ArticleStructural dynamics (Melville, N.Y.)2020
A tool for visualizing protein motions in time-resolved crystallography.
Article in Structural dynamics (Melville, N.Y.), 2020. 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.
- Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography.Nature communications · 2025Article
- Structural Insights Into the Opening Mechanism of C1C2 Channelrhodopsin.Journal of the American Chemical Society · 2025Article
- Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate.Nature communications · 2024Article
- ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering.Journal of chemical information and modeling · 2024Article
- Appraising protein conformational changes by resampling time-resolved serial x-ray crystallography data.Structural dynamics (Melville, N.Y.) · 2024Article
- Dynamic three-dimensional structures of a metal-organic framework captured with femtosecond serial crystallography.Nature chemistry · 2024Article
- Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.Nature chemistry · 2024Article
- Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.Nature chemistry · 2023Article
- Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.Journal of the American Chemical Society · 2023Article
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- Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography.Nature communications · 2023Article
- Simulation toolkits at the molecular scale for trans-scale thermal signaling.Computational and structural biotechnology journal · 2023Review
- Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization.Nature communications · 2022Article
- Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.Annual review of biophysics · 2022Review
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- Discerning best practices in XFEL-based biological crystallography - standards for nonstandard experiments.IUCrJ · 2021Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature of electron density changes and their correlation with modeled protein structural changes. Here, we use TR-SFX data from bacteriorhodopsin to develop and validate a method for quantifying time-dependent electron density changes and correlating them throughout the protein. We define a spherical volume of difference electron density about selected atoms, average separately the positive and negative electron difference densities within each volume, and walk this spherical volume through all atoms within the protein. By correlating the resulting difference electron density amplitudes with time, our approach facilitates an initial assessment of the number and timescale of structural intermediates and highlights quake-like motions on the sub-picosecond timescale. This tool also allows structural models to be compared with experimental data using theoretical difference electron density changes calculated from refined resting and photo-activated structures.
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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.