Implications of different membrane compartmentalization models in particle-based
membrane
particle-based simulation
restricted diffusion
Journal
Royal Society open science
ISSN: 2054-5703
Titre abrégé: R Soc Open Sci
Pays: England
ID NLM: 101647528
Informations de publication
Date de publication:
Jul 2023
Jul 2023
Historique:
received:
08
09
2022
accepted:
12
06
2023
medline:
7
7
2023
pubmed:
7
7
2023
entrez:
7
7
2023
Statut:
epublish
Résumé
Studying membrane dynamics is important to understand the cellular response to environmental stimuli. A decisive spatial characteristic of the plasma membrane is its compartmental structure created by the actin-based membrane-skeleton (fences) and anchored transmembrane proteins (pickets). Particle-based reaction-diffusion simulation of the membrane offers a suitable temporal and spatial resolution to analyse its spatially heterogeneous and stochastic dynamics. Fences have been modelled via hop probabilities, potentials or explicit picket fences. Our study analyses the different approaches' constraints and their impact on simulation results and performance. Each of the methods comes with its own constraints; the picket fences require small timesteps, potential fences might induce a bias in diffusion in crowded systems, and probabilistic fences, in addition to carefully scaling the probability with the timesteps, induce higher computational costs for each propagation step.
Identifiants
pubmed: 37416823
doi: 10.1098/rsos.221177
pii: rsos221177
pmc: PMC10320350
doi:
Banques de données
figshare
['10.6084/m9.figshare.c.6700181']
Types de publication
Journal Article
Langues
eng
Pagination
221177Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
We declare we have no competing interests.
Références
PLoS Comput Biol. 2019 Feb 28;15(2):e1006830
pubmed: 30818351
Biol Proced Online. 2009 May 15;11:32-51
pubmed: 19495910
Sci Rep. 2015 Jun 29;5:11454
pubmed: 26118385
Bioinformatics. 2018 Oct 15;34(20):3591-3593
pubmed: 29762723
BMC Biophys. 2014 Nov 26;7:13
pubmed: 25774289
Biophys J. 2020 Jun 16;118(12):3026-3040
pubmed: 32470324
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82(4 Pt 1):041914
pubmed: 21230320
J Chem Phys. 2015 Aug 28;143(8):084117
pubmed: 26328828
Philos Trans R Soc Lond B Biol Sci. 2012 Dec 24;368(1611):20120029
pubmed: 23267182
Integr Biol (Camb). 2009 Feb;1(2):205-11
pubmed: 20023804
Nat Protoc. 2019 Apr;14(4):1054-1083
pubmed: 30842616
EMBO J. 2016 Jan 4;35(1):77-88
pubmed: 26598531
Biophys J. 2018 Jun 19;114(12):2945-2950
pubmed: 29925030
Biophys J. 2005 Mar;88(3):2266-77
pubmed: 15613635
Biophys J. 2006 Jun 1;90(11):3951-65
pubmed: 16533838
Biochim Biophys Acta. 2013 Aug;1828(8):1765-76
pubmed: 23500617
Biophys J. 2010 Jun 16;98(12):2886-94
pubmed: 20550901
BMC Bioinformatics. 2020 Jan 29;21(1):33
pubmed: 31996129
Curr Opin Biotechnol. 2010 Oct;21(5):677-82
pubmed: 20829029
Mol Biol Cell. 2016 Apr 1;27(7):1101-19
pubmed: 26864625
J Cell Biol. 2002 Jun 10;157(6):1071-81
pubmed: 12058021
Int J Mol Sci. 2012;13(6):7798-7827
pubmed: 22837728
Cancer Res. 2015 Apr 1;75(7):1169-76
pubmed: 25788696
PLoS Comput Biol. 2013 Apr;9(4):e1003033
pubmed: 23592975
Langmuir. 2006 Feb 28;22(5):2384-91
pubmed: 16489833
J Orthop Res. 2013 Feb;31(2):322-7
pubmed: 22912342
Mol Biol Cell. 2021 Jan 15;32(2):186-210
pubmed: 33237849
Biophys J. 2014 Nov 18;107(10):2274-86
pubmed: 25418296
PLoS Comput Biol. 2013;9(1):e1002803
pubmed: 23341757
Biomedicines. 2020 Nov 08;8(11):
pubmed: 33171654
Biophys J. 2016 Feb 2;110(3):523-529
pubmed: 26840718
Biophys J. 1989 Sep;56(3):615-22
pubmed: 2790141
Curr Opin Cell Biol. 2018 Aug;53:15-21
pubmed: 29656224
Annu Rev Cell Dev Biol. 2012;28:215-50
pubmed: 22905956
Bioinformatics. 2017 Mar 1;33(5):710-717
pubmed: 28365760
Science. 1972 Feb 18;175(4023):720-31
pubmed: 4333397
PLoS One. 2013 Sep 11;8(9):e74261
pubmed: 24040218
Cell. 2019 May 2;177(4):806-819
pubmed: 31051105
J Biotechnol. 2011 Feb 10;151(3):261-70
pubmed: 21167222
Biophys J. 2008 Mar 1;94(5):1551-64
pubmed: 17993499
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 1):061916
pubmed: 23005136
BMC Biophys. 2014 Oct 24;7:11
pubmed: 25737778
Trends Cell Biol. 2012 Oct;22(10):515-26
pubmed: 22917551
Chem Rev. 2019 May 8;119(9):6184-6226
pubmed: 30623647
J Phys Chem Lett. 2017 Sep 7;8(17):4308-4313
pubmed: 28823153
J Phys Chem B. 2016 Sep 1;120(34):8873-81
pubmed: 27483109
Biomater Res. 2019 Dec 5;23:25
pubmed: 31844552
Biomaterials. 2018 Jan;150:60-86
pubmed: 29032331
Chem Rev. 2019 May 8;119(9):5607-5774
pubmed: 30859819
Phys Biol. 2007 Feb 14;4(1):16-28
pubmed: 17406082
Biophys J. 2008 Mar 1;94(5):L41-3
pubmed: 18192354
Biophys J. 2013 Jul 16;105(2):455-62
pubmed: 23870266
Nano Lett. 2019 Aug 14;19(8):4827-4835
pubmed: 31314539
FASEB J. 2002 Jun;16(8):857-9
pubmed: 11967227
RSC Adv. 2018;8(22):12017-12028
pubmed: 30761211
Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8568-8573
pubmed: 28739955
Biochim Biophys Acta. 2014 Jun;1838(6):1467-76
pubmed: 24440423