2019
DOI: 10.1101/715383
|View full text |Cite
Preprint
|
Sign up to set email alerts
|

Insights into actin polymerization and nucleation using a coarse grained model

Abstract: We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the C α atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polyme… Show more

Help me understand this report
View published versions

Search citation statements

Order By: Relevance

Paper Sections

Select...
1

Citation Types

1
2
0

Year Published

2020
2020
2022
2022

Publication Types

Select...
2
1
1

Relationship

0
4

Authors

Journals

citations
Cited by 4 publications
(3 citation statements)
references
References 69 publications
1
2
0
Order By: Relevance
“…However, the close match to existing structural data of the pointed end (15) suggests that our allatom approach adequately sampled conformational space in order to reach equilibrium distributions. Furthermore, recent coarse-grained Monte Carlo simulations of an actin monomer associating with an actin dimer reported high-probability barbed end conformations similar to ones sampled in our all-atom simulations (18).…”
supporting
confidence: 82%
“…However, the close match to existing structural data of the pointed end (15) suggests that our allatom approach adequately sampled conformational space in order to reach equilibrium distributions. Furthermore, recent coarse-grained Monte Carlo simulations of an actin monomer associating with an actin dimer reported high-probability barbed end conformations similar to ones sampled in our all-atom simulations (18).…”
supporting
confidence: 82%
“…Molecular Dynamics (MD) simulations have become increasingly popular over the last 20 years for studying biological systems at different scales ( Vanommeslaeghe et al, 2010 ; Maier et al, 2015 ; Souza et al, 2021 ; Kim and Hummer, 2008 ; Chu and Voth, 2005 ). This method was extensively used to characterize properties of actin protein such as differences between nucleotide states ( Splettstoesser et al, 2009 ; Saunders et al, 2014 ; Jepsen and Sept, 2020 ), waters located in the cavity and their impact on protein plasticity and enzymatic properties ( Saunders and Voth, 2011 ; Mc-Cullagh et al, 2014 ), interactions with small molecules ( Rennebaum and Caflisch, 2012 ; Helal et al, 2013 ) and the dynamics of filaments in various environments ( Chu and Voth, 2005 ; Splettstoesser et al, 2011 ; Zsolnay et al, 2020 ; Schroer et al, 2020 ; Shamloo and Mehrafrooz, 2018 ; Jaswandkar et al, 2021 ; Horan et al, 2020 ; Castaneda et al, 2019 ) but, to our knowledge, these computational works focus exclusively on α -actin while the β -actin isoform remains understudied.…”
Section: Introductionmentioning
confidence: 99%
“…Actin monomers, either in free or bound filament form, can be represented as spheres or ellipsoids, [13][14][15] in a more detailed 4-bead description, 12,16 or an even greater level of detail that begins to bridge the gap in resolution to all-atom simulations. 17,18 Parameters for these coarse-grained models can be set either from experimental data or by inferring them, using various techniques, 16,19 from all-atom MD simulation data.. 20,21 In this paper, we will use a monomer-based description of actin, which was developed by De La Cruz et al, 22 who parametrised it using atomistic MD simulations. This model will form our monomer-based description of actin introduced in Section II A.…”
mentioning
confidence: 99%