Conservation of conformational dynamics across prokaryotic actins

The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins, these techniques cannot probe molecular-scale conformation...

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Bibliographic Details
Published in:PLoS computational biology Vol. 15; no. 4; p. e1006683
Main Authors: Ng, Natalie, Shi, Handuo, Colavin, Alexandre, Huang, Kerwyn Casey
Format: Journal Article
Language:English
Published: United States Public Library of Science 01.04.2019
Public Library of Science (PLoS)
Subjects:
Actin
Actins - chemistry
Archaea
Bacteria
Bacterial Proteins - chemistry
Bioengineering
Biology and Life Sciences
Biophysics
Cell division
Computational Biology
Crystallography
Crystallography, X-Ray
Cytoskeletal proteins
Cytoskeletal Proteins - chemistry
Cytoskeleton
Dihedral angle
Dimers
E coli
Electron microscopy
Escherichia coli Proteins - chemistry
Eukaryotes
Family relations
Funding
Homology
Microscopy
Models, Molecular
Molecular dynamics
Molecular Dynamics Simulation
Molecular structure
Monomers
Morphogenesis
Muscle proteins
Mutation
Nucleotides
Physical Sciences
Physiological aspects
Polymerization
Prokaryotes
Protein Conformation
Protein Interaction Domains and Motifs
Proteins
Pyrobaculum - chemistry
Rigid structures
Software
Structural Homology, Protein
Supervision
X-ray crystallography
United States > US
ISSN:1553-7358, 1553-734X, 1553-7358
Online Access:Get full text
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Description
Summary:The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins, these techniques cannot probe molecular-scale conformational dynamics. Here, we use all-atom molecular dynamic simulations to reveal conserved dynamical behaviors in four prokaryotic actin homologs: MreB, FtsA, ParM, and crenactin. We demonstrate that the majority of the conformational dynamics of prokaryotic actins can be explained by treating the four subdomains as rigid bodies. MreB, ParM, and FtsA monomers exhibited nucleotide-dependent dihedral and opening angles, while crenactin monomer dynamics were nucleotide-independent. We further show that the opening angle of ParM is sensitive to a specific interaction between subdomains. Steered molecular dynamics simulations of MreB, FtsA, and crenactin dimers revealed that changes in subunit dihedral angle lead to intersubunit bending or twist, suggesting a conserved mechanism for regulating filament structure. Taken together, our results provide molecular-scale insights into the nucleotide and polymerization dependencies of the structure of prokaryotic actins, suggesting mechanisms for how these structural features are linked to their diverse functions.
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The authors have declared that no competing interests exist.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1006683