ArticleBiophysical journal2008
Simulation of structure, orientation, and energy transfer between AlexaFluor molecules attached to MscL.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Integrating Molecular Dynamics Simulations and Single-molecule FRET Spectroscopy: From Computational FRET Estimation to Experimental Data Interpretation.The journal of physical chemistry. B · 2026Review
- Computational biophysical characterization of a superradiant virus-like particle in its ground state.bioRxiv : the preprint server for biology · 2025Article
- Determination of FRET orientation factor between artificial fluorophore and photosynthetic light-harvesting 2 complex (LH2).Scientific reports · 2022Article
- Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation.RSC advances · 2022Article
- Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex.RNA (New York, N.Y.) · 2020Article
- Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase.eLife · 2018Article
- Multifunctional, Micropipette-based Method for Incorporation And Stimulation of Bacterial Mechanosensitive Ion Channels in Droplet Interface Bilayers.Journal of visualized experiments : JoVE · 2015Article
- Activation of bacterial channel MscL in mechanically stimulated droplet interface bilayers.Scientific reports · 2015Article
- Quantitative interpretation of FRET experiments via molecular simulation: force field and validation.Biophysical journal · 2015Article
- A starting point for fluorescence-based single-molecule measurements in biomolecular research.Molecules (Basel, Switzerland) · 2014Review
- Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study.Biophysical journal · 2014Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Simulation vs. reality: a comparison of in silico distance predictions with DEER and FRET measurements.PloS one · 2012Article
- Article
- Fluorescence lifetime measurements and biological imaging.Chemical reviews · 2010Review
- Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins.European biophysics journal : EBJ · 2010Article
- Structural changes in the cytoplasmic domain of the mechanosensitive channel MscS during opening.Biophysical journal · 2009Article
- Nicotine normalizes intracellular subunit stoichiometry of nicotinic receptors carrying mutations linked to autosomal dominant nocturnal frontal lobe epilepsy.Molecular pharmacology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Measurements of time-resolved fluorescence anisotropy and fluorescence resonance energy transfer are finding many applications in the study of biological macromolecules as they enable structural properties of the host molecules to be determined in their natural environment. A difficulty in interpreting these experiments is that they both require knowledge of the relative orientation of the fluorophores, a property that is almost impossible to measure. Here we conduct simulations of AlexaFluor488 and AlexaFluor568 attached to two sites on the membrane channel MscL to provide an alternative mechanism for determining the likely configurations and orientational freedom of the fluorophores, as well as the most likely value of the orientation factor kappa(2) for energy transfer between them. The fluorophores are relatively mobile, and are found to be more so when immersed in bulk water than when they interact with the lipid membrane. The fluorophores never insert deeply into the lipid, despite their hydrophobic linkers and aromatic headgroup structures. Properties such as the fluorescence anisotropy decay can be predicted from simulations of the fluorophores in bulk water that closely match experimental data. In contrast, when the fluorophores were attached to the large MscL protein it was difficult to sample all the possible configurations of the fluorophores due to the computational time required. While this approach is likely to provide useful data on solvent-accessible fluorophores attached to small proteins, simulations lasting >50 ns or the use of biasing forces are required to accurately predict orientation factors for use in energy transfer experiments on larger membrane-bound proteins.
Indexed as
Identifiers
What OpenQuestion holds
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.