Nanomaterials in biological environment: A review of computer modelling studies

European Biophysics Journal

Volumn 40, Issue 2, 2011, Pages 103-115

  Makarucha, A J ^a   Todorova, N ^a   Yarovsky, I ^a  

^a RMIT UNIVERSITY   (Australia)

Author keywords

Biological membranes; DNA; Molecular simulation; Nanomaterials; Nanoparticles; Nanotoxicology; Peptide decorated nanoparticles; Proteins; Water

Indexed keywords

NANOMATERIAL;

BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ENVIRONMENTAL MONITORING; METHODOLOGY; REVIEW;

COMPUTER SIMULATION; ENVIRONMENTAL MONITORING; MODELS, BIOLOGICAL; NANOSTRUCTURES;

EID: 79955668060     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-010-0651-6     Document Type: Review

References (106)

1. Alexeev A, Uspal WE, Balazs AC (2008) Harnessing Janus nanoparticles to create controllable pores in membranes. ACS Nano 2:1117-1122
2. Alivisatos AP, Gu WW, Larabell C (2005) Quantum dots as cellular probes. Annu Rev Biomed Eng 7:55-76 (Pubitemid 41170185)
3. Aubin-Tam ME, Hwang W, Hamad-Schifferli K (2009) Site-directed nanoparticle labeling of cytochrome c. Proc Natl Acad Sci USA 106:4095-4100
4. Auer S, Trovato A, Vendruscolo M (2009) A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation. PLoS Comput Biol 5:e1000458
5. Barth JV, Costantini G, Kern K (2005) Engineering atomic and molecular nanostructures at surfaces. Nature 437:671-679 (Pubitemid 41486530)
6. Barlow PG, Donaldson K, MacCallum J, Clouter A, Stone V (2005) Serum exposed to nanoparticle carbon black displays increased potential to induce macrophage migration. Toxicol Lett 155:397-401 (Pubitemid 40093003)
7. Bedrov D, Smith GD, Davande H, Li LW (2008) Passive transport of C-60 fullerenes through a lipid membrane: a molecular dynamics simulation study. J Phys Chem B 112:2078-2084 (Pubitemid 351316332)
8. Bjelkmar P, Niemela PS, Vattulainen I, Lindahl E (2009) Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel. PLoS Comput Biol 5:e1000289
9. Brunner TJ, Wick P, Manser P, Spohn P, Grass RN, Limbach LK, Bruinink A, Stark WJ (2006) In vitro cytotoxicity of oxide nanoparticles: comparison to asbestos, silica, and the effect of particle solubility. Environ Sci Technol 40:4374-4381 (Pubitemid 44092369)
10. Burcham P (2010) Nanotoxicology: a primer for chemists chemistry in australia, vol 77. Royal Australian Chemical Institute Inc., Australia, pp 18-22
11. Carlsson F, Hyltner E, Arnebrant T, Malmsten M, Linse P (2004) Lysozyme adsorption to charged surfaces. A Monte Carlo study. J Phys Chem B 108:9871-9881
12. Chang CI, Lee WJ, Young TF, Ju SP, Chang CW, Chen HL, Chang JG (2008) Adsorption mechanism of water molecules surrounding Au nanoparticles of different sizes. J Chem Phys 128:154703
13. Chen Q, Wang Q, Liu YC, Wu T, Kang Y, Moore JD, Gubbins KE (2009) Energetics investigation on encapsulation of protein/ peptide drugs in carbon nanotubes. J Chem Phys 131:015101
14. Chiu CC, Dieckmann GR, Nielsen SO (2008) Molecular dynamics study of a nanotube-binding amphiphilic helical peptide at different water/hydrophobic interfaces. J Phys Chem B 112:16326-16333
15. Chiu CC, Dieckmann GR, Nielsen SO (2009a) Role of peptidepeptide interactions in stabilizing peptide-wrapped single-walled carbon nanotubes: a molecular dynamics study. Biopolymers 92:156-163
16. Chiu CC, Moore PB, Shinoda W, Nielsen SO (2009b) Size-dependent hydrophobic to hydrophilic transition for nanoparticles: a molecular dynamics study. J Chem Phys 131:244706
17. Chiu CC, Maher MC, Dieckmann GR, Nielsen SO (2010) Molecular dynamics study of a carbon nanotube binding reversible cyclic peptide. ACS Nano 4:2539-2546
18. Choe S, Chang R, Jeon J, Violi A (2008) Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle. Biophys J 95:4102-4114
19. D'Rozario RS, Wee CL, Wallace EJ, Sansom MS (2009) The interaction of C60 and its derivatives with a lipid bilayer via molecular dynamics simulations. Nanotechnology 20:115102
20. De Jong WH, Borm PJA (2008) Drug delivery and nanoparticles: applications and hazards. Int J Nanomed 3:133-149 (Pubitemid 352042401)
21. Debouck C, Goodfellow PN (1999) DNA microarrays in drug discovery and development. Nat Genet 21:48-50 (Pubitemid 29031492)
22. Deng XY, Luan QX, Chen WT, Wang YL, Wu MH, Zhang HJ, Jiao Z (2009) Nanosized zinc oxide particles induce neural stem cell apoptosis. Nanotechnology 20:115101
23. Dong XL, Wang Q, Wu T, Pan HH (2007) Understanding adsorptiondesorption dynamics of BMP-2 on hydroxyapatite (001) surface. Biophys J 93:750-759 (Pubitemid 47219770)
24. Dror RO, Arlow DH, Borhani DW, Jensen MO, Piana S, Shaw DE (2009) Identification of two distinct inactive conformations of the beta(2)-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 106:4689-4694
25. Dror RO, Jensen MO, Borhani DW, Shaw DE (2010) Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol 135:555-562
26. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet 21:10-14 (Pubitemid 29031485)
27. Feris K, Otto C, Tinker J, Wingett D, Punnoose A, Thurber A, Kongara M, Sabetian M, Quinn B, Hanna C, Pink D (2010) Electrostatic interactions affect nanoparticle-mediated toxicity to gram-negative bacterium Pseudomonas aeruginosa PAO1. Langmuir 26:4429-4436
28. Fischer HC, Chan WCW (2007) Nanotoxicity: the growing need for in vivo study. Curr Opin Biotechnol 18:565-571
29. Friling SR, Notman R, Walsh TR (2010) Probing diameter-selective solubilisation of carbon nanotubes by reversible cyclic peptides using molecular dynamics simulations. Nanoscale 2:98-106
30. Gao HJ, Kong Y, Cui DX, Ozkan CS (2003) Spontaneous insertion of DNA oligonucleotides into carbon nanotubes. Nano Lett 3:471-473 (Pubitemid 37140647)
31. Geiser M, Rothen-Rutishauser B, Kapp N, Schurch S, Kreyling W, Schulz H, Semmler M, Im Hof V, Heyder J, Gehr P (2005) Ultrafine particles cross cellular membranes by nonphagocytic mechanisms in lungs and in cultured cells. Environ Health Perspect 113:1555-1560 (Pubitemid 41614911)
32. Ghorai PK, Glotzer SC (2007) Molecular dynamics simulation study of self-assembled monolayers of alkanethiol surfactants on spherical gold nanoparticles. J Phys Chem C 111:15857-15862 (Pubitemid 350097651)
33. Ginzburg VV, Balijepailli S (2007) Modeling the thermodynamics of the interaction of nanoparticles with cell membranes. Nano Lett 7:3716-3722
34. Gu FX, Karnik R, Wang AZ, Alexis F, Levy-Nissenbaum E, Hong S, Langer RS, Farokhzad OC (2007) Targeted nanoparticles for cancer therapy. Nano Today 2:14-21 (Pubitemid 46672835)
35. Gunasekera UA, Pankhurst QA, Douek M (2009) Imaging applications of nanotechnology in cancer. Target Oncol 4:169-181
36. Hanley C, Layne J, Punnoose A, Reddy KM, Coombs I, Coombs A, Feris K, Wingett D (2008) Preferential killing of cancer cells and activated human T cells using ZnO nanoparticles. Nanotechnology 19:295103
37. Houili H, Tutis E, Izquierdo R (2010) Modeling nanoparticle embedded organic memory devices. Org Electron 11:514-520
38. Hung A, Mwenifumbo S, Mager M, Hembury M, Stellacci F, Yarovsky I, Stevens M (2011) Ordering surfaces on the nanoscale: implications for protein adsorption. J Am Chem Soc (in press)
39. Hwang H, Schatz GC, Ratner MA (2009) Coarse-grained molecular dynamics study of cyclic peptide nanotube insertion into a lipid bilayer. J Phys Chem A 113:4780-4787
40. Jackson AM, Myerson JW, Stellacci F (2004) Spontaneous assembly of subnanometre-ordered domains in the ligand shell of monolayer- protected nanoparticles. Nat Mater 3:330-336
41. Johnson RR, Johnson AT, Klein ML (2008) Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics. Nano Lett 8:69-75 (Pubitemid 351177777)
42. Johnson RR, Kohlmeyer A, Johnson ATC, Klein ML (2009) Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics. Nano Lett 9:537-541
43. Kilpadi KL, Chang PL, Bellis SL (2001) Hydroxylapatite binds more serum proteins, purified integrins, and osteoblast precursor cells than titanium or steel. J Biomed Mater Res 57:258-267 (Pubitemid 32988505)
44. Klein J (2007) Probing the interactions of proteins and nanoparticles. Proc Natl Acad Sci USA 104:2029-2030 (Pubitemid 46391345)
45. Kubiak K, Mulheran PA (2009) Molecular dynamics simulations of hen egg white lysozyme adsorption at a charged solid surface. J Phys Chem B 113:12189-12200
46. Kuna JJ, Voitchovsky K, Singh C, Jiang H, Mwenifumbo S, Ghorai PK, Stevens MM, Glotzer SC, Stellacci F (2009) The effect of nanometre-scale structure on interfacial energy. Nat Mater 8:837-842
47. Kyani A, Goliaei B (2009) Binding free energy calculation of peptides to carbon nanotubes using molecular dynamics with a linear interaction energy approach. J Mol Struct-Theochem 913:63-69
48. Leach AR (2001) Molecular modelling: principles and applications, 2nd edn. Pearson Education, Harlow, England.
49. Lee OS, Schatz GC (2009a) Interaction between DNAs on a gold surface. J Phys Chem C 113:15941-15947
50. Lee OS, Schatz GC (2009b) Molecular dynamics simulation of dnafunctionalized gold nanoparticles. J Phys Chem C 113:2316-2321
51. Lewinski N, Colvin V, Drezek R (2008) Cytotoxicity of nanoparticles. Small 4:26-49
52. Li Y, Gu N (2010) Thermodynamics of charged nanoparticle adsorption on charge-neutral membranes: a simulation study. J Phys Chem B 114:2749-2754
53. Li LW, Bedrov D, Smith GD (2006) Water-induced interactions between carbon nanoparticles. J Phys Chem B 110:10509-10513 (Pubitemid 43952946)
54. Li LW, Davande H, Bedrov D, Smith GD (2007) A molecular dynamics simulation study of C-60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer. J Phys Chem B 111:4067-4072 (Pubitemid 46732954)
55. Li Y, Chen X, Gu N (2008) Computational investigation of interaction between nanoparticles and membranes: hydrophobic/ hydrophilic effect. J Phys Chem B 112:16647-16653 ]
56. Liang LJ, Wang Q, Wu T, Shen JW, Kang Y (2009) Molecular dynamics simulation on stability of insulin on graphene. Chin J Chem Phys 22:627-634
57. Lin YW, Liu CW, Chang HT (2009) DNA functionalized gold nanoparticles for bioanalysis. Anal Methods 1:14-24
58. Lin J, Zhang H, Chen Z, Zheng Y (2010) Penetration of lipid membranes by gold nanoparticles: insights into cellular uptake, cytotoxicity, and their relationship. ACS Nano 4:5421-5429
59. Linse S, Cabaleiro-Lago C, Xue WF, Lynch I, Lindman S, Thulin E, Radford SE, Dawson KA (2007) Nucleation of protein fibrillation by nanoparticles. Proc Natl Acad Sci USA 104:8691-8696 (Pubitemid 47175373)
60. Lu G, Maragakis P, Kaxiras E (2005) Carbon nanotube interaction with DNA. Nano Lett 5:897-900 (Pubitemid 40749050)
61. Mailander V, Landfester K (2009) Interaction of nanoparticles with cells. Biomacromolecules 10:2379-2400
62. Marrink SJ, de Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108:750-760
63. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111:7812-7824 (Pubitemid 47169693)
64. Martin W, Zhu W, Krilov G (2008) Simulation study of noncovalent hybridization of carbon nanotubes by single-stranded dna in water. J Phys Chem B 112(50):16076-16089
65. McBain SC, Yiu HHP, Dobson J (2008) Magnetic nanoparticles for gene and drug delivery. Int J Nanomed 3:169-180 (Pubitemid 352037850)
66. Mills NL, Tornqvist H, Robinson SD, Gonzalez M, Darnley K, MacNee W, Boon NA, Donaldson K, Blomberg A, Sandstrom T, Newby DE (2005) Diesel exhaust inhalation causes vascular dysfunction and impaired endogenous fibrinolysis. Circulation 112:3930-3936 (Pubitemid 43739491)
67. Monticelli L, Salonen E, Ke PC, Vattulainen I (2009) Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective. Soft Matter 5:4433-4445
68. Nel A, Xia T, Madler L, Li N (2006) Toxic potential of materials at the nanolevel. Science 311:622-627 (Pubitemid 43191298)
69. Noon WH, Kong YF, Ma JP (2002) Molecular dynamics analysis of a buckyball-antibody complex. Proc Natl Acad Sci USA 99:6466-6470 (Pubitemid 34492352)
70. Ohno Y, Maehashi K, Yamashiro Y, Matsumoto K (2009) Electrolyte- gated graphene field-effect transistors for detecting pH protein adsorption. Nano Lett 9:3318-3322
71. Patil AJ, Vickery JL, Scott TB, Mann S (2009) Aqueous stabilization and self-assembly of graphene sheets into layered bio-nanocomposites using DNA. Adv Mater 21:3159
72. Peetla C, Rao KS, Labhasetwar V (2009) Relevance of biophysical interactions of nanoparticles with a model membrane in predicting cellular uptake: study with tat peptide-conjugated nanoparticles. Mol Pharm 6:1311-1320
73. Pei QX, Lim CG, Cheng Y, Gao HJ (2008) Molecular dynamics study on DNA oligonucleotide translocation through carbon nanotubes. J Chem Phys 129:125101
74. Pellenc D, Bennett RA, Green RJ, Sperrin M, Mulheran PA (2008) New insights on growth mechanisms of protein clusters at surfaces: an AFM and simulation study. Langmuir 24:9648-9655
75. Qiao R, Roberts AP, Mount AS, Klaine SJ, Ke PC (2007) Translocation of C-60 and its derivatives across a lipid bilayer. Nano Lett 7:614-619 (Pubitemid 46516035)
76. Raffaini G, Ganazzoli F (2004) Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface. Langmuir 20:3371-3378
77. Reddy KM, Feris K, Bell J, Wingett DG, Hanley C, Punnoose A (2007) Selective toxicity of zinc oxide nanoparticles to prokaryotic and eukaryotic systems. Appl Phys Lett 90:213902
78. Roman T, Dino WA, Nakanishi H, Kasai H (2006) Amino acid adsorption on single-walled carbon nanotubes. Eur Phys J D 38:117-120 (Pubitemid 43401972)
79. Rueckerl F, Kaes JA, Selle C (2008) Diffusion of nanoparticles in monolayers is modulated by domain size. Langmuir 24:3365-3369 (Pubitemid 351549177)
80. Sachs JN, Woolf TB (2003) Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations. J Am Chem Soc 125:8742-8743 (Pubitemid 36886209)
81. Salata O (2004) Applications of nanoparticles in biology and medicine. J Nanobiotech 2:3
82. Shan CS, Yang HF, Song JF, Han DX, Ivaska A, Niu L (2009) Direct electrochemistry of glucose oxidase and biosensing for glucose based on graphene. Anal Chem 81:2378-2382
83. Shen JW, Wu T, Wang Q, Kang Y (2008a) Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces. Biomaterials 29:3847-3855
84. Shen JW, Wu T, Wang Q, Pan HH (2008b) Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. Biomaterials 29:513-532 (Pubitemid 350100806)
85. Shi XH, Kong Y, Gao HJ (2008) Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane. Acta Mech Sin 24:161-169
86. Smith GD, Bedrov D (2007) Transport of C-60 fullerenes through a lipid membrane: a molecular dynamics simulation study. In: Abstracts of the 51st annual meeting of the biophysical-society, Biophysical society, Baltimore, 65a-66a
87. Suzuki O, Kamakura S, Katagiri T, Nakamura M, Zhao BH, Honda Y, Kamijo R (2006) Bone formation enhanced by implanted octacalcium phosphate involving conversion into Ca-deficient hydroxyapatite. Biomaterials 27:2671-2681 (Pubitemid 43122071)
88. Theron J, Walker JA, Cloete TE (2008) Nanotechnology and water treatment: applications and emerging opportunities. Critical Rev Microbiol 34:43-69 (Pubitemid 351225501)
89. Titov AV, Kral P, Pearson R (2010) Sandwiched graphene- membrane superstructures. ACS Nano 4:229-234
90. Todorova N, Marakucha A, Yarovsky I (in preparation) Effect of carbonaceous nanoparticles on peptide structure and dynamics: insights from all-atom simulations
91. Todorova N, Legge FS, Treutlein H, Yarovsky I (2008) Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin. J Phys Chem B 112:11137-11146
92. Verma A, Stellacci F (2010) Effect of surface properties on nanoparticle-cell interactions. Small 6:12-21
93. Wallace EJ, Sansom MSP (2007) Carbon nanotube/detergent interactions via coarse-grained molecular dynamics. Nano Lett 7:1923-1928 (Pubitemid 47197568)
94. Wallace EJ, Sansom MSP (2008) Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study. Nano Lett 8:2751-2756
95. Wallace EJ, Sansom MSP (2009) Carbon nanotube self-assembly with lipids and detergent: a molecular dynamics study. Nanotechnology 20:045101
96. Wang HW, Michielssens S, Moors SLC, Ceulemans A (2009) Molecular dynamics study of dipalmitoylphosphatidylcholine lipid layer self-assembly onto a single-walled carbon nanotube. Nano Res 2:945-954
97. Weiss DR, Raschke TM, Levitt M (2008) How hydrophobic Buckminsterfullerene affects surrounding water structure. J Phys Chem B 112:2981-2990
98. Wong-Ekkabut J, Baoukina S, Triampo W, Tang IM, Tieleman DP, Monticelli L (2008) Computer simulation study of fullerene translocation through lipid membranes. Nat Nanotechnol 3:363-368 (Pubitemid 351809610)
99. Xie YH, Kong Y, Soh AK, Gao HJ (2007) Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane. J Chem Phys 127:225101
100. Yang K, Ma YQ (2010) Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer. Nat Nanotechnol 5:579-583
101. Yang WR, Thordarson P, Gooding JJ, Ringer SP, Braet F (2007) Carbon nanotubes for biological and biomedical applications. Nanotechnology 18:412001
102. Yarovsky I, Hearn MTW, Aguilar MI (1997) Molecular simulation of peptide interactions with an RP-HPLC sorbent. J Phys Chem B 101:10962-10970 (Pubitemid 127585252)
103. Yiapanis G, Henry DJ, Evans E, Yarovsky I (2007) Effect of surface composition and atomic roughness on interfacial adhesion between polyester and amorphous carbon. J Phys Chem C 111:3000-3009 (Pubitemid 46384311)
104. Zhang L, Pornpattananangkul D, Hu CMJ, Huang CM (2010) Development of nanoparticles for antimicrobial drug delivery. Curr Med Chem 17:585-594
105. Zhao X, Striolo A, Cummings PT (2005) C60 binds to and deforms nucleotides. Biophys J 89:3856-3862 (Pubitemid 41725607)
106. Zhao WT, Lin L, Hsing IM (2009) Rapid synthesis of DNAfunctionalized gold nanoparticles in salt solution using mononucleotide- mediated conjugation. Bioconjug Chem 20:1218-1222