Stepwise design of non-covalent wrapping of large diameter carbon nanotubes by peptides

Journal of Molecular Graphics and Modelling

Volumn 46, Issue , 2013, Pages 83-92

  Chen, Xin ^a   Yu, Xiaohan ^a   Liu, Yafang ^a   Zhang, Jinglai ^a  

^a HENAN UNIVERSITY   (China)

Author keywords

Molecular design; Molecular dynamics; Non covalent functionalization; Peptide; Single walled carbon nanotubes (SWCNTs)

Indexed keywords

ADSORPTION CAPABILITY; ADSORPTION DYNAMICS; ADSORPTION OF PROTEINS; MOLECULAR DESIGN; NANOSCALE ELECTRONICS; NON-COVALENT FUNCTIONALIZATION; SINGLE-WALLED CARBON NANOTUBE (SWCNTS); SINGLEWALLED CARBON NANOTUBE (SWCNT);

ADSORPTION; AROMATIC COMPOUNDS; MEDICAL NANOTECHNOLOGY; MOLECULAR DYNAMICS; SINGLE-WALLED CARBON NANOTUBES (SWCN);

PEPTIDES;

AROMATIC COMPOUND; HISTIDINE; HYDROGEN; METHIONINE; PEPTIDE; SERINE; SINGLE WALLED NANOTUBE; THREONINE; TRYPTOPHAN;

ADSORPTION; ARTICLE; BIOCOMPATIBILITY; CONFORMATIONAL TRANSITION; DISPERSION; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STATIC ELECTRICITY; TUBE;

MOLECULAR DESIGN; MOLECULAR DYNAMICS; NON-COVALENT FUNCTIONALIZATION; PEPTIDE; SINGLE-WALLED CARBON NANOTUBES (SWCNTS);

ADSORPTION; AMINO ACID SEQUENCE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INSULIN; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; NANOTUBES, CARBON; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 84886550744     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.09.012     Document Type: Article

References (66)

1. H.K. Li, J.H. Huang, J.H. Lv, H.J. An, X.D. Zhang, Z.Z. Zhang, C.H. Fan, and J. Hu Nanoparticle PCR: Nanogold-assisted PCR with enhanced specificity Angew. Chem. Int. Ed. 44 2005 5100 5103
2. R.F. Service Is nanotechnology dangerous Science 290 2000 1526 1527
3. K. Donaldson, R. Aitken, L. Tran, V. Stone, R. Duffin, G. Forrest, and A. Alexander Carbon nanotubes: a review of their properties in relation to pulmonary toxicology and workplace safety Toxicol. Sci. 92 2006 5 22
4. N. Gilbert Nanoparticle safety in doubt Nature 460 2009 937
5. R. Saito, G. Dresselhaus, and M.S. Dresselhaus Physical Properties of Carbon Nanotubes 1998 Imperial College Press London
6. A. Bianco, K. Kostarlos, C.D. Partidos, and M. Prato Biomedical applications of functionalized carbon nanotubes Chem. Commun. 5 2005 571 577
7. L. Lacerda, A. Bianco, M. Prato, and K. Kostarelos Carbon nanotubes as nanomedicines: from toxicology to pharmacology Adv. Drug Deliver. Rev. 58 2006 1460 1470
8. W. Zhao, C. Song, and P.E. Pehrsson Water-soluble and optically pH-sensitive single-walled carbon nanotubes from surface modification J. Am. Chem. Soc. 124 2002 12418 12419
9. K. Kurppa, H. Jiang, G.R. Szilvay, A.G. Nasibulin, E.I. Kauppinen, and M.B. Linder Controlled hybrid nanostructures through protein-mediated noncovalent functionalization of carbon nanotubes Angew. Chem. 119 2007 6566 6569
10. K. Kurppa, H. Jiang, G.R. Szilvay, A.G. Nasibulin, E.I. Kauppinen, and M.B. Linder Controlled hybrid nanostructures through protein-mediated noncovalent functionalization of carbon nanotubes Angew. Chem. Int. Ed. 46 2007 6446 6449
11. A. Bianco, J. Hoebeke, S. Godefroy, O. Chaloin, D. Pantarotto, J.P. Briand, S. Muller, M. Prato, and C.D. Partidos Cationic carbon nanotubes bind to CpG oligodeoxynucleotides and enhance their immunostimulatory properties J. Am. Chem. Soc. 127 2005 58 59
12. V.C. Moore, M.S. Strano, E.H. Haroz, R.H. Hauge, J.L. Margrave, R.E. Smalley, J. Schmidt, and Y. Talmon Individually suspended single-walled carbon nanotubes in various surfactants Nano. Lett. 3 2003 1379 1382
13. L.Y. Li, Y. Yang, G.L. Yang, X.M. Chen, B.S. Hsiao, B. Chu, J.E. Spanier, and C.Y. Li Patterning polyethylene oligomers on carbon nanotubes using physical vapor deposition Nano. Lett. 6 2006 1007 1012
14. Y. Chen, H.P. Liu, T. Ye, J. Kim, and C.D. Mao DNA-directed assembly of single-wall carbon nanotubes J. Am. Chem. Soc. 129 2007 8696 8697
15. S. Wang, E.S. Humphreys, S.Y. Chung, D.F. Delduco, S.R. Lustig, H. Wang, K.N. Parker, N.W. Rizzo, S. Subramoney, Y.M. Chiang, and A. Jagota Peptides with selective affinity for carbon nanotubes Nat. Mater. 2 2003 196 200
16. S.S. Karajanagi, H. Yang, P. Asuri, E. Sellitto, J.S. Dordick, and R.S. Kane Protein-assisted solubilization of single-walled carbon nanotubes Langmuir 22 2006 1392 1395
17. G.R. Dieckmann, A.B. Dalton, P.A. Johnson, J. Razal, J. Chen, G.M. Giordano, E. Munoz, I.H. Musselman, R.H. Baughman, and R.K. Draper Controlled assembly of carbon nanotubes by designed amphiphilic peptide helices J. Am. Chem. Soc. 125 2003 1770 1777
18. A.B. Dalton, A. Ortiz-Acevedo, V. Zorbas, E. Brunner, W.M. Sampson, S. Collins, J.M. Razal, M.M. Yoshida, R.H. Baughman, R.K. Draper, I.H. Musselman, M. Jose-Yaca-man, and G.R. Dieckmann Controlled assembly of carbon nanotubes by designed amphiphilic peptide helices Adv. Funct. Mater. 14 2004 1147 1151
19. V. Zorbas, A.L. Smith, A. Ortiz-Acevedo, H. Xie, A.B. Dalton, G.R. Dieckmann, R.K. Draper, R.H. Baughman, and I.H. Mussel-man Importance of aromatic content for peptide/single-walled carbon nanotube interactions J. Am. Chem. Soc. 127 2005 12323 12328
20. V. Zorbas, A. Ortiz-Acevedo, A.B. Dalton, M.M. Yoshida, G.R. Die-ckmann, R.K. Draper, R.H. Baughman, M. Jose-Yacaman, and I.H. Musselman Preparation and characterization of individual peptide-wrapped single-walled carbon nanotubes J. Am. Chem. Soc. 126 2004 7222 7227
21. C.C. Chiu, G.R. Dieckmann, and S.O. Nielsen Molecular dynamics study of a nanotube-binding amphiphilic helical peptide at different water/hydrophobic interfaces J. Phys. Chem. B 112 2008 16326 16333
22. C.C. Chiu, G.R. Dieckmann, and S.O. Nielsen Role of peptide-peptide interactions in stabilizing peptide-wrapped single-walled carbon nanotubes: a molecular dynamics study Peptide Sci. 2009 156 163
23. G.H. Zuo, Q. Huang, G.h. Wei, R.H. Zhou, and H.P. Fang Plugging into proteins: Poisoning protein function by a hydrophobic nanoparticle ACS. Nano. 4 2010 7508 7514
24. J.W. Shen, T. Wu, Q. Wang, Y. Kang, and X. Chen Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules Chem. Phys. Chem. 10 2009 1260 1269
25. Y. Kang, Y.C. Liu, Q. Wang, J.W. Shen, T. Wu, and W.J. Guan On the spontaneous encapsulation of proteins in carbon nanotubes Biomaterials 30 14 2009 2807 2815
26. Y. Kang, Q. Wang, Y.C. Liu, J.W. Shen, and T. Wu Diameter selectivity of protein encapsulation in carbon nanotubes J. Phys. Chem. B 114 8 2010 2869 2875
27. M.J. Macias, M. Hyvonen, E. Baraldi, J. Schultz, M. Sudol, M. Saraste, and H. Oschkinat Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide Nature 382 1996 646 649
28. I.C. Yeh, and G.H. Proc Nucleic acid transport through carbon nanotube membranes Natl. Acad. Sci. 101 2004 12177 12182
29. R.R. Johnson, A.T.C. Johnson, and M.L. Klein Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics Nano. Lett. 8 2008 69 75
30. J.W. Shen, T. Wu, Q. Wang, and Y. Kang Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces Biomaterial 29 2008 3847 3855
31. H. Gao, Y. Kong, D. Cui, and C.S. Ozkan Spontaneous insertion of DNA oligonucleotides into carbon nanotubes Nano. Lett. 3 2003 471 473
32. E.J. Sorin, and V.S. Pande Nanotube confinement denatures protein helices J. Am. Chem. Soc. 128 2006 6316 6317
33. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gusteren, and J. Hermans Interaction models for water in relation to protein hydration B. Pullman, Intermolecular Forces 1981 Reidel Dordrecht 331 342
34. H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma The missing term in effective pair potentials J. Phys. Chem. 91 1987 6269 6271
35. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
36. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evan-seck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher III, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wi-rkiewicz-Kuczera, D. Yin, and M. Kar-plus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
37. J.H. Walther, R. Jaffe, T. Halicioglu, and P. Koumoutsakos Carbon nanotubes in water: structural characteristics and energetics J. Phys. Chem. B 105 2001 9980 9987
38. J.W. Shen, T. Wu, Q. Wang, and H.H. Pan Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces Biomaterials 29 2008 513 532
39. X. Chen, T. Wu, Q. Wang, and J.W. Shen Shield effect of silicate on adsorption of protein onto silicon-doped hydroxyapatite (100) surface Biomaterials 29 2008 2423 2432
40. H.J. Gao, and Y. Kong Simulation of DNA-nanotube interactions Annu. Rev. Mater. Res. 34 2004 123 150
41. S. Ravichandran, J.D. Madura, and J. Talbot A Brownian dynamics study of the initial stages of hen egg-white lysozyme adsorption at a solid interface J. Phys. Chem. B 105 2001 3610 3613
42. D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y.B. Shan, and W. Wriggers Atomic-level characterization of the structural dynamics of proteins Science 330 2010 341 346
43. A.B. Guliaev, S. Cheng, and B. Hang Protein dynamics via computational microscope World J. Methodol. 2 2012 42 49
44. H.L. Zhou, T. Wu, X.L. Dong, Q. Wang, and J.W. Shen Adsorption mechanism of BMP-7 on hydroxyapatite (001) surfaces Biochem. Biophys. Res. Commun. 361 2007 91 96
45. P. Bjelkmar, P. Laesson, M.A. Cuendet, B. Hess, and E. Lindahl Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models J. Chem. Theory Comput. 6 2010 459 466
46. Q.X. Mu, W. Liu, Y.H. Xing, H.Y. Zhou, Z.W. Li, Y. Zhang, L.H. Ji, F. Wang, Z.K. Si, B. Zhang, and B. Yan Protein binding by functionalized multiwalled carbon nanotubes is governed by the surface chemistry of both parties and the nanotube diameter J. Phys. Chem. C 112 2008 3300 3307
47. C. Rajesh, C. Majumder, H. Mizuseki, and Y. Kawazoe A theoretical study on the interaction of aromatic amino acids with graphene and single walled carbon nanotube J. Chem. Phys. 130 2009 124911 124917
48. Y.Z. Liu, C. Chipot, X.G. Shao, and W.S. Cai Edge effects control helical wrapping of carbon nanotubes by polysaccharides Nanoscale 4 2012 2584 2589
49. A.C. Camproux, R. Gautier, and P. Tuffery A hidden markov model derived structural alphabet for proteins J. Mol. Biol. 339 3 2004 591 605
50. J. Maupetit, P. Derreumaux, and P. Tuffery A fast and accurate method for large-scale de novo peptide structure prediction J. Comput. Chem. 31 4 2010 726 738
51. J. Maupetit, P. Tuffery, and P. Derreumaux A coarse-grained protein force field for folding and structure prediction Proteins 69 2 2007 394 408
52. H. Kaur, A. Garg, and G.P. Raghava PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides Protein. Pept. Lett. 14 7 2007 626 631
53. Z. Wang, J. Eickholt, and J. Cheng APOLLO: a quality assessment service for single and multiple protein models Bioinformatics 27 12 2011 1715 1716
54. J. Beaufays, L. Lins, A. Thomas, and R. Brasseur In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues J. Pept. Sci. 18 2012 17 24
55. M.L. Connolly Solvent-accessible surfaces of proteins and nucleic-acids Science 221 1983 709 713
56. A.T. Macias, and A.D. MacKerell CH/π interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field J. Comput. Chem. 26 2005 1452 1463
57. C.A. Hunter, and J.K.M. Sanders Dabco-metalloporphyrin binding: ternary complexes, host-guest chemistry and the measurement of pi-pi interactions J. Am. Chem. Soc. 112 1990 5525 5534
58. G. Raffaini, and F. Ganazzoli Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface Langmuir 20 2004 3371 3378
59. G. Raffaini, and F. Ganazzoli Simulation study of the interaction of some albumin subdomains with a flat graphite surface Langmuir 19 2003 3403 3412
60. G. Raffaini, and F. Ganazzoli Surface ordering of proteins adsorbed on graphite J. Phys. Chem. B 108 2004 13850 13854
61. G. Raffaini, and F. Ganazzoli Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface Langmuir 20 2004 3371 3378
62. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graphics 14 1996 33 38
63. J. Zielkiewicz Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water J. Chem. Phys. 123 2005 104501 104506
64. W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
65. S.S. Karajanagi, A.A. Vertegel, R.S. Kane, and J.S. Dordick Structure and function of enzymes adsorbed onto single-walled carbon nanotubes Langmuir 20 2004 11594 11599
66. D. Dutta, S.K. Sundaram, J.G. Teeguarden, B. Joseph, L.S. Fifield, and J.M. Jacobs Adsorbed proteins influence the biological activity and molecular targeting of nano-materials Toxicol. Sci. 100 2007 303 315