Please wait a minute...
Chin. Phys. B, 2016, Vol. 25(1): 018704    DOI: 10.1088/1674-1056/25/1/018704
Special Issue: TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics
TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics Prev   Next  

Amyloid-β peptide aggregation and the influence of carbon nanoparticles

Wen-Hui Xi(郗文辉) and Guang-Hong Wei(韦广红)
Key Laboratory for Computational Physical Sciences (Ministry of Education), State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China
Abstract  Soluble peptides or proteins can self-aggregate into insoluble, ordered amyloid fibrils under appropriate conditions. These amyloid aggregates are the hallmarks of several human diseases ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we first introduce the common structural features of amyloid fibrils and the amyloid fibrillation kinetics determined from experimental studies. Then, we discuss the structural models of Alzheimer's amyloid-β (Aβ) fibrils derived from solid-state nuclear magnetic resonance spectroscopy. On the computational side, molecular dynamics simulations can provide atomic details of structures and the underlying oligomerization mechanisms. We finally summarize recent progress in atomistic simulation studies on the oligomerization of Aβ (including full-length Aβ and its fragments) and the influence of carbon nanoparticles.
Keywords:  Amyloid-β      oligomerization      carbon nanoparticles      molecular dynamics  
Received:  12 May 2015      Revised:  16 August 2015      Accepted manuscript online: 
PACS:  87.14.em (Fibrils (amyloids, collagen, etc.))  
  87.15.nr (Aggregation)  
  87.15.bk (Structure of aggregates)  
  87.15.ap (Molecular dynamics simulation)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11274075 and 91227102).
Corresponding Authors:  Guang-Hong Wei     E-mail:  ghwei@fudan.edu.cn

Cite this article: 

Wen-Hui Xi(郗文辉) and Guang-Hong Wei(韦广红) Amyloid-β peptide aggregation and the influence of carbon nanoparticles 2016 Chin. Phys. B 25 018704

[1] Maji S K, Perrin M H, Sawaya M R, Jessberger S, Vadodaria K, Rissman R A, Singru P S, Nilsson K P, Simon R, Schubert D, Eisenberg D, Rivier J, Sawchenko P, Vale W and Riek R 2009 Science 325 328
[2] Knowles T P, Vendruscolo M and Dobson C M 2014 Nat. Rev. Mol. Cell Biol. 15 384
[3] Selkoe D J 2001 Physiol. Rev. 81 741
[4] Shulman J M, De Jager P L and Feany M B 2011 Annu. Rev. Pathol. 6 193
[5] Prusiner S B 1991 Science 252 1515
[6] Walker F O 2007 Lancet 369 218
[7] Hoppener J W, Ahren B and Lips C J 2000 N. Engl. J. Med. 343 411
[8] Dunker A K, Silman I, Uversky V N and Sussman J L 2008 Curr. Opin. Struct. Biol. 18 756
[9] Sisodia S S, Koo E H, Beyreuther K, Unterbeck A and Price D L 1990 Science 248 492
[10] Buee L, Bussiere T, Buee-Scherrer V, Delacourte A and Hof P R 2000 Brain Res. Brain Res. Rev. 33 95
[11] Westermark P, Wernstedt C, Wilander E, Hayden D W, O'Brien T D and Johnson K H 1987 Proc. Natl. Acad. Sci. USA 84 3881
[12] Spillantini M G, Crowther R A, Jakes R, Hasegawa M and Goedert M 1998 Proc. Natl. Acad. Sci. USA 95 6469
[13] Sunde M, Serpell L C, Bartlam M, Fraser P E, Pepys M B and Blake C C 1997 J. Mol. Biol. 273 729
[14] Jan A, Adolfsson O, Allaman I, Buccarello A L, Magistretti P J, Pfeifer A, Muhs A and Lashuel H A 2011 J. Biol. Chem. 286 8585
[15] Cleary J P, Walsh D M, Hofmeister J J, Shankar G M, Kuskowski M A, Selkoe D J and Ashe K H 2005 Nat. Neurosci. 8 79
[16] Nelson R, Sawaya M R, Balbirnie M, Madsen A O, Riekel C, Grothe R and Eisenberg D 2005 Nature 435 773
[17] Eisenberg D and Jucker M 2012 Cell 148 1188
[18] Sawaya M R, Sambashivan S, Nelson R, Ivanova M I, Sievers S A, Apostol M I, Thompson M J, Balbirnie M, Wiltzius J J, McFarlane H T, Madsen A O, Riekel C and Eisenberg D 2007 Cah. Rev. The. 447 453
[19] Tycko R 2011 Annu. Rev. Phys. Chem. 62 279
[20] Jarrett J T and Lansbury Jr P T 1993 Cell 73 1055
[21] Lomakin A, Teplow D B, Kirschner D A and Benedek G B 1997 Proc. Natl. Acad. Sci. USA 94 7942
[22] Bartolini M, Naldi M, Fiori J, Valle F, Biscarini F, Nicolau D V and Andrisano V 2011 Anal. Biochem. 414 215
[23] DeToma A S, Salamekh S, Ramamoorthy A and Lim M H 2012 Chem. Soc. Rev. 41 608
[24] Theillet F X, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley P B, Gierasch L, Pielak G J, Elcock A H, Gershenson A and Selenko P 2014 Chem. Rev. 114 6661
[25] Curtain C C, Ali F E, Smith D G, Bush A I, Masters C L and Barnham K J 2003 J. Biol. Chem. 278 2977
[26] Aisenbrey C, Borowik T, Bystrom R, Bokvist M, Lindstrom F, Misiak H, Sani M A and Grobner G 2008 Eur. Biophys. J. 37 247
[27] Linse S, Cabaleiro-Lago C, Xue W F, Lynch I, Lindman S, Thulin E, Radford S E and Dawson K A 2007 Proc. Natl. Acad. Sci. USA 104 8691
[28] Cabaleiro-Lago C, Quinlan-Pluck F, Lynch I, Lindman S, Minogue A M, Thulin E, Walsh D M, Dawson K A and Linse S 2008 J. Am. Chem. Soc. 130 15437
[29] Iwatsubo T, Odaka A, Suzuki N, Mizusawa H, Nukina N and Ihara Y 1994 Neuron 13 45
[30] Petkova A T, Ishii Y, Balbach J J, Antzutkin O N, Leapman R D, Delaglio F and Tycko R 2002 Proc. Natl. Acad. Sci. USA 99 16742
[31] Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Dobeli H, Schubert D and Riek R 2005 Proc. Natl. Acad. Sci. USA 102 17342
[32] Petkova A T, Yau W M and Tycko R 2006 Biochemistry-us. 45 498
[33] Luca S, Yau W M, Leapman R and Tycko R 2007 Biochemistry-us. 46 13505
[34] Andronesi O C, von Bergen M, Biernat J, Seidel K, Griesinger C, Mandelkow E and Baldus M 2008 J. Am. Chem. Soc. 130 5922
[35] Vilar M, Chou H T, Luhrs T, Maji S K, Riek-Loher D, Verel R, Manning G, Stahlberg H and Riek R 2008 Proc. Natl. Acad. Sci. USA 105 8637
[36] Qiang W, Yau W M, Luo Y, Mattson M P and Tycko R 2012 Proc. Natl. Acad. Sci. USA 109 4443
[37] Paravastu A K, Leapman R D, Yau W M and Tycko R 2008 Proc. Natl. Acad. Sci. USA 105 18349
[38] Lu J X, Qiang W, Yau W M, Schwieters C D, Meredith S C and Tycko R 2013 Cell 154 1257
[39] Lindorff-Larsen K, Piana S, Dror R O and Shaw D E 2011 Science 334 517
[40] Morriss-Andrews A and Shea J E 2015 Annu. Rev. Phys. Chem. 66 643
[41] Sugita Y and Okamoto Y 1999 Chem. Phys. Lett. 314 141
[42] Baumketner A, Bernstein S L, Wyttenbach T, Lazo N D, Teplow D B, Bowers M T and Shea J E 2006 Protein Sci. 15 1239
[43] Nishino M, Sugita Y, Yoda T and Okamoto Y 2005 Febs. Lett. 579 5425
[44] Tsai H H, Reches M, Tsai C J, Gunasekaran K, Gazit E and Nussinov R 2005 Proc. Natl. Acad. Sci. USA 102 8174
[45] Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre J F, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen P H and Derreumaux P 2014 Chem. Soc. Rev. 43 4871
[46] Cheon M, Chang I and Hall C K 2010 Proteins 78 2950
[47] Wu C and Shea J E 2011 Curr. Opin. Struct. Biol. 21 209
[48] Urbanc B, Cruz L, Teplow D B and Stanley H E 2006 Curr. Alzheimer Res. 3 493
[49] Ma B and Nussinov R 2006 Curr. Opin. Chem. Biol. 10 445
[50] Balbach J J, Ishii Y, Antzutkin O N, Leapman R D, Rizzo N W, Dyda F, Reed J and Tycko R 2000 Biochemistry 39 13748
[51] Ma B and Nussinov R 2002 Proc. Natl. Acad. Sci. USA 99 14126
[52] Ma B and Nussinov R 2006 Biophys. J. 90 3365
[53] Takeda T and Klimov D K 2007 J. Mol. Biol. 368 1202
[54] Gnanakaran S, Nussinov R and Garcia A E 2006 J. Am. Chem. Soc. 128 2158
[55] Wei G and Shea J E 2006 Biophys. J. 91 1638
[56] Wu C, Murray M M, Bernstein S L, Condron M M, Bitan G, Shea J E and Bowers M T 2009 J. Mol. Biol. 387 492
[57] Krone M G, Baumketner A, Bernstein S L, Wyttenbach T, Lazo N D, Teplow D B, Bowers M T and Shea J E 2008 J. Mol. Biol. 381 221
[58] Tarus B, Straub J E and Thirumalai D 2008 J. Mol. Biol. 379 815
[59] Han W and Wu Y D 2005 J. Am. Chem. Soc. 127 15408
[60] Jang S and Shin S 2008 J. Phys. Chem. B 112 3479
[61] Campanera J M and Pouplana R 2010 Molecules 15 2730
[62] Baumketner A and Shea J E 2006 J. Mol. Biol. 362 567
[63] Ikebe J, Kamiya N, Ito J, Shindo H and Higo J 2007 Protein Sci. 16 1596
[64] Baumketner A, Krone M G and Shea J E 2008 Proc. Natl. Acad. Sci. USA 105 6027
[65] Baumketner A and Shea J E 2007 J. Mol. Biol. 366 275
[66] Kittner M and Knecht V 2010 J. Phys. Chem. B 114 15288
[67] Wei G, Jewett A I and Shea J E 2010 Phys. Chem. Chem. Phys. 12 3622
[68] Smith M D, Srinivasa Rao J and Cruz L 2014 Phys. Chem. Chem. Phys. 16 13069
[69] Jang S and Shin S 2006 J. Phys. Chem. B 110 1955
[70] Li H, Luo Y, Derreumaux P and Wei G 2011 Biophys. J. 101 2267
[71] Laganowsky A, Liu C, Sawaya M R, Whitelegge J P, Park J, Zhao M, Pensalfini A, Soriaga A B, Landau M, Teng P K, Cascio D, Glabe C and Eisenberg D 2012 Science 335 1228
[72] Xie L, Luo Y and Wei G 2013 J. Phys. Chem. B 117 10149
[73] Larini L and Shea J E 2012 Biophys. J. 103 576
[74] Cao Z, Liu L, Zhao L and Wang J 2011 Int. J. Mol. Sci. 12 8259
[75] Nguyen P H, Li M S and Derreumaux P 2011 Phys. Chem. Chem. Phys. 13 9778
[76] Baumketner A, Bernstein S L, Wyttenbach T, Bitan G, Teplow D B, Bowers M T and Shea J E 2006 Protein Sci. 15 420
[77] Sgourakis N G, Yan Y, McCallum S A, Wang C and Garcia A E 2007 J. Mol. Biol. 368 1448
[78] Anand P, Nandel F S and Hansmann U H 2008 J. Chem. Phys. 128 165102
[79] Yang M and Teplow D B 2008 J. Mol. Biol. 384 450
[80] Sgourakis N G, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C and Garcia A E 2011 J. Mol. Biol. 405 570
[81] Roychaudhuri R, Yang M, Deshpande A, Cole G M, Frautschy S, Lomakin A, Benedek G B and Teplow D B 2013 J. Mol. Biol. 425 292
[82] Rosenman D J, Connors C R, Chen W, Wang C and Garcia A E 2013 J. Mol. Biol. 425 3338
[83] Yano A, Okamoto A, Nomura K, Higai S I and Kurita N 2014 Chem. Phys. Lett. 595--596 242
[84] Triguero L, Singh R and Prabhakar R 2008 J. Phys. Chem. B 112 7123
[85] Velez-Vega C and Escobedo F A 2011 J. Phys. Chem. B 115 4900
[86] Lin Y S and Pande V S 2012 Biophys. J. 103 L47
[87] Truong P M, Viet M H, Nguyen P H, Hu C K and Li M S 2014 J. Phys. Chem. B 118 8972
[88] Das P, Murray B and Belfort G 2015 Biophys. J. 108 738
[89] Kim S, Takeda T and Klimov D K 2010 Biophys. J. 99 1949
[90] Zhu X, Bora R P, Barman A, Singh R and Prabhakar R 2012 J. Phys. Chem. B 116 4405
[91] Zhang T, Zhang J, Derreumaux P and Mu Y 2013 J. Phys. Chem. B 117 3993
[92] Tarus B, Tran T T, Nasica-Labouze J, Sterpone F, Nguyen P H and Derreumaux P 2015 J. Phys. Chem. B 119 10478
[93] Ball K A, Phillips A H, Nerenberg P S, Fawzi N L, Wemmer D E and Head-Gordon T 2011 Biochemistry-us. 50 7612
[94] Li W, Zhang J, Su Y, Wang J, Qin M and Wang W 2007 J. Phys. Chem. B 111 13814
[95] Nasica-Labouze J, Nguyen P H, Sterpone F, et al. 2015 Chem. Rev. 115 3518
[96] Brambilla D, Le Droumaguet B, Nicolas J, Hashemi S H, Wu L P, Moghimi S M, Couvreur P and Andrieux K 2011 Nanomedicine-Uk 7 521
[97] Zaman M, Ahmad E, Qadeer A, Rabbani G and Khan R H 2014 Int. J. Nanomed. 9 899
[98] Kim J E and Lee M 2003 Biochem. Biophys. Res. Commun. 303 576
[99] Podolski I Y, Podlubnaya Z A, Kosenko E A, Mugantseva E A, Makarova E G, Marsagishvili L G, Shpagina M D, Kaminsky Y G, Andrievsky G V and Klochkov V K 2007 J. Nanosci. Nanotechnol. 7 1479
[100] Makarova E G, Gordon R Y and Podolski I Y 2012 J. Nanosci. Nanotechnol. 12 119
[101] Kowalewski T and Holtzman D M 1999 Proc. Natl. Acad. Sci. USA 96 3688
[102] Losic D, Martin L L, Aguilar M I and Small D H 2006 Biopolymers 84 519
[103] Arce F T, Jang H, Ramachandran S, Landon P B, Nussinov R and Lal R 2011 Soft Matter 7 5267
[104] Fu Z, Luo Y, Derreumaux P and Wei G 2009 Biophys. J. 97 1795
[105] Xie L, Lin D, Luo Y, Li H, Yang X and Wei G 2014 Biophys. J. 107 1930
[106] Jana A K and Sengupta N 2012 Biophys. J. 102 1889
[107] Jana A K, Jose J C and Sengupta N 2013 Phys. Chem. Chem. Phys. 15 837
[108] Andujar S A, Lugli F, Hofinger S, Enriz R D and Zerbetto F 2012 Phys. Chem. Chem. Phys. 14 8599
[109] Huy P D and Li M S 2014 Phys. Chem. Chem. Phys. 16 20030
[110] Zhou X, Xi W, Luo Y, Cao S and Wei G 2014 J. Phys. Chem. B 118 6733
[111] Xie L, Luo Y, Lin D, Xi W, Yang X and Wei G 2014 Nanoscale 6 9752
[112] Takeda T and Klimov D K 2009 Biophys. J. 96 442
[113] Han M and Hansmann U H E 2011 J. Chem. Phys. 135
[114] Gurry T and Stultz C M 2014 Biochemistry-us. 53 6981
[115] Han W and Schulten K 2014 J. Am. Chem. Soc. 136 12450
[116] Morales R, Moreno-Gonzalez I and Soto C 2013 PLoS Pathog. 9 e1003537
[117] Xi W, Li W and Wang W 2012 J. Phys. Chem. B 116 7398
[1] Molecular dynamics study of interactions between edge dislocation and irradiation-induced defects in Fe–10Ni–20Cr alloy
Tao-Wen Xiong(熊涛文), Xiao-Ping Chen(陈小平), Ye-Ping Lin(林也平), Xin-Fu He(贺新福), Wen Yang(杨文), Wang-Yu Hu(胡望宇), Fei Gao(高飞), and Hui-Qiu Deng(邓辉球). Chin. Phys. B, 2023, 32(2): 020206.
[2] Formation of nanobubbles generated by hydrate decomposition: A molecular dynamics study
Zilin Wang(王梓霖), Liang Yang(杨亮), Changsheng Liu(刘长生), and Shiwei Lin(林仕伟). Chin. Phys. B, 2023, 32(2): 023101.
[3] Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions
Mengjiao Wu(吴梦娇), Huishu Ma(马慧姝), Haiping Fang(方海平), Li Yang(阳丽), and Xiaoling Lei(雷晓玲). Chin. Phys. B, 2023, 32(1): 018701.
[4] Prediction of flexoelectricity in BaTiO3 using molecular dynamics simulations
Long Zhou(周龙), Xu-Long Zhang(张旭龙), Yu-Ying Cao(曹玉莹), Fu Zheng(郑富), Hua Gao(高华), Hong-Fei Liu(刘红飞), and Zhi Ma(马治). Chin. Phys. B, 2023, 32(1): 017701.
[5] Effect of spatial heterogeneity on level of rejuvenation in Ni80P20 metallic glass
Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Chin. Phys. B, 2022, 31(9): 096401.
[6] Spatial correlation of irreversible displacement in oscillatory-sheared metallic glasses
Shiheng Cui(崔世恒), Huashan Liu(刘华山), and Hailong Peng(彭海龙). Chin. Phys. B, 2022, 31(8): 086108.
[7] Effect of void size and Mg contents on plastic deformation behaviors of Al-Mg alloy with pre-existing void: Molecular dynamics study
Ning Wei(魏宁), Ai-Qiang Shi(史爱强), Zhi-Hui Li(李志辉), Bing-Xian Ou(区炳显), Si-Han Zhao(赵思涵), and Jun-Hua Zhao(赵军华). Chin. Phys. B, 2022, 31(6): 066203.
[8] Strengthening and softening in gradient nanotwinned FCC metallic multilayers
Yuanyuan Tian(田圆圆), Gangjie Luo(罗港杰), Qihong Fang(方棋洪), Jia Li(李甲), and Jing Peng(彭静). Chin. Phys. B, 2022, 31(6): 066204.
[9] Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations
Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Chin. Phys. B, 2022, 31(5): 058702.
[10] Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations
Song Hu(胡松), C Y Zhao(赵长颖), and Xiaokun Gu(顾骁坤). Chin. Phys. B, 2022, 31(5): 056301.
[11] Evolution of defects and deformation mechanisms in different tensile directions of solidified lamellar Ti-Al alloy
Yutao Liu(刘玉涛), Tinghong Gao(高廷红), Yue Gao(高越), Lianxin Li(李连欣), Min Tan(谭敏), Quan Xie(谢泉), Qian Chen(陈茜), Zean Tian(田泽安), Yongchao Liang(梁永超), and Bei Wang(王蓓). Chin. Phys. B, 2022, 31(4): 046105.
[12] Evaluation on performance of MM/PBSA in nucleic acid-protein systems
Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Chin. Phys. B, 2022, 31(4): 048701.
[13] Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution
Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Chin. Phys. B, 2022, 31(4): 048702.
[14] Effect of the number of defect particles on the structure and dispersion relation of a two-dimensional dust lattice system
Rangyue Zhang(张壤月), Guannan Shi(史冠男), Hanyu Tang(唐瀚宇), Yang Liu(刘阳), Yanhong Liu(刘艳红), and Feng Huang(黄峰). Chin. Phys. B, 2022, 31(3): 035204.
[15] Molecular dynamics simulations on the wet/dry self-latching and electric fields triggered wet/dry transitions between nanosheets: A non-volatile memory nanostructure
Jianzhuo Zhu(朱键卓), Xinyu Zhang(张鑫宇), Xingyuan Li(李兴元), and Qiuming Peng(彭秋明). Chin. Phys. B, 2022, 31(2): 024703.
No Suggested Reading articles found!