A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation.
Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self-assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered as their size increases.
Auer
Stefan
S
Centre for Self Organising Molecular Systems, University of Leeds, Leeds, UK. s.auer@leeds.ac.uk
Trovato
Antonio
A
Vendruscolo
Michele
M
D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008968:Molecular Conformation; D053758:Nanoparticles / Q000737:chemistry*; D010316:Particle Size; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011108:Polymers / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D055503:Protein Multimerization; D017433:Protein Structure, Secondary
D010455:Peptides; D011108:Polymers
J Mol Biol. 2009 Mar 27;387(2):407-15
19133272
Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):111-6
17190811
Trends Biotechnol. 2008 Aug;26(8):425-33
18514941
J Chem Phys. 2007 Jun 28;126(24):245104
17614592
Annu Rev Biophys Biomol Struct. 2007;36:261-80
17477839
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14126-31
12391326
J Mol Biol. 2008 Dec 5;384(1):279-97
18824003
Front Biosci. 2008 May 01;13:5614-22
18508610
J Chem Phys. 2009 Jan 21;130(3):035102
19173542
J Mol Biol. 2004 Aug 27;341(5):1175-87
15321714
Protein Sci. 2002 May;11(5):1036-49
11967361
J Mol Biol. 2007 Dec 7;374(4):917-24
18028943
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8691-6
17485668
J Chem Phys. 2008 Nov 7;129(17):175101
19045373
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2029-30
17284585
Proc Natl Acad Sci U S A. 2004 May 25;101(21):7960-4
15148372
Curr Opin Biotechnol. 2007 Dec;18(6):565-71
18160274
J Mol Biol. 2006 Jul 21;360(4):882-92
16797587
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14265-70
18809927
J Mol Biol. 2008 Jun 13;379(4):815-29
18479708
Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10016-21
17540728
PLoS Comput Biol. 2007 Sep;3(9):1727-38
17941703
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct;70(4 Pt 1):041905
15600433
J Am Chem Soc. 2001 Jan 31;123(4):775-6
11456608
J Am Chem Soc. 2008 Nov 19;130(46):15437-43
18954050
EMBO J. 2002 Nov 1;21(21):5682-90
12411486
Small. 2008 Jan;4(1):26-49
18165959
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Apr;69(4 Pt 1):041908
15169044
Proteins. 2003 Feb 15;50(3):437-50
12557186
J Mol Biol. 2007 May 4;368(3):894-901
17368485
Science. 1997 Sep 26;277(5334):1975-8
9302288
J Am Chem Soc. 2003 Apr 2;125(13):3751-7
12656605
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8679-80
17502593
J Biol Chem. 2001 Nov 23;276(47):44284-96
11553618
Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16180-5
15534217
Nature. 2003 Dec 18;426(6968):884-90
14685248
J Chem Phys. 2007 Jan 14;126(2):025101
17228975
Phys Rev Lett. 2008 Dec 19;101(25):258101
19113754
J Chromatogr B Biomed Sci Appl. 2000 Jun 23;743(1-2):151-67
10942282
Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11857-62
11592996
Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17345-50
15583128
Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12916-21
15326301
Proc Natl Acad Sci U S A. 2006 May 2;103(18):6883-8
16624879
HFSP J. 2007 Jul;1(2):137-46
19404419
Cell. 1993 Jun 18;73(6):1055-8
8513491
Annu Rev Biochem. 2006;75:333-66
16756495
Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6027-32
18408165
Science. 2000 Aug 25;289(5483):1317-21
10958771
PLoS Comput Biol. 2008 Nov;4(11):e1000222
19008938
J Mol Biol. 2007 Feb 9;366(1):275-85
17166516
Nature. 1985 Mar 21-27;314(6008):235-8
3845322
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2050-5
17267609
J Mol Biol. 2005 Nov 4;353(4):804-21
16213524