvatures on binding affinity. J. Phys. Chem. C 115, 23323-23328 (2011).
63. Kang, S.-g. et al. Dual inhibitory pathways of metallofullerenol Gd@C82(OH)22 on matrix metalloproteinase-2: molecular insight into drug-like nanomedicine. Sci Rep 4, 4775 (2014).
64. Wang, S. Q. et al. Peptides with selective affinity for carbon nanotubes. Nat. Mater. 2, 196-200 (2003).
65. Zorbas, V. et al. Importance of aromatic content for peptide/single-walled carbon nanotube interactions. J. Am. Chem. Soc. 127, 12323-12328 (2005).
66. Li, X. J. et al. Direct measurements of interactions between polypeptides and carbon nanotubes. J. Phys. Chem. B 110, 12621-12625 (2006).
67. Salzmann, C. G., Ward, M. A. H., Jacobs, R. M. J., Tobias, G. & Green, M. L. H. Interaction of tyrosine-, tryptophan-, and lysinecontaining polypeptides with single-wall carbon nanotubes and its relevance for the rational design of dispersing agents. J. Phys. Chem. C 111, 18520-18524 (2007).
68. Su, Z., Mui, K., Daub, E., Leung, T. & Honek, J. Single-walled carbon nanotube binding peptides: Probing tryptophan's importance by unnatural amino acid substitution. J. Phys. Chem. B 111, 14411-14417 (2007).
69. Xie, H., Becraft, E. J., Baughman, R. H., Dalton, A. B. & Dieckmann, G. R. Ranking the affinity of aromatic residues for carbon nanotubes by using designed surfactant peptides. J. Pept. Sci. 14, 139-151 (2008).
70. Yang, Z. X., Wang, Z. G., Tian, X. L., Xiu, P. & Zhou, R. H. Amino acid analogues bind to carbon nanotube via pi-pi interactions: Comparison of molecular mechanical and quantum mechanical calculations. J. Chem. Phys. 136, 10 (2012).
71. Gao, Z. H., Zhi, C. Y., Bando, Y., Golberg, D. & Serizawa, T. Isolation of individual boron nitride nanotubes via peptide wrapping. J. Am. Chem. Soc. 132, 4976-4977 (2010).
72. Hoare, T. et al. Magnetically triggered nanocomposite membranes: a versatile platform for triggered drug release. Nano Lett. 11, 1395-1400 (2011).
73. Zhang, X., Yang, R., Wang, C. & Heng, C. L. Cell biocompatibility of functionalized graphene oxide. Acta Phys.-Chim. Sin. 28, 1520-1524 (2012).
74. Zhang, X. Y. et al. Distribution and biocompatibility studies of graphene oxide in mice after intravenous administration. Carbon 49, 986-995 (2011).
75. Wang, K. et al. Biocompatibility of graphene oxide. Nanoscale Res. Lett. 6, 8 (2011).