ArticleBiophysical journal2012
Coarse-graining provides insights on the essential nature of heterogeneity in actin filaments.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows.The journal of physical chemistry. B · 2025Article
- Molecular Dynamics Assessment of Mechanical Properties of the Thin Filaments in Cardiac Muscle.International journal of molecular sciences · 2023Article
- Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament.The journal of physical chemistry letters · 2021Article
- Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Plastic Deformation and Fragmentation of Strained Actin Filaments.Biophysical journal · 2019Article
- Multiscale simulation of actin filaments and actin-associated proteins.Biophysical reviews · 2018Review
- Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments.Biophysical journal · 2018Article
- Molecular Consequences of the Myopathy-Related D286G Mutation on Actin Function.Frontiers in physiology · 2018Article
- Coarse-Grained Directed Simulation.Journal of chemical theory and computation · 2017Article
- Actin Filament Strain Promotes Severing and Cofilin Dissociation.Biophysical journal · 2017Article
- Highly Coarse-Grained Representations of Transmembrane Proteins.Journal of chemical theory and computation · 2017Article
- Myopathy-inducing mutation H40Y in ACTA1 hampers actin filament structure and function.Biochimica et biophysica acta · 2016Article
- Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits.The journal of physical chemistry. B · 2016Article
- The Importance of Intrinsically Disordered Segments of Cardiac Troponin in Modulating Function by Phosphorylation and Disease-Causing Mutations.Frontiers in physiology · 2016Review
- Unraveling the mystery of ATP hydrolysis in actin filaments.Journal of the American Chemical Society · 2014Article
- Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain.Biophysical journal · 2013Article
- Molecular origins of cofilin-linked changes in actin filament mechanics.Journal of molecular biology · 2013Article
- MICAL, the flavoenzyme participating in cytoskeleton dynamics.International journal of molecular sciences · 2013Review
- Calcium induced regulation of skeletal troponin--computational insights from molecular dynamics simulations.PloS one · 2013Article
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3 authors.
Funding
Abstract
Experiments have shown that actin is structurally polymorphic, but knowledge of the details of molecular level heterogeneity in both the dynamics of a single subunit and the interactions between subunits is still lacking. Here, using atomistic molecular dynamics simulations of the actin filament, we identify domains of atoms that move in a correlated fashion, quantify interactions between these domains using coarse-grained (CG) analysis methods, and perform CG simulations to explore the importance of filament heterogeneity. The persistence length and torsional stiffness calculated from molecular dynamics simulation data agree with experimental values. We additionally observe that distinct actin conformations coexist in actin filaments. The filaments also exhibit random twist angles that are broadly distributed. CG analysis reveals that interactions between equivalent CG pairs vary from one subunit to another. To explore the importance of heterogeneity on filament dynamics, we perform CG simulations using different methods of parameterization to show that only by including heterogeneous interactions can we reproduce the twist angles and related properties. Free energy calculations further suggest that in general the actin filament is best represented as a set of subunits with differing CG sites and interactions, and the incorporating heterogeneity into the CG interactions is more important than including that in the CG sites. Our work therefore presents a systematic method to explore molecular level detail in this large and complex biopolymer.
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