ArticleThe journal of physical chemistry. B2013
Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Seven inducible promoters for Zymomonas mobilis.Microbial cell factories · 2026Article
- Dark-State-Mediated Photobleaching in mCherry-Based Red Fluorescent Proteins.The journal of physical chemistry letters · 2026Article
- Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis.Protein engineering, design & selection : PEDS · 2026Article
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation.Nature communications · 2023Article
- Fluorescence Microscopy Study of the Intracellular Sulfur Globule Protein SgpD in the Purple Sulfur BacteriumMicroorganisms · 2023Article
- Molecular Dynamics Force Field Parameters for the EGFP Chromophore and Some of Its Analogues.The journal of physical chemistry. B · 2023Article
- Over the rainbow: structural characterization of the chromoproteins gfasPurple, amilCP, spisPink and eforRed.Acta crystallographica. Section D, Structural biology · 2022Article
- A Red Fluorescent Protein Reporter System Developed for Measuring Gene Expression in Photosynthetic Bacteria under Anaerobic Conditions.Microorganisms · 2022Article
- Monomerization of far-red fluorescent proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Cysteine Sulfoxidation Increases the Photostability of Red Fluorescent Proteins.ACS chemical biology · 2016Article
- Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting.Scientific reports · 2016Article
- pH-dependent transient conformational states control optical properties in cyan fluorescent protein.Journal of the American Chemical Society · 2015Article
- Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching.Integrative biology : quantitative biosciences from nano to macro · 2015Article
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Authors and funding
4 authors.
Funding
Abstract
The development of fluorescent proteins (FPs) has revolutionized cell biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for tagging and tracking cellular processes in vivo. Determining oxygen diffusion pathways in FPs can be important for improving photostability and for understanding maturation of the chromophore. We use molecular dynamics (MD) calculations to investigate the diffusion of molecular oxygen in one of the most useful monomeric RFPs, mCherry. We describe a pathway that allows oxygen molecules to enter from the solvent and travel through the protein barrel to the chromophore. We calculate the free-energy of an oxygen molecule at points along the path. The pathway contains several oxygen hosting pockets, which are identified by the amino acid residues that form the pocket. We also investigate an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.
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