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

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography (Online)
 [1];  [2];  [3];  [3];  [4]
  1. CNRS–INSERM–UdS, Illkirch (France). Centre for Integrative Biology; Universite´ de Lorraine, Nancy (France). Faculte des Sciences et Technolgoies
  2. Lawrence Berkeley National Lab., Berkeley, CA (United States). Physical Biosciences Div
  3. Univ. of California, San Francisco, CA (United States). Dept. of Bioengineering and Therapeutic Sciences
  4. Lawrence Berkeley National Lab., Berkeley, CA (United States). Physical Biosciences Div.; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1213057
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 71, Issue 8; ISSN 1399-0047
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 13 works
Citation information provided by
Web of Science

References (40)

Validation of crystallographic models containing TLS or other descriptions of anisotropy journal July 2010
Exploring the Structural Dynamics of the E.coli Chaperonin GroEL Using Translation-libration-screw Crystallographic Refinement of Intermediate States journal September 2004
The analysis of the anisotropic thermal motion of molecules in crystals journal September 1956
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage1 1Edited by K. Morikawa journal April 2001
Correlation of Internal Torsional Motion with Overall Molecular Motion in Crystals journal October 1998
Refinement of the arginine kinase transition-state analogue complex at 1.2 Å resolution: mechanistic insights journal November 2002
The Structure and Function of a Novel Glycerophosphodiesterase from Enterobacter aerogenes journal April 2007
TLSANL : TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures journal August 1993
Domain flexibility in aspartic proteinases journal February 1992
Description of overall anisotropy in diffraction from macromolecular crystals journal January 1987
Use of TLS parameters to model anisotropic displacements in macromolecular refinement journal January 2001
Coupling between the translational and rotational brownian motions of rigid particles of arbitrary shape journal March 1967
Bulk-solvent and overall scaling revisited: faster calculations, improved results journal March 2013
TLS from fundamentals to practice journal October 2013
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps.acidophila at 2.0Å Resolution and 100K: New Structural Features and Functionally Relevant Motions journal March 2003
Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms journal April 2013
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
TLSMD web server for the generation of multi-group TLS models journal January 2006
Macromolecular TLS Refinement in REFMAC at Moderate Resolutions book January 2003
A molecular viewer for the analysis of TLS rigid-body motion in macromolecules journal March 2005
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework journal January 2002
The segmented anisotropic refinement of monoclinic papain by the application of the rigid-body TLS model and comparison to bovine ribonuclease A journal February 1992
Refinement at atomic resolution book April 2012
Rigid protein motion as a model for crystallographic temperature factors. journal April 1991
On the handling of atomic anisotropic displacement parameters journal July 2002
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion journal March 2006
The Protein Data Bank journal January 2000
Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III: Implications for Ca journal November 1999
A lattice-dynamical interpretation of molecular rigid-body vibration tensors journal September 1973
Efficient anisotropic refinement of macromolecular structures using FFT journal January 1999
On the rigid-body motion of molecules in crystals journal January 1968
The protein data bank: A computer-based archival file for macromolecular structures journal May 1977
Dynamics of folded proteins journal June 1977
Intersubunit Bridge Formation Governs Agonist Efficacy at Nicotinic Acetylcholine α4β2 Receptors: UNIQUE ROLE OF HALOGEN BONDING REVEALED journal December 2011
The 1.0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity journal September 2000
The structure factor book October 2006
Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles journal July 2015
Non-rigid-body thermal-motion analysis journal January 1973
Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model journal December 1989

Cited By (2)

Measuring and modeling diffuse scattering in protein X-ray crystallography journal March 2016
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

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
TLS model
TLS matrices
model validation
molecular mobility
ensemble of models
diffuse scattering
libration
vibration
correlated motion