From deep TLS validation to ensembles of atomic models built from elemental motions
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.
- Authors:
-
- CNRS–INSERM–UdS, Illkirch (France). Centre for Integrative Biology; Universite´ de Lorraine, Nancy (France). Faculte des Sciences et Technolgoies
- Lawrence Berkeley National Lab., Berkeley, CA (United States). Physical Biosciences Div
- Univ. of California, San Francisco, CA (United States). Dept. of Bioengineering and Therapeutic Sciences
- Lawrence Berkeley National Lab., Berkeley, CA (United States). Physical Biosciences Div.; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1213057
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D: Biological Crystallography (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 8; Journal ID: ISSN 1399-0047
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; TLS model; TLS matrices; model validation; molecular mobility; ensemble of models; diffuse scattering; libration; vibration; correlated motion
Citation Formats
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., and Adams, Paul D. From deep TLS validation to ensembles of atomic models built from elemental motions. United States: N. p., 2015.
Web. doi:10.1107/S1399004715011426.
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., & Adams, Paul D. From deep TLS validation to ensembles of atomic models built from elemental motions. United States. https://doi.org/10.1107/S1399004715011426
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., and Adams, Paul D. Tue .
"From deep TLS validation to ensembles of atomic models built from elemental motions". United States. https://doi.org/10.1107/S1399004715011426. https://www.osti.gov/servlets/purl/1213057.
@article{osti_1213057,
title = {From deep TLS validation to ensembles of atomic models built from elemental motions},
author = {Urzhumtsev, Alexandre and Afonine, Pavel V. and Van Benschoten, Andrew H. and Fraser, James S. and Adams, Paul D.},
abstractNote = {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.},
doi = {10.1107/S1399004715011426},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 8,
volume = 71,
place = {United States},
year = {Tue Jul 28 00:00:00 EDT 2015},
month = {Tue Jul 28 00:00:00 EDT 2015}
}
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Works referencing / citing this record:
Measuring and modeling diffuse scattering in protein X-ray crystallography
journal, March 2016
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- Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
journal, June 2018
- Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre
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