Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin

Autor: Kotila, Tommi, Wioland, Hugo, Enkavi, Giray, Kogan, Konstantin, Vattulainen, Ilpo, Jégou, Antoine, Romet-Lemonne, Guillaume, Lappalainen, Pekka
Přispěvatelé: Institute of Biotechnology, Materials Physics, Department of Physics, Pekka Lappalainen / Principal Investigator, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Tampere University, Physics, Research group: Biological Physics and Soft Matter, Research area: Computational Physics
Jazyk: angličtina
Rok vydání: 2019
Předmět:
General Physics and Astronomy
CELL-SHAPE
Plasma protein binding
Crystallography
X-Ray
Protein filament
Mice
0302 clinical medicine
DOMAIN
Cytoskeleton
lcsh:Science
ComputingMilieux_MISCELLANEOUS
0303 health sciences
Multidisciplinary
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Structural Biology [q-bio.BM]
Chemistry
GELSOLIN
Cofilin
Actin filament depolymerization
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
3. Good health
Actin Cytoskeleton
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
cyclase-associated-protein (CAP)
CAP1
Rabbits
SIDE-CHAIN
Protein Binding
NUCLEATION
Cofilin 1
STRUCTURAL BASIS
Science
cofilin
macromolecular substances
Molecular Dynamics Simulation
SRV2/CAP COMPLEX
114 Physical sciences
Article
General Biochemistry
Genetics and Molecular Biology
PARAMETERS
03 medical and health sciences
Animals
Protein Interaction Domains and Motifs
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biochemistry [q-bio.BM]
Actin
030304 developmental biology
X-ray crystallography
Depolymerization
actin filament turnover
actin disassembly
General Chemistry
Actins
molecular dynamics
Cytoskeletal proteins
MOLECULAR-DYNAMICS
Biophysics
1182 Biochemistry
cell and molecular biology
lcsh:Q
Carrier Proteins
Gelsolin
030217 neurology & neurosurgery
Zdroj: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Nature Communications
Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-13213-2⟩
ISSN: 2041-1723
Popis: HFD-bound and HFD-free simulation systems presented in the paper; see table_of_simulations.pdf Contents of the simulation_archive: _FORCEFIELD: Force field parameters and topologies in GROMACS format amber-ff14SB.ff: The required force field parameters compiled for all systems.*** actin: chicken actin | topology (mol.itp)***, structure (mol.gro) ncap: mouse HFD domain (CAP) | topology (mol.itp)***, structure (mol.gro) ADP: ADP | topology (mol.itp)***, structure (mol.gro) MMG: multisite Mg2+ | topology (mol.itp)***, structure (mol.gro) cofilin: rabbit cofilin | topology (mol.itp)***, structure (mol.gro) dock: the "platform" region | topology (mol.itp), structure (mol.gro), the position restraints (position_restraints.itp) _parametrize_HIC: Amber format parameters for methyl-histidine (Nτ-Methyl-L-histidine, HIC) to be used together with amber-ff14SB force field. Charges were calculated based on the protocol by Duan, Y. et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24, 1999–2012 (2003). Missing bonded parameters were adopted from GAFF2. *** Converted to GROMACS from amber format using the ParmEd tool (https://github.com/ParmEd/ParmEd) HFD-bound: contains the directories for each simulation repeat listed in the table of simulations. 1, 2, and 3: simulations that were started by replacing the terminal actins with HFD-bound actins. 1' and 2': simulations that were started by docking HFD after some simulation without HFD (see below HFD-free simulations 1 and 2) HFD-free: contains the directories for each simulation repeat listed in the table of simulations. 1, 2, and 3: simulations of the cofilin-decorated actin filament. 2': simulations that was started by removing HFD from the HFD-bound system (see above HFD-bound simulation 2) Each subdirectory (under 1 2 3, etc.) contains prod.mdp: simulation setting file topol.top: GROMACS topology file t0.pdb: initial coordinates for simulation obtained after a set of restrained NVT and NpT equilibration steps prod0.tpr: the GROMACS tpr file index.ndx: index file nW.pdb: t0.pdb with all water molecules removed nW.xtc: the simulation trajectory with all water molecules removed. _FORCEFIELD: link to ../../_FORCEFIELD
{"references":["Kotila, T., Wioland, H., Enkavi, G. et al. Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin. Nat Commun 10, 5320 (2019) doi:10.1038/s41467-019-13213-2"]}
Databáze: OpenAIRE
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