Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model.
UNRES model
molecular dynamics
peptide aggregation
replica exchange
Journal
Biomolecules
ISSN: 2218-273X
Titre abrégé: Biomolecules
Pays: Switzerland
ID NLM: 101596414
Informations de publication
Date de publication:
18 08 2022
18 08 2022
Historique:
received:
14
07
2022
revised:
13
08
2022
accepted:
16
08
2022
entrez:
26
8
2022
pubmed:
27
8
2022
medline:
30
8
2022
Statut:
epublish
Résumé
The UNited RESidue (UNRES) model of polypeptide chains was applied to study the association of 20 peptides with sizes ranging from 6 to 32 amino-acid residues. Twelve of those were potentially aggregating hexa- or heptapeptides excised from larger proteins, while the remaining eight contained potentially aggregating sequences, functionalized by attaching larger ends rich in charged residues. For 13 peptides, the experimental data of aggregation were used. The remaining seven were synthesized, and their properties were measured in this work. Multiplexed replica-exchange simulations of eight-chain systems were conducted at 12 temperatures from 260 to 370 K at concentrations from 0.421 to 5.78 mM, corresponding to the experimental conditions. The temperature profiles of the fractions of monomers and octamers showed a clear transition corresponding to aggregate dissociation. Low simulated transition temperatures were obtained for the peptides, which did not precipitate after incubation, as well as for the H-GNNQQNY-NH
Identifiants
pubmed: 36009034
pii: biom12081140
doi: 10.3390/biom12081140
pmc: PMC9406146
pii:
doi:
Substances chimiques
Peptides
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Références
J Phys Chem B. 2005 Jul 21;109(28):13798-810
pubmed: 16852728
J Chem Theory Comput. 2008 Mar;4(3):435-47
pubmed: 26620784
Methods Mol Biol. 2022;2340:51-78
pubmed: 35167070
Int J Mol Sci. 2022 May 22;23(10):
pubmed: 35628610
J Biol Chem. 2001 Dec 21;276(51):48165-74
pubmed: 11606569
Curr Pharm Biotechnol. 2013;14(5):501-12
pubmed: 22429133
J Phys Chem B. 2007 Jan 11;111(1):260-85
pubmed: 17201450
Nat Chem. 2018 Feb;10(2):170-176
pubmed: 29359764
ACS Chem Neurosci. 2017 Jan 18;8(1):201-209
pubmed: 28095675
J Chem Theory Comput. 2010 Mar 9;6(3):890-909
pubmed: 20305729
Brief Bioinform. 2021 Nov 5;22(6):
pubmed: 34181000
Trends Neurosci. 2008 Oct;31(10):521-8
pubmed: 18778858
J Chem Phys. 2009 Jun 21;130(23):235106
pubmed: 19548767
Curr Opin Biotechnol. 2014 Dec;30:211-7
pubmed: 25173826
Nature. 1991 Feb 21;349(6311):704-6
pubmed: 1671712
Nat Protoc. 2008;3(12):1832-47
pubmed: 18989261
J Comput Chem. 2008 Jul 15;29(9):1460-5
pubmed: 18196502
Nat Rev Drug Discov. 2021 Apr;20(4):309-325
pubmed: 33536635
J Protein Chem. 1994 Feb;13(2):195-215
pubmed: 8060493
J Mol Graph Model. 2018 Jan;79:118-132
pubmed: 29161634
J Pept Sci. 2018 Jun;24(4-5):e3073
pubmed: 29573035
J Phys Chem B. 2018 Jul 19;122(28):7049-7056
pubmed: 29940109
Proc Natl Acad Sci U S A. 2000 May 9;97(10):5129-34
pubmed: 10805776
Phys Chem Chem Phys. 2021 Sep 22;23(36):20615-20626
pubmed: 34514491
J Chem Theory Comput. 2009 Mar 10;5(3):627-640
pubmed: 20161452
Nature. 2007 May 24;447(7143):453-7
pubmed: 17468747
Nat Rev Drug Discov. 2008 Mar;7(3):255-70
pubmed: 18219308
Science. 2002 Jul 19;297(5580):353-6
pubmed: 12130773
Nature. 2005 Jun 9;435(7043):773-8
pubmed: 15944695
Methods Mol Biol. 2022;2340:235-279
pubmed: 35167078
J Chem Phys. 2006 May 7;124(17):174903
pubmed: 16689600
J Chem Phys. 2017 Mar 28;146(12):124106
pubmed: 28388107
J Mol Biol. 1982 May 5;157(1):105-32
pubmed: 7108955
J Mol Model. 2014 Aug;20(8):2306
pubmed: 25024008
ISRN Pharm. 2012;2012:195727
pubmed: 22830056
Int J Mol Sci. 2019 May 14;20(10):
pubmed: 31091705
Int J Mol Sci. 2021 Apr 07;22(8):
pubmed: 33917000
J Phys Chem B. 2005 Jul 21;109(28):13785-97
pubmed: 16852727
J Mol Graph Model. 2021 Nov;108:108008
pubmed: 34419932
J Mol Biol. 2010 Dec 3;404(3):537-52
pubmed: 20888834
QJM. 1999 Jan;92(1):1-4
pubmed: 10209665
Soft Matter. 2020 Jun 7;16(21):5071-5080
pubmed: 32453328
Nucleic Acids Res. 2021 Jul 2;49(W1):W216-W227
pubmed: 33849055
Phys Chem Chem Phys. 2018 Jul 18;20(28):19057-19070
pubmed: 29972174
Methods Mol Biol. 2022;2376:399-416
pubmed: 34845623
J Phys Chem B. 2011 Nov 10;115(44):12978-83
pubmed: 21939202
Biophys J. 2003 Feb;84(2 Pt 1):775-86
pubmed: 12547762
Adv Mater. 2020 May;32(18):e1901690
pubmed: 31183916
J Chem Phys. 2019 Apr 21;150(15):155104
pubmed: 31005069
Anal Biochem. 2000 Dec 15;287(2):252-60
pubmed: 11112271
J Chem Theory Comput. 2007 Jul;3(4):1236-48
pubmed: 26633198
Adv Drug Deliv Rev. 2020;160:78-104
pubmed: 33091503