ArticleActa crystallographica. Section D, Biological crystallography2015
From deep TLS validation to ensembles of atomic models built from elemental motions.
Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A method for intuitively extracting macromolecular dynamics from structural disorder.Nature communications · 2021Article
- Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor HJournal of computer-aided molecular design · 2020Article
- Article
- From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.Acta crystallographica. Section D, Structural biology · 2018Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Germinal-center kinase-like kinase co-crystal structure reveals a swapped activation loop and C-terminal extension.Protein science : a publication of the Protein Society · 2017Article
- From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.Acta crystallographica. Section D, Structural biology · 2016Article
- Measuring and modeling diffuse scattering in protein X-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Identifying and Visualizing Macromolecular Flexibility in Structural Biology.Frontiers in molecular biosciences · 2016Review
- Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.Acta crystallographica. Section D, Biological crystallography · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
The translation-libration-screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
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