ArticleProceedings of the National Academy of Sciences of the United States of America2011
Excited states of ribosome translocation revealed through integrative molecular modeling.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.Nature communications · 2026Article
- Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.Communications biology · 2026Article
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
- Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution.Research square · 2025Article
- Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.Scientific reports · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Cryo-electron tomography reveals structural insights into the membrane remodeling mode of dynamin-like EHD filaments.Nature communications · 2022Article
- Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022).Current research in structural biology · 2022Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution.Frontiers in molecular biosciences · 2021Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Article
- Role of integrative structural biology in understanding transcriptional initiation.Methods (San Diego, Calif.) · 2019Review
- Rapid interpretation of small-angle X-ray scattering data.PLoS computational biology · 2019Article
- Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.Journal of chemical theory and computation · 2018Article
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.International journal of molecular sciences · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model.Bioscience reports · 2017Review
- A fragment based method for modeling of protein segments into cryo-EM density maps.BMC bioinformatics · 2017Article
- Enzymatic Activity and Thermodynamic Stability of Biliverdin IXβ Reductase Are Maintained by an Active Site Serine.Chemistry (Weinheim an der Bergstrasse, Germany) · 2017Article
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8 authors.
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Abstract
The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them.
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