Key factors governing fibril formation of proteins: insights from simulations and experiments

• Autorzy: Co N. T. , Viet M. H. , Truong P. M. , Kouza M. , Li M. S.
• Języki publikacji: EN

Abstrakty

EN

Fibril formation of proteins and peptides is associated with a large group of major human diseases, including Alzheimer’s disease, prion disorders, amy otrophic lateral sclerosis, type 2 diabetes, etc. Therefore, understanding the key factors th at govern this process is of paramount importance. The fibrillogenesis of polypeptide chains depends on their intrinsic properties as well as on the external conditions. In this mini-review w e discuss the relationship between fibril formation kinetics and the sequence, aromaticity, hydr ophobicity, charge and population of the so called fibril-prone conformation in a monomer state. The high er the population, the faster is the fibril elongation and this dependence may b e described by a single exponential function. This observation opens up a new way to unders tand the fibrillogenesis of bio-molecules at the monomer level. We will also discuss the influence of t he environment with focus on the recently observed dual effect of crowders on the aggregation rat es of polypeptide chains.

Słowa kluczowe

EN

fibre formation; binding free energy

PL

tworzenie włókienek; swobodna energia wiązania

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2014
• Tom: Vol. 18, No 3
• Strony: 245--254
• Opis fizyczny: Bibliogr. 50 poz., rys., wykr.

Twórcy

autor

Co N. T.

• Institute for Computational Science and Technology, SBI Bui lding
• Institute for Computational Science and Technology, SBI Bui lding Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Ch i Minh City, Vietnam

autor

Viet M. H.

• Institute of Physics, Polish Academy of Sciences, Al. Lotni kow 32/46, 02-668 Warsaw, Poland

autor

Truong P. M.

• Institute for Computational Science and Technology, SBI Bui lding
• Institute for Computational Science and Technology, SBI Bui lding Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Ch i Minh City, Vietnam

autor

Kouza M.

• Faculty of Chemistry, Faculty of Chemistry University of Warsa w Pasteura 1, 02-093 Warsaw, Poland

autor

Li M. S.

• Institute for Computational Science and Technology, SBI Bui lding Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Ch i Minh City, Vietnam
• Institute of Physics, Polish Academy of Sciences, Al. Lotni kow 32/46, 02-668 Warsaw, Poland

Bibliografia

• [1] Dobson C M 2003 Nature 426 884
• [2] Chiti F, Dobson C M 2006 Annual Rev. Biochemistry 75 333
• [3] Tycko R 2004 Curr. Opin. Struct. Biol. 14 96
• [4] Li M S, Co N T, Hu C K, Straub J E, Thirumalai D 2010 Phys. Rev. Lett. 105 218101
• [5] Tomiyama T, Nagata T, Shimada H, Teraoka R, Fukushima A, Kanemitsu H, Takuma H, Kuwano R, Imagawa M, Ataka S et al. 2008 Ann. Nerol. 63 377
• [6] Coskuner O, Wise-Scira O, Perry G, Kitahara T 2013 ACS Chemical Neuroscience 4 310
• [7] Lu Y, Wei G H, Derreumaux P 2011 J. Phys. Chem. B 115 1282
• [8] Paravastu A K, Leapman R D, Yau W M, Tycko R 2008 PNAS 105 18349
• [9] Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Doeli H, Schubert D, Riek R 2005 Proc. Natl. Acad. Sci. USA 102 17342
• [10] Lu J X, Qiang W, Yau W M, Schwieters C D, Meredith S C, Tycko R 2013 Cell 154 1257
• [11] Hori Y, Hashimoto T, Wakutani Y, Urakami K, Nakashima K, Condron M M, Tsubuki S, Saido T C, Teplow D B, Iwatsubo T 2007 J. Bio. Chem. 282 4916
• [12] Chen W T, Hong C J, Lin Y T, Chang W H, Huang H T, Liao J Y, Chang Y J, Hsieh Y F, Cheng C Y, Liu H C, Chen Y R, Cheng I H 2012 Plos One 7 , e35807
• [13] Ono K, Condron M M, Teplow D B 2010 J. Bio. Chem. 285 23186
• [14] Fede G D, Catania M, Morbin M, Rossi G, Suardi S, Mazzoleni G, Merlin M, Giovagnoli A R, Prioni S, Erbetta A et al. 2009 Science 323 1473
• [15] Lin Y-S, Pande V S 2012 Biophys. J. 103 , L47
• [16] Viet M H, Nguyen P H, Ngo S T, Li M S, Derreumaux P 2013 ACS Chem. Neurosci. 4 1446
• [17] Viet M H, Nguyen P H, Derreumaux P, Li M S 2014 ACS Chem. Neurosci. DOI: 10.1021/cn500007j
• [18] Truong P M, Viet M H, Nguyen P H, Hu C K, Li M S 2014 J. Phys. Chem. B 118 8972
• [19] Otzen D E, Kristensen O, Oliveberg M 2000 Proc. Natl. Acad. Sci. (USA) 97 9907
• [20] Gazit E 2002 FASEB Journal 16 77
• [21] Adler-Abramovich L, Gazit E 2014 Chem. Soc. Rev. 43 6881
• [22] Bowerman C J, Ryan D M, Nissan D A, Nilsson B L 2009 Mol Biosyst 5 1058
• [23] Senguen F T, Lee N R, Gu X, Ryan D M, Doran T M, Anderson E A, Nilsson B L 2011 Mol Biosyst 7 486
• [24] Li M S, Klimov D K, Straub J E, Thirumalai D 2008 J. Chem. Phys. 129 175101
• [25] Straub J E, Thirumalai D 2010 Curr. Opin. Struct. Biol. 20 187
• [26] Nam H B, Kouza M, Zung H, Li M S 2010 J. Chem. Phys. 132 165104
• [27] Reddy G, Straub J E, Thirumalai D 2009 J. Phys. Chem. B 113 1162
• [28] Sciarretta K, Gordon D, Petkova A, Tycko R, Meredith S 2005 Biochemistry 44 6003
• [29] Snyder S W, Ladror U S, Wade W S, Wang G T, Barrett L W, Matayoshi E D, Huffaker H J, Krafft G A, Holzman T F 1994 Biophys. J. 67 1216
• [30] Sgourakis N G, Yan Y L, McCallum S A, Wang C Y, Garcia A E 2007 J. Mol. Biol 368 1448
• [31] Yang M, Teplow D B 2008 J. Mol. Biol. 384 450
• [32] Kaminski G A, Friesner R A 2001 J. Phys. Chem. B 105 6474
• [33] Jorgensen J W, Chandrasekhar J, Madura J D, Imprey R W, Klein M L 1983 J. Chem. Phys. 79 926
• [34] Dobson C M 2001 Nature 410 165
• [35] Nielsen L, Khurana R, Coats A, Frokjaer S, Brange J, Vyas S, Uversky V N, Fink A L 2001 Biochemistry 40 6036 PMID: 11352739
• [36] Nielsen L, Khurana R, Coats A, Frokjaer S, Brange J, Vyas S, Uversky V N, Fink A L 2001 Biochemistry 40 6036
• [37] Jang H, Arce F T, Ramachandran S, Kagan B L, Lal R, Nussinov R 2014 Chem Soc Rev 43 6750
• [38] Zhou H X, Rivas G N, Minton A P 2008 Annual Rev. Biophys. 37 375
• [39] Kuriyan J, Eisenberg D 2007 Nature 450 983
• [40] White D A, Buell A K, Knowles T P J, Welland M E, Dobson C M 2010 J. Am. Chem. Soc. 132 5170
• [41] Magno A, Caflisch A, Pellarin R 2010 J. Phys. Chem. Lett. 1 3027
• [42] O’Brien E P, Straub J E, Brooks B R, Thirumalai D 2011 J. Phys. Chem. Lett. 2 1171
• [43] Asakura S, Oosawa F 1954 J. Chem. Phys. 22 1255
• [44] Linse S, Cabaleiro-Lago C, Xue W F, Lynch I, Lindman S, Thulin E, Radford S E, Dawson K A 2007 Proc. Natl. Acad. Sci. (USA) 104 8691
• [45] Cabaleiro-Lago C, Quinlan-Pluck F, Lynch I, Lindman S, Minogue A M, Thulin E, Walsh D M, Dawson K A, Linse S 2008 J. Am. Chem. Soc. 130 15437
• [46] Cabaleiro-Lago C, Quinlan-Pluck F, Lynch I, Dawson K A, Linse S 2010 ACS Chem. NeuroSci. 1 279
• [47] Wu W H, Sun X, Yu Y P, Hu J, Zhao L, Liu Q, Zhao Y F, Li Y M 2008 Biochem. Biophys. Res. Commun. 373 315
• [48] Klajnert B, Cortijo-Arellano M, Bryszewska M, Cladera J 2006 Biochem. Biophys. Res. Commun. 339 577
• [49] Co N T, Hu C K, Li M S 2013 J. Chem Phys 138 185101
• [50] Cieplak M, Hoang T X, Li M S 1999 Phys. Rev. Lett. 83 1684