From deep TLS validation to ensembles of atomic models built from elemental motions
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:

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 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:
 Grant/Contract Number:
 AC0205CH11231
 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 13990047
 Publisher:
 International Union of Crystallography
 Research Org:
 Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
 Sponsoring Org:
 USDOE
 Country of Publication:
 United States
 Language:
 English
 Subject:
 TLS model; TLS matrices; model validation; molecular mobility; ensemble of models; diffuse scattering; libration; vibration; correlated motion
 OSTI Identifier:
 1213057
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.,
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. doi:10.1107/S1399004715011426.
Urzhumtsev, Alexandre, Afonine, Pavel V., Van Benschoten, Andrew H., Fraser, James S., and Adams, Paul D.. 2015.
"From deep TLS validation to ensembles of atomic models built from elemental motions". United States.
doi: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 = {2015},
month = {7}
}