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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Vydané v:PLoS computational biology Ročník 15; číslo 4; s. e1006683
Hlavní autori: Ng, Natalie, Shi, Handuo, Colavin, Alexandre, Huang, Kerwyn Casey
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 01.04.2019
Public Library of Science (PLoS)
Predmet:
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
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Abstract 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.
AbstractList 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.
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. Simulations are a critical tool for uncovering the molecular mechanisms underlying biological form and function. Here, we use molecular-dynamics simulations to identify common and specific dynamical behaviors in four prokaryotic homologs of actin, a cytoskeletal protein that plays important roles in cellular structure and division in eukaryotes. The four actin homologs have diverse functions including cell division, cell shape maintenance, and DNA segmentation. Dihedral angles and opening angles in monomers of bacterial MreB, FtsA, and ParM were all sensitive to whether the subunit was bound to ATP or ADP, unlike in the archaeal homolog crenactin. In simulations of MreB, FtsA, and crenactin dimers, changes in subunit dihedral angle led to bending or twisting in filaments of these proteins, suggesting a mechanism for regulating the properties of large filaments. Taken together, our simulations set the stage for understanding and exploiting structure-function relationships of prokaryotic cytoskeletons.
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.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.
Audience Academic
Author Ng, Natalie
Huang, Kerwyn Casey
Shi, Handuo
Colavin, Alexandre
AuthorAffiliation 2 Biophysics Program, Stanford University, Stanford, CA, United States of America
4 Chan Zuckerberg Biohub, San Francisco, CA, United States of America
3 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States of America
1 Department of Bioengineering, Stanford University, Stanford, CA, United States of America
Yale University, UNITED STATES
AuthorAffiliation_xml – name: 4 Chan Zuckerberg Biohub, San Francisco, CA, United States of America
– name: Yale University, UNITED STATES
– name: 2 Biophysics Program, Stanford University, Stanford, CA, United States of America
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– name: 3 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States of America
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CitedBy_id crossref_primary_10_1016_j_csbj_2022_10_008
crossref_primary_10_3389_fmicb_2021_639883
crossref_primary_10_1038_s41467_020_14752_9
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Snippet The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and...
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StartPage e1006683
SubjectTerms 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
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Title Conservation of conformational dynamics across prokaryotic actins
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Volume 15
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