Cargando…
The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models
Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformationa...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042166/ https://www.ncbi.nlm.nih.gov/pubmed/33859629 http://dx.doi.org/10.3389/fmicb.2021.639883 |
_version_ | 1783678071243538432 |
---|---|
author | Lv, Dashuai Li, Jingyuan Ye, Sheng |
author_facet | Lv, Dashuai Li, Jingyuan Ye, Sheng |
author_sort | Lv, Dashuai |
collection | PubMed |
description | Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity. |
format | Online Article Text |
id | pubmed-8042166 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-80421662021-04-14 The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models Lv, Dashuai Li, Jingyuan Ye, Sheng Front Microbiol Microbiology Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity. Frontiers Media S.A. 2021-03-30 /pmc/articles/PMC8042166/ /pubmed/33859629 http://dx.doi.org/10.3389/fmicb.2021.639883 Text en Copyright © 2021 Lv, Li and Ye. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Lv, Dashuai Li, Jingyuan Ye, Sheng The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title | The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title_full | The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title_fullStr | The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title_full_unstemmed | The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title_short | The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models |
title_sort | assembly switch mechanism of ftsz filament revealed by all-atom molecular dynamics simulations and coarse-grained models |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042166/ https://www.ncbi.nlm.nih.gov/pubmed/33859629 http://dx.doi.org/10.3389/fmicb.2021.639883 |
work_keys_str_mv | AT lvdashuai theassemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels AT lijingyuan theassemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels AT yesheng theassemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels AT lvdashuai assemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels AT lijingyuan assemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels AT yesheng assemblyswitchmechanismofftszfilamentrevealedbyallatommoleculardynamicssimulationsandcoarsegrainedmodels |