title: Mechanisms of the self-assembly of EAK16-family peptides into fibrillar and globular structures: molecular dynamics simulations from nano- to micro-seconds.
abstract: The self-assembly of EAK16-family peptides in a bulk solution was studied using a combination of all-atom and coarse-grained molecular dynamics simulations. In addition, specified concentrations of EAK16 peptides were induced to form fibrillary or globular assemblies in vitro. The results show that the combination of all-atom molecular dynamics simulations on the single- and double-chain levels and coarse-grained simulations on the many-chain level predicts the experimental observations reasonably well. At neutral pH conditions, EAK16-I and EAK16-II assemble into fibrillary structures, whereas EAK16-IV aggregates into globular assemblies. Mechanisms of the formation of fibrillar and globular assemblies are described using the simulation results.
authors.affiliation: Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731, Zanjan, Iran.
authors.forename: Soheila
authors.initials: S
authors.lastname: Emamyari
authors.forename: Faezeh
authors.initials: F
authors.lastname: Kargar
authors.forename: Vahid
authors.initials: V
authors.lastname: Sheikh-Hasani
authors.forename: Saeed
authors.initials: S
authors.lastname: Emadi
authors.forename: Hossein
authors.initials: H
authors.lastname: Fazli
mesh_terms: D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D066329:Protein Aggregates; D055503:Protein Multimerization
chemical_list: C098329:EAK16 peptide; D009842:Oligopeptides; D066329:Protein Aggregates
references.citation: J Biol Chem. 1999 Sep 3;274(36):25945-52
references.pmid: 10464339
references.citation: J Am Chem Soc. 2007 Oct 10;129(40):12200-10
references.pmid: 17850149
references.citation: Trends Biotechnol. 2007 May;25(5):211-8
references.pmid: 17379339
references.citation: J Phys Chem B. 2006 Aug 10;110(31):15045-8
references.pmid: 16884212
references.citation: Biomaterials. 2013 Nov;34(34):8776-85
references.pmid: 23953841
references.citation: Biophys J. 2008 Nov 1;95(9):4337-47
references.pmid: 18676652
references.citation: Acta Biomater. 2014 Nov;10 (11):4759-4767
references.pmid: 25117952
references.citation: Biomacromolecules. 2003 Sep-Oct;4(5):1433-42
references.pmid: 12959616
references.citation: PLoS One. 2007 Dec 19;2(12):e1325
references.pmid: 18091996
references.citation: J Biol Chem. 1997 Aug 29;272(35):22364-72
references.pmid: 9268388
references.citation: Tissue Eng Part A. 2008 Dec;14(12):2051-8
references.pmid: 18636949
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4623-8
references.pmid: 19273853
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5133-8
references.pmid: 11929981
references.citation: J Mol Biol. 2004 Aug 6;341(2):575-88
references.pmid: 15276845
references.citation: J Phys Chem B. 2007 Jul 12;111(27):7812-24
references.pmid: 17569554
references.citation: Chem Biol. 1997 Dec;4(12):951-9
references.pmid: 9427660
references.citation: Biopolymers. 1983 Dec;22(12):2577-637
references.pmid: 6667333
references.citation: Nat Neurosci. 2012 Jan 29;15(3):349-57
references.pmid: 22286176
references.citation: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5355-60
references.pmid: 11929973
references.citation: J Control Release. 2012 Jun 28;160(3):451-8
references.pmid: 22465676
references.citation: J Am Chem Soc. 1988 Mar 1;110(6):1657-66
references.pmid: 27557051
references.citation: ACS Nano. 2013 Sep 24;7(9):7562-72
references.pmid: 23977885
references.citation: J Phys Chem B. 2008 Feb 28;112(8):2326-34
references.pmid: 18251531
references.citation: Nat Rev Mol Cell Biol. 2007 Feb;8(2):101-12
references.pmid: 17245412
references.citation: J Biol Chem. 2009 Feb 20;284(8):4749-53
references.pmid: 18845536
references.citation: J Am Chem Soc. 2003 Oct 22;125(42):12680-1
references.pmid: 14558795
references.citation: Soft Matter. 2014 Jun 28;10(24):4248-57
references.pmid: 24740580
references.citation: Trends Biotechnol. 2002 Jan;20(1):16-21
references.pmid: 11742673
references.citation: J Phys Chem B. 2005 Feb 24;109(7):2469-73
references.pmid: 16851243
references.citation: Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11857-62
references.pmid: 11592996
references.citation: Proteins. 2008 Jul;72(1):150-62
references.pmid: 18214962
references.citation: Chem Biol. 1997 Feb;4(2):119-25
references.pmid: 9190286
references.citation: J Biol Chem. 2002 Apr 5;277(14):11970-8
references.pmid: 11812782
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Biomaterials. 2014 Jun;35(19):5196-205
references.pmid: 24680662
references.citation: Annu Rev Biochem. 2006;75:333-66
references.pmid: 16756495
references.citation: Mol Pharm. 2013 Mar 4;10(3):1035-44
references.pmid: 23419203
references.citation: J Comput Chem. 2005 Dec;26(16):1701-18
references.pmid: 16211538
references.citation: Protein Sci. 2010 Sep;19(9):1639-48
references.pmid: 20572020
references.citation: Eur Biophys J. 2014 May;43(4-5):143-55
references.pmid: 24623551
references.citation: Biophys J. 2004 Aug;87(2):1249-59
references.pmid: 15298927
references.citation: EMBO J. 1992 Oct;11(10):3787-96
references.pmid: 1396572
references.citation: J Biol Chem. 2004 Nov 5;279(45):46363-6
references.pmid: 15385542
references.citation: Biomaterials. 1999 Jul;20(13):1213-20
references.pmid: 10395390
references.citation: Biopolymers. 2012;98(3):169-84
references.pmid: 22782560
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):622-7
references.pmid: 20080728
references.citation: Biophys J. 2007 Jun 15;92(12):4289-303
references.pmid: 17400700
references.citation: Phys Chem Chem Phys. 2009 Mar 28;11(12):2077-86
references.pmid: 19280018
references.citation: J Chem Theory Comput. 2008 May;4(5):819-34
references.pmid: 26621095
references.citation: Colloids Surf B Biointerfaces. 2005 Dec 20;46(3):152-61
references.pmid: 16321511
references.citation: Science. 2000 Aug 25;289(5483):1317-21
references.pmid: 10958771
references.citation: J Chem Theory Comput. 2008 Mar;4(3):435-47
references.pmid: 26620784