ArticleJournal of the American Chemical Society2017
The Impact of Protonation on Early Translocation of Anthrax Lethal Factor: Kinetics from Molecular Dynamics Simulations and Milestoning Theory.
Article in Journal of the American Chemical Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.Journal of chemical theory and computation · 2022Article
- Design of Peptides for Membrane Insertion: The Critical Role of Charge Separation.The journal of physical chemistry. B · 2022Article
- Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation.The journal of physical chemistry. B · 2022Article
- Anthrax toxin translocation complex reveals insight into the lethal factor unfolding and refolding mechanism.Scientific reports · 2021Article
- Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning.The journal of physical chemistry. B · 2021Article
- Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction.Life (Basel, Switzerland) · 2021Article
- Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2021Article
- A Minimal, Adaptive Binning Scheme for Weighted Ensemble Simulations.The journal of physical chemistry. A · 2021Article
- Exploring the Reaction Mechanism of HIV Reverse Transcriptase with a Nucleotide Substrate.The journal of physical chemistry. B · 2020Article
- The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.Biochimica et biophysica acta. General subjects · 2020Article
- ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.Journal of chemical theory and computation · 2020Article
- Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW.The journal of physical chemistry. B · 2019Article
- Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability.Journal of chemical theory and computation · 2019Article
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- Probing Translocation in Mutants of the Anthrax Channel: Atomically Detailed Simulations with Milestoning.The journal of physical chemistry. B · 2018Article
- Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.The journal of physical chemistry letters · 2018Article
- Pyrophosphate Release in the Protein HIV Reverse Transcriptase.The journal of physical chemistry. B · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
We report atomically detailed molecular dynamics simulations of the permeation of the lethal factor (LF) N-terminal segment through the anthrax channel. The N-terminal chain is unstructured and leads the permeation process for the LF protein. The simulations were conducted in explicit solvent with milestoning theory, making it possible to extract kinetic information from nanosecond to millisecond time scales. We illustrate that the initial event is strongly influenced by the protonation states of the permeating amino acids. While the N-terminal segment passes easily at high protonation state through the anthrax channel (and the ϕ clamp), the initial permeation represents a critical step, which can be irreversible and establishes a hook in the channel mouth.
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Registered trials
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.