ArticleProceedings of the National Academy of Sciences of the United States of America2009
Nucleotide-dependent conformational states of actin.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 113 citations in OpenAlex.
- Mechanism of phosphate release from actin filaments.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.Journal of chemical theory and computation · 2024Article
- Mechanism of Phosphate Release from Actin Filaments.bioRxiv : the preprint server for biology · 2024Article
- Molecular Dynamics Assessment of Mechanical Properties of the Thin Filaments in Cardiac Muscle.International journal of molecular sciences · 2023Article
- Structural basis for receptor selectivity and inverse agonism in S1PNature communications · 2022Article
- New Insights into Cellular Functions of Nuclear Actin.Biology · 2021Review
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- Biased localization of actin binding proteins by actin filament conformation.Nature communications · 2020Article
- Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription.Cell reports · 2020Article
- Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model.Biophysical journal · 2020Article
- D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-Actin.Structure (London, England : 1993) · 2020Article
- 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
- Direct Interaction between the Two Z Ring Membrane Anchors FtsA and ZipA.Journal of bacteriology · 2019Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- 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
- Coarse-Grained Directed Simulation.Journal of chemical theory and computation · 2017Article
- Actin Filament Strain Promotes Severing and Cofilin Dissociation.Biophysical journal · 2017Article
- The allosteric switching mechanism in bacteriophage MS2.The Journal of chemical physics · 2016Article
- Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits.The journal of physical chemistry. B · 2016Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
The influence of the state of the bound nucleotide (ATP, ADP-Pi, or ADP) on the conformational free-energy landscape of actin is investigated. Nucleotide-dependent folding of the DNase-I binding (DB) loop in monomeric actin and the actin trimer is carried out using all-atom molecular dynamics (MD) calculations accelerated with a multiscale implementation of the metadynamics algorithm. Additionally, an investigation of the opening and closing of the actin nucleotide binding cleft is performed. Nucleotide-dependent free-energy profiles for all of these conformational changes are calculated within the framework of metadynamics. We find that in ADP-bound monomer, the folded and unfolded states of the DB loop have similar relative free-energy. This result helps explain the experimental difficulty in obtaining an ordered crystal structure for this region of monomeric actin. However, we find that in the ADP-bound actin trimer, the folded DB loop is stable and in a free-energy minimum. It is also demonstrated that the nucleotide binding cleft favors a closed conformation for the bound nucleotide in the ATP and ADP-Pi states, whereas the ADP state favors an open confirmation, both in the monomer and trimer. These results suggest a mechanism of allosteric interactions between the nucleotide binding cleft and the DB loop. This behavior is confirmed by an additional simulation that shows the folding free-energy as a function of the nucleotide cleft width, which demonstrates that the barrier for folding changes significantly depending on the value of the cleft width.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.