Special Issue:
TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics
|
TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics |
Prev
Next
|
|
|
Computational studies on the interactions of nanomaterials with proteins and their impacts |
An De-Yi (安德义)a b, Su Ji-Guo (苏计国)b, Li Chun-Hua (李春华)c, Li Jing-Yuan (李敬源)a |
a CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Science (CAS), Beijing 100049, China;
b College of Science, Yanshan University, Qinhuangdao 066004, China;
c College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China |
|
|
Abstract The intensive concern over the biosafety of nanomaterials demands the systematic study of the mechanisms underlying their biological effects. Many of the effects of nanomaterials can be attributed to their interactions with proteins and their impacts on protein function. On the other hand, nanomaterials show potential for a variety of biomedical applications, many of which also involve direct interactions with proteins. In this paper, we review some recent computational studies on this subject, especially those investigating the interactions of carbon and gold nanomaterials. Beside hydrophobic and π-stacking interactions, the mode of interaction of carbon nanomaterials can also be regulated by their functional groups. The coatings of gold nanomaterials similarly adjust their mode of interaction, in addition to coordination interactions with the sulfur groups of cysteine residues and the imidazole groups of histidine residues. Nanomaterials can interact with multiple proteins and their impacts on protein activity are attributed to a wide spectrum of mechanisms. These findings on the mechanisms of nanomaterial-protein interactions can further guide the design and development of nanomaterials to realize their application in disease diagnosis and treatment.
|
Received: 01 May 2015
Revised: 08 July 2015
Accepted manuscript online:
|
PACS:
|
05.70.Np
|
(Interface and surface thermodynamics)
|
|
81.07.Nb
|
(Molecular nanostructures)
|
|
83.10.Rs
|
(Computer simulation of molecular and particle dynamics)
|
|
87.15.ap
|
(Molecular dynamics simulation)
|
|
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 21273240, 11204267, and 11474013). |
Corresponding Authors:
Li Chun-Hua, Li Jing-Yuan
E-mail: chunhuali@bjut.edu.cn;lijingyuan@ihep.ac.cn
|
Cite this article:
An De-Yi (安德义), Su Ji-Guo (苏计国), Li Chun-Hua (李春华), Li Jing-Yuan (李敬源) Computational studies on the interactions of nanomaterials with proteins and their impacts 2015 Chin. Phys. B 24 120504
|
[1] |
Ball P and Garwin L 1992 Nature 355 761
|
[2] |
Halperin W P 1986 Rev. Mod. Phys. 58 533
|
[3] |
Steigerwald M L and Brus L E 1990 ACC Chem. Res. 23 183
|
[4] |
Wang Y 1991 ACC Chem. Res. 24 133
|
[5] |
Weller H 1993 Adv. Mater. 5 88
|
[6] |
Wang X F, Zhu M T and Li J Y 2012 Chin. J. Chem. 30 1931
|
[7] |
Zuo G H, Kang S G, Xiu P, Zhao Y L and Zhou R H 2013 Small 9 1546
|
[8] |
Subbiah R, Veerapandian M and Yun K S 2010 Curr. Med. Chem. 17 4559
|
[9] |
Kim B Y, Rutka J T and Chan W C 2010 N. Engl. J. Med. 363 2434
|
[10] |
Delehanty J B, Boeneman K, Bradburne C E, Robertson K and Medintz I L 2009 Expert Opin. Drug Deliv. 6 1091
|
[11] |
Choi H S and Frangioni J V 2010 Mol. Imaging 9 291
|
[12] |
Janib S M, Moses A S and MacKay J A 2010 Adv. Drug Deliv. Rev. 62 1052
|
[13] |
Oliveira J M, Salgado A J, Sousa N, Mano J F and Reis R L 2010 Prog. Polym. Sci. 35 1163
|
[14] |
Ahmad M Z, Akhter S, Jain G K, Rahman M, Pathan S A, Ahmad F J and Khar R K 2010 Expert Opin. Drug Deliv. 7 927
|
[15] |
Mahmoudi M, Lynch I, Ejtehadi M R, Monopoli M P, Bombelli F B and Laurent S 2011 Chem. Rev. 111 5610
|
[16] |
Dror R O, Jensen M O, Borhani D W and Shaw D E 2010 J. Gen. Physiol. 135 555
|
[17] |
Cai W B and Chen X Y 2007 Small 3 1840
|
[18] |
Son S J, Bai X and Lee S B 2007 Drug Discov. Today 12 650
|
[19] |
Son S J, Bai X and Lee S 2007 Drug Discov. Today 12 657
|
[20] |
Foldvari M and Bagonluri M 2008 Nanomedicine 4 173
|
[21] |
Foldvari M and Bagonluri M 2008 Nanomedicine 4 183
|
[22] |
Nel A 2005 Science 308 804
|
[23] |
Nel A, Xia T, Madler L and Li N 2006 Science 311 622
|
[24] |
Oberdorster G, Oberdorster E and Oberdorster J 2005 Environ. Health Perspect. 113 823
|
[25] |
Ma-Hock L, Treumann S, Strauss V, Brill S, Luizi F, Mertler M, Wiench K, Gamer A O, van Ravenzwaay B and Landsiedel R 2009 Toxicol. Sci. 112 468
|
[26] |
Schipper M L, Nakayama-Ratchford N, Davis C R, Kam N W S, Chu P, Liu Z, Sun X M, Dai H J and Gambhir S S 2008 Nat. Nanotechnol. 3 216
|
[27] |
Shvedova A A, Kisin E R, Mercer R, Murray A R, Johnson V J, Potapovich A I, Tyurina Y Y, Gorelik O, Arepalli S, Schwegler-Berry D, Hubbs A F, Antonini J, Evans D E, Ku B K, Ramsey D, Maynard A, Kagan V E, Castranova V and Baron P 2005 Am. J. Physiol. Lung Cell Mol. Physiol. 289 698
|
[28] |
Li Z, Hulderman T, Salmen R, Chapman R, Leonard S S, Young S H, Shvedova A, Luster M I and Simeonova P P 2007 Environ. Health Perspect. 115 377
|
[29] |
Noon W H, Kong Y and Ma J 2002 Proc. Natl. Acad. Sci. USA 99 6466
|
[30] |
Da Ros T and Prato M 1999 Chem. Commun. No. 8 663
|
[31] |
Montellano A, Da Ros T, Bianco A and Prato M 2011 Nanoscale 3 4035
|
[32] |
Anilkumar P, Lu F, Cao L, Luo P G, Liu J H, Sahu S, Tackett K N, Wang Y and Sun Y P 2011 Curr. Med. Chem. 18 2045
|
[33] |
Liang X J, Meng H, Wang Y Z, He H Y, Meng J, Lu J, Wang P C, Zhao Y L, Gao X Y, Sun B Y, Chen C Y, Xing G M, Shen D W, Gottesman M M, Wu Y, Yin J J and Jia L 2010 Proc. Natl. Acad. Sci. USA 107 7449
|
[34] |
Chen C Y, Xing G M, Wang J X, Zhao Y L, Li B, Tang J, Jia G, Wang T C, Sun J, Xing L, Yuan H, Gao Y X, Meng H, Chen Z, Zhao F, Chai Z F and Fang X H 2005 Nano Lett. 5 2050
|
[35] |
Yang D, Zhao Y L, Guo H, Li Y N, Tewary P, Xing G M, Hou W, Oppenheim J J and Zhang N 2010 ACS Nano 4 1178
|
[36] |
Liu Y, Jiao F, Qiu Y, Li W, Lao F, Zhou G Q, Sun B Y, Xing G M, Dong J Q, Zhao Y L, Chai Z F and Chen C Y 2009 Biomaterials 30 3934
|
[37] |
Wang J X, Chen C Y, Li B, Yu H W, Zhao Y L, Sun J, Li Y F, Xing G M, Yuan H, Tang J, Chen Z, Meng H, Gao Y X, Ye C, Chai Z F, Zhu C F, Ma B C, Fang X H and Wan L J 2006 Biochem. Pharmacol. 71 872
|
[38] |
Meng H, Xing G M, Sun B Y, Zhao F, Lei H, Li W, Song Y, Chen Z, Yuan H, Wang X X, Long J, Chen C Y, Liang X J, Zhang N, Chai Z F and Zhao Y L 2010 ACS Nano 4 2773
|
[39] |
Meng H, Xing G M, Blanco E, Song Y, Zhao L N, Sun B Y, Li X D, Wang P C, Korotcov A, Li W, Liang X J, Chen C Y, Yuan H, Zhao F, Chen Z, Sun T, Chai Z F, Ferrari M and Zhao Y L 2012 Nanomedicine 8 136
|
[40] |
Kang S G, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y and Zhou R 2012 Proc. Natl. Acad. Sci. USA 109 15431
|
[41] |
Kadler K E, Holmes D F, Trotter J A and Chapman J A 1996 Biochem. J. 316 1
|
[42] |
Myllyharju J and Kivirikko K I 2001 Ann. Med. 33 7
|
[43] |
Myllyharju J and Kivirikko K I 2004 Trends Genet. 20 33
|
[44] |
Viguet-Carrin S, Garnero P and Delmas P D 2006 Osteoporos. Int. 17 319
|
[45] |
Grabowska M 1959 Nature 183 1186
|
[46] |
Yin X, Zhao L, Kang S G, Pan J, Song Y, Zhang M, Xing G, Wang F, Li J, Zhou R and Zhao Y 2013 Nanoscale 5 7341
|
[47] |
Balamurugan K, Gopalakrishnan R, Raman S S and Subramanian V 2010 J. Phys. Chem. B 114 14048
|
[48] |
Zuo G H, Huang Q, Wei G H, Zhou R H and Fang H P 2010 ACS Nano 4 7508
|
[49] |
Balamurugan K, Singam E R A and Subramanian V 2011 J. Phys. Chem. C 115 8886
|
[50] |
Ge C C, Du J F, Zhao L N, Wang L M, Liu Y, Li D H, Yang Y L, Zhou R H, Zhao Y L, Chai Z F and Chen C Y 2011 Proc. Natl. Acad. Sci. USA 108 16968
|
[51] |
Bachmann A, Kiefhaber T, Boudko S, Engel J and Bachinger H P 2005 Proc. Natl. Acad. Sci. USA 102 13897
|
[52] |
Engel J and Bachinger H P
|
[53] |
Dai N, Wang X J and Etzkorn F A 2008 J. Am. Chem. Soc. 130 5396
|
[54] |
Veld P J and Stevens M J 2008 Biophys. J. 95 33
|
[55] |
Gurry T, Nerenberg P S and Stultz C M 2010 Biophys. J. 98 2634
|
[56] |
Raman S S, Gopalakrishnan R, Wade R C and Subramanian V 2011 J. Phys. Chem. B 115 2593
|
[57] |
Iijima S 1991 Nature 354 56
|
[58] |
Zanello L P, Zhao B, Hu H and Haddon R C 2006 Nano Lett. 6 562
|
[59] |
Prato M, Kostarelos K and Bianco A 2008 ACC Chem. Res. 41 60
|
[60] |
Bhirde A A, Patel V, Gavard J, Zhang G F, Sousa A A, Masedunskas A, Leapman R D, Weigert R, Gutkind J S and Rusling J F 2009 ACS Nano 3 307
|
[61] |
Tu X M, Manohar S, Jagota A and Zheng M 2009 Nature 460 250
|
[62] |
Thakare V S, Das M, Jain A K, Patil S and Jain S 2010 Nanomedicine 5 1277
|
[63] |
Chen H I and Sudol M 1995 Proc. Natl. Acad. Sci. USA 92 7819
|
[64] |
Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K and Lehman D 1995 J. Biol. Chem. 270 14733
|
[65] |
Lu P J, Wulf G, Zhou X Z, Davies P and Lu K P 1999 Nature 399 784
|
[66] |
Garrus J E, von Schwedler U K, Pornillos O W, Morham S G, Zavitz K H, Wang H E, Wettstein D A, Stray K M, Cote M, Rich R L, Myszka D G and Sundquist W I 2001 Cell 107 55
|
[67] |
Zheng H W, You H, Zhou X Z, Murray S A, Uchida T, Wulf G, Gu L, Tang X R, Lu K P and Xiao Z X J 2002 Nature 419 849
|
[68] |
Gao J, Wang L, Kang S G, Zhao L, Ji M, Chen C, Zhao Y, Zhou R and Li J 2014 Nanoscale 6 12828
|
[69] |
Chin D and Means A R 2000 Trends Cell Biol. 10 322
|
[70] |
Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee C B and Bax A 1995 Nat. Struct. Biol. 2 768
|
[71] |
Shen X C, Valencia C A, Szostak J, Dong B and Liu R H 2005 Proc. Natl. Acad. Sci. USA 102 5969
|
[72] |
Ikura M, Clore G M, Gronenborn A M, Zhu G, Klee C B and Bax A 1992 Science 256 632
|
[73] |
Crivici A and Ikura M 1995 Ann. Rev. Biophys. Biomol. Struct. 24 85
|
[74] |
Brokx R D, Lopez M M, Vogel H J and Makhatadze G I 2001 J. Biol. Chem. 276 14083
|
[75] |
Yang C, Jas G S and Kuczera K 2004 Biochim. Biophys. Acta 1697 289
|
[76] |
Novoselov K S, Geim A K, Morozov S V, Jiang D, Katsnelson M I, Grigorieva I V, Dubonos S V and Firsov A A 2005 Nature 438 197
|
[77] |
Feng L Z and Liu Z A 2011 Nanomedicine 6 317
|
[78] |
Zuo G, Zhou X, Huang Q, Fang H and Zhou R 2011 J. Phys. Chem. C 115 23323
|
[79] |
Tu Y, Lv M, Xiu P, Huynh T, Zhang M, Castelli M, Liu Z, Huang Q, Fan C, Fang H and Zhou R 2013 Nat. Nanotechnol. 8 594
|
[80] |
Li Y, Yuan H, von dem Bussche A, Creighton M, Hurt R H, Kane A B and Gao H 2013 Proc. Natl. Acad. Sci. USA 110 12295
|
[81] |
Chen J Y, Wang D L, Xi J F, Au L, Siekkinen A, Warsen A, Li Z Y, Zhang H, Xia Y N and Li X D 2007 Nano Lett. 7 1318
|
[82] |
Chithrani B D, Ghazani A A and Chan W C W 2006 Nano Lett. 6 662
|
[83] |
Qiu Y, Liu Y, Wang L M, Xu L G, Bai R, Ji Y L, Wu X C, Zhao Y L, Li Y F and Chen C Y 2010 Biomaterials 31 7606
|
[84] |
Maiorano G, Sabella S, Sorce B, Brunetti V, Malvindi M A, Cingolani R and Pompa P P 2010 ACS Nano 4 7481
|
[85] |
Hu W B, Peng C, Lv M, Li X M, Zhang Y J, Chen N, Fan C H and Huang Q 2011 ACS Nano 5 3693
|
[86] |
Lesniak A, Fenaroli F, Monopoli M R, Aberg C, Dawson K A and Salvati A 2012 ACS Nano 6 5845
|
[87] |
Wang F J, Yu L, Monopoli M P, Sandin P, Mahon E, Salvati A and Dawson K A 2013 Nanomedicine 9 1159
|
[88] |
Wang L M, Liu Y, Li W, Jiang X M, Ji Y L, Wu X C, Xu L G, Qiu Y, Zhao K, Wei T T, Li Y F, Zhao Y L and Chen C Y 2011 Nano Lett. 11 772
|
[89] |
Larson T A, Joshi P R and Sokolov K 2012 ACS Nano 6 9182
|
[90] |
Walkey C D, Olsen J B, Guo H B, Emili A and Chan W C W 2012 J. Am. Chem. Soc. 134 2139
|
[91] |
Deng Z J, Liang M T, Monteiro M, Toth I and Minchin R F 2011 Nat. Nanotechnol. 6 39
|
[92] |
Wang L, Li J, Pan J, Jiang X, Ji Y, Li Y, Qu Y, Zhao Y, Wu X and Chen C 2013 J. Am. Chem. Soc. 135 17359
|
[93] |
Rompel A, Cinco R M, Latimer M J, McDermott A E, Guiles R D, Quintanilha A, Krauss R M, Sauer K, Yachandra V K and Klein M P 1998 Proc. Natl. Acad. Sci. USA 95 6122
|
[94] |
Zhang F C 2003 Phys. Rev. Lett. 90 207002
|
[95] |
Chai Z F, Zhang Z Y, Feng W Y, Chen C Y, Xu D D and Hou X L 2004 J. Anal. At. Spectrom. 19 26
|
[96] |
Qu Y, Li W, Zhou Y L, Liu X F, Zhang L L, Wang L M, Li Y F, Iida A, Tang Z Y, Zhao Y L, Chai Z F and Chen C Y 2011 Nano Lett. 11 3174
|
[97] |
Chen C Y, Li Y F, Qu Y, Chai Z F and Zhao Y L 2013 Chem. Soc. Rev. 42 8266
|
[98] |
Vairavamurthy A 1998 Spectrochim. Acta, Part A: Mol. Biomol. Spectrosc. 54 2009
|
[99] |
Mcrae R, Lai B, Vogt S and Fahrni C J 2006 J. Struct. Biol. 155 22
|
[100] |
Bohic S, Murphy K, Paulus W, Cloetens P, Salome M, Susini J and Double K 2008 Anal. Chem. 80 9557
|
[101] |
Corezzi S, Urbanelli L, Cloetens P, Emiliani C, Helfen L, Bohic S, Elisei F and Fioretto D 2009 Anal. Biochem. 388 33
|
[102] |
Zheng J, Zhang C W and Dickson R M 2004 Phys. Rev. Lett. 93 077402
|
[103] |
Zheng J, Nicovich P R and Dickson R M 2007 Ann. Rev. Phys. Chem. 58 409
|
[104] |
Guo W W, Yuan J P and Wang E K 2009 Chem. Commun. 3395
|
[105] |
Huang C C, Yang Z, Lee K H and Chang H T 2007 Angew. Chem. Int. Ed. 46 6824
|
[106] |
Luedtke W D and Landman U 1996 J. Phys. Chem. 100 13323
|
[107] |
Le Guevel X, Hotzer B, Jung G, Hollemeyer K, Trouillet V and Schneider M 2011 J. Phys. Chem. C 115 10955
|
[108] |
Padovan-Merhar O, Lara F V and Starr F W 2011 J. Chem. Phys. 134 244701
|
[109] |
Sun C J, Yuan Y, Xu Z H, Ji T J, Tian Y H, Wu S, Lei J L, Li J Y, Gao N and Nie G J 2015 Bioconjugate Chem. 26 193
|
[110] |
Sun C J, Yang H, Yuan Y, Tian X, Wang L M, Guo Y, Xu L, Lei J L, Gao N, Anderson G J, Liang X J, Chen C Y, Zhao Y L and Nie G J 2011 J. Am. Chem. Soc. 133 8617
|
[111] |
Wang Y L, Cui Y Y, Liu R, Wei Y T, Jiang X G, Zhu H R, Gao L, Zhao Y L, Chai Z F and Gao X Y 2013 Chem. Commun. 49 10724
|
[112] |
Liu R, Wang Y L, Yuan Q, An D Y, Li J Y and Gao X Y 2014 Chem. Commun. 50 10687
|
[113] |
Soderberg A, Sahaf B and Rosen A 2000 Cancer Res. 60 2281
|
[114] |
Fang J G, Lu J and Holmgren A 2005 J. Biol. Chem. 280 25284
|
[115] |
Berggren M, Gallegos A, Gasdaska J R, Gasdaska P Y, Warneke J and Powis G 1996 Anticancer Res. 16 3459
|
[116] |
Kahlos K, Soini Y, Saily M, Koistinen P, Kakko S, Paakko P, Holmgren A and Kinnula V L 2001 Int. J. Cancer 95 198
|
[117] |
Chen R, Li L and Weng Z P 2003 Proteins: Struct. Funct. Bioinform. 52 80
|
[118] |
An D, Su J, Weber J K, Gao X, Zhou R and Li J 2015 J. Am. Chem. Soc. in press
|
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
Altmetric
|
blogs
Facebook pages
Wikipedia page
Google+ users
|
Online attention
Altmetric calculates a score based on the online attention an article receives. Each coloured thread in the circle represents a different type of online attention. The number in the centre is the Altmetric score. Social media and mainstream news media are the main sources that calculate the score. Reference managers such as Mendeley are also tracked but do not contribute to the score. Older articles often score higher because they have had more time to get noticed. To account for this, Altmetric has included the context data for other articles of a similar age.
View more on Altmetrics
|
|
|