Amyloid-β peptide aggregation and the influence of carbon nanoparticles

doi:10.1088/1674-1056/25/1/018704

摘要/Abstract

摘要： 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.

关键词: Amyloid-β, oligomerization, carbon nanoparticles, molecular dynamics

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.

Key words: Amyloid-β, oligomerization, carbon nanoparticles, molecular dynamics

中图分类号: (Fibrils (amyloids, collagen, etc.))

87.14.em

87.15.nr (Aggregation) 87.15.bk (Structure of aggregates) 87.15.ap (Molecular dynamics simulation)

郗文辉, 韦广红. Amyloid-β peptide aggregation and the influence of carbon nanoparticles[J]. 中国物理B, 2016, 25(1): 18704-018704.

Wen-Hui Xi(郗文辉) and Guang-Hong Wei(韦广红). Amyloid-β peptide aggregation and the influence of carbon nanoparticles[J]. Chin. Phys. B, 2016, 25(1): 18704-018704.

参考文献 117

[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