ArticleThe journal of physical chemistry. B2017
Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Assembly and Functional Coordination of Two Families of Metabolic Organelles in Salmonella.Microbial biotechnology · 2026Article
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment.The journal of physical chemistry. B · 2025Article
- Robust Synthetic Biology Toolkit to Advance Carboxysome Study and Redesign.ACS synthetic biology · 2025Article
- Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System.ACS synthetic biology · 2025Article
- Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation.Frontiers in plant science · 2024Review
- A single shell protein plays a major role in choline transport across the shell of the choline utilization microcompartment ofMicrobiology (Reading, England) · 2023Article
- Monatomic ions influence substrate permeation across bacterial microcompartment shells.Scientific reports · 2023Article
- Pore structure controls stability and molecular flux in engineered protein cages.Science advances · 2022Article
- Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments.Acta crystallographica. Section F, Structural biology communications · 2021Article
- Selective molecular transport across the protein shells of bacterial microcompartments.Current opinion in microbiology · 2021Review
- Recent structural insights into bacterial microcompartment shells.Current opinion in microbiology · 2021Review
- Advances in the World of Bacterial Microcompartments.Trends in biochemical sciences · 2021Review
- Article
- Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein.Scientific reports · 2020Article
- Prokaryotic Organelles: Bacterial Microcompartments inEcoSal Plus · 2020Review
- Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment ofMicrobiology (Reading, England) · 2019Article
- Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.Scientific reports · 2018Article
- A Bacterial Microcompartment Is Used for Choline Fermentation by Escherichia coli 536.Journal of bacteriology · 2018Article
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Authors and funding
5 authors.
Funding
Abstract
Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, propionaldehyde. Using both metadynamics and replica-exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic propionaldehyde generated within the microcompartment. The energetic effect is consistent with a lower capacity of a serine side chain, which protrudes into the pore at a point of constriction, to form hydrogen bonds with propionaldehyde relative to the more freely permeable propanediol. The results highlight the importance of molecular diffusion and transport in a new biological context.
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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.