ArticleNucleic acids research2014
Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 20 citations in OpenAlex.
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- Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes.Molecular biology and evolution · 2016Article
- Modeling and fitting protein-protein complexes to predict change of binding energy.Scientific reports · 2016Article
- MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.Nucleic acids research · 2016Article
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Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
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Abstract
Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.
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