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Literature DB >> 25249713

TLS from fundamentals to practice.

Alexandre Urzhumtsev¹, Pavel V Afonine², Paul D Adams³.

Abstract

The Translation-Libration-Screw-rotation (TLS) model of rigid-body harmonic displacements introduced in crystallography by Schomaker & Trueblood (1968) is now a routine tool in macromolecular studies and is a feature of most modern crystallographic structure refinement packages. In this review we consider a number of simple examples that illustrate important features of the TLS model. Based on these examples simplified formulae are given for several special cases that may occur in structure modeling and refinement. The derivation of general TLS formulae from basic principles is also provided. This manuscript describes the principles of TLS modeling, as well as some select algorithmic details for practical application. An extensive list of applications references as examples of TLS in macromolecular crystallography refinement is provided.

Entities: Chemical Disease Gene Species

Keywords: ADP; TLS; atomic displacement parameter; rigid body motion; structure refinement; translation libration screw model

Year: 2013 PMID： 25249713 PMCID： PMC4170067 DOI： 10.1080/0889311X.2013.835806

Source DB: PubMed Journal: Crystallogr Rev ISSN： 0889-311X Impact factor: 2.467

49 in total

1. The three-dimensional structure of human S100A12.

Authors: O V Moroz; A A Antson; G N Murshudov; N J Maitland; G G Dodson; K S Wilson; I Skibshøj; E M Lukanidin; I B Bronstein
Journal: Acta Crystallogr D Biol Crystallogr Date: 2001-01

2. Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis.

Authors: V M Ducros; R J Lewis; C S Verma; E J Dodson; G Leonard; J P Turkenburg; G N Murshudov; A J Wilkinson; J A Brannigan
Journal: J Mol Biol Date: 2001-03-02 Impact factor: 5.469

Review 3. Expanding the model: anisotropic displacement parameters in protein structure refinement.

Authors: E A Merritt
Journal: Acta Crystallogr D Biol Crystallogr Date: 1999-06

4. Validation of crystallographic models containing TLS or other descriptions of anisotropy.

Authors: Frank Zucker; P Christoph Champ; Ethan A Merritt
Journal: Acta Crystallogr D Biol Crystallogr Date: 2010-07-09

5. Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

Authors: A Kidera; N Go
Journal: J Mol Biol Date: 1992-05-20 Impact factor: 5.469

6. The segmented anisotropic refinement of monoclinic papain by the application of the rigid-body TLS model and comparison to bovine ribonuclease A.

Authors: G W Harris; R W Pickersgill; B Howlin; D S Moss
Journal: Acta Crystallogr B Date: 1992-02-01

7. On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor.

Authors: R Diamond
Journal: Acta Crystallogr A Date: 1990-06-01 Impact factor: 2.290

8. Local mobility of nucleic acids as determined from crystallographic data. I. RNA and B form DNA.

Authors: S R Holbrook; S H Kim
Journal: J Mol Biol Date: 1984-03-05 Impact factor: 5.469

9. Structure of 6-phosphogluconate dehydrogenase refined at 2 A resolution.

Authors: C Phillips; S Gover; M J Adams
Journal: Acta Crystallogr D Biol Crystallogr Date: 1995-05-01

10. Modelling dynamics in protein crystal structures by ensemble refinement.

Authors: B Tom Burnley; Pavel V Afonine; Paul D Adams; Piet Gros
Journal: Elife Date: 2012-12-18 Impact factor: 8.140

18 in total

1. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment.

Authors: Ivan G Shabalin; Przemyslaw J Porebski; Wladek Minor
Journal: Crystallogr Rev Date: 2018-09-21 Impact factor: 2.467

2. Uses and Abuses of the Atomic Displacement Parameters in Structural Biology.

Authors: Oliviero Carugo
Journal: Methods Mol Biol Date: 2022

3. Why are large conformational changes well described by harmonic normal modes?

Authors: Yves Dehouck; Ugo Bastolla
Journal: Biophys J Date: 2021-10-26 Impact factor: 4.033

4. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs.

Authors: Gianluca Veggiani; Bradley P Yates; Gregory D Martyn; Noah Manczyk; Alex U Singer; Igor Kurinov; Frank Sicheri; Sachdev S Sidhu
Journal: ACS Chem Biol Date: 2022-04-06 Impact factor: 4.634

5. Allostery and Hysteresis Are Coupled in Human UDP-Glucose Dehydrogenase.

Authors: Nathaniel R Beattie; Nicholas D Keul; Andrew M Sidlo; Zachary A Wood
Journal: Biochemistry Date: 2016-12-22 Impact factor: 3.162

6. Characterizing human α-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases.

Authors: Bhargavi M Boruah; Renuka Kadirvelraj; Lin Liu; Annapoorani Ramiah; Chao Li; Guanghui Zong; Gerlof P Bosman; Jeong-Yeh Yang; Lai-Xi Wang; Geert-Jan Boons; Zachary A Wood; Kelley W Moremen
Journal: J Biol Chem Date: 2020-10-01 Impact factor: 5.157