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

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2015)

Bottom Line: 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.The description of valid underlying motions can then be output as a structural ensemble.All methods are implemented as part of the PHENIX project.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.

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.

No MeSH data available.


Related in: MedlinePlus

phenix.tls_as_xyz ensembles replicate TLS anisotropic motion. (a) GpdQ backbone with thermal ellipsoid representation of ‘entire molecule’ TLS anisotropic B factors. (b) phenix.tls_as_xyz ensemble backbones produced from ‘entire molecule’ TLS refinement. (c) Complete electron density predicted by ‘entire molecule’ TLS refinement. (d) Global correlation coefficient between experimental structure-factor amplitudes Fobs of the original GpdQ ‘entire motion’ refinement and phenix.tls_as_xyz ensembles of various sizes. Convergence values plateau at 0.935.
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fig5: phenix.tls_as_xyz ensembles replicate TLS anisotropic motion. (a) GpdQ backbone with thermal ellipsoid representation of ‘entire molecule’ TLS anisotropic B factors. (b) phenix.tls_as_xyz ensemble backbones produced from ‘entire molecule’ TLS refinement. (c) Complete electron density predicted by ‘entire molecule’ TLS refinement. (d) Global correlation coefficient between experimental structure-factor amplitudes Fobs of the original GpdQ ‘entire motion’ refinement and phenix.tls_as_xyz ensembles of various sizes. Convergence values plateau at 0.935.

Mentions: We generated the ensembles produced by alternative TLS refinements of the glycerophosphodiesterase GpdQ (Jackson et al., 2007 ▸). GpdQ is found in Enterobacter aerogenes and contributes to the homeostasis of the cell membrane by hydrolyzing the 3′–5′ phosphodiester bond in glycerophos­phodiesters. Each dimer contains three distinct domains per monomer: an α/β sandwich fold containing the active site, a domain-swapped active-site cap and a novel dimerization domain comprised of dual-stranded antiparallel β-sheets connected by a small β-sheet. Owing to the high global B factors and the presence of diffuse signal (Fig. 4 ▸), Jackson et al. (2007 ▸) performed three separate TLS refinements to model the crystalline disorder: entire molecule, monomer and subdomain. All TLS refinement attempts improved the Rfree values when compared with the standard isotropic B-factor refinement; however, there was no significant difference among the final Rfree values from the various TLS runs. We hypothesized that the diffuse scattering produced by each TLS motion would contain significant differences, as diffuse signal is a direct result of correlated motion. The notion that TLS refinement produces unique diffuse signal has been suggested previously (Tickle & Moss, 1999 ▸). Physical ensembles of the TLS motion, rather than a mathematical description, were required to generate three-dimensional diffuse scattering maps from phenix.diffuse. Visual inspection confirmed that the ensembles produced by phenix.tls_as_xyz replicated the anisotropic motion predicted by TLS thermal ellipsoids (Fig. 5 ▸). Additionally, we calculated the structure factors predicted by the original TLS refinement ‘entire molecule’ and compared them with the Fmodel values (for example, as defined in Afonine et al., 2012 ▸) produced by various phenix.tls_as_xyz ensemble sizes. The structure factors converged to a global correlation value of 0.965, demonstrating that phenix.tls_as_xyz ensembles accurately represent the motions predicted by TLS refinement. Physical representation of the underlying motion also revealed that while two of the TLS refinements produced motion with small variances (a necessity within TLS theory), using each functional region as a TLS group produced fluctuations that are clearly improbable (Fig. 4 ▸). Thus, viewing TLS refinement in the form of a structural ensemble is a valuable check of the validity of the results, as matrix elements that satisfy the previously described conditions may still produce motions that are clearly implausible.


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

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2015)

phenix.tls_as_xyz ensembles replicate TLS anisotropic motion. (a) GpdQ backbone with thermal ellipsoid representation of ‘entire molecule’ TLS anisotropic B factors. (b) phenix.tls_as_xyz ensemble backbones produced from ‘entire molecule’ TLS refinement. (c) Complete electron density predicted by ‘entire molecule’ TLS refinement. (d) Global correlation coefficient between experimental structure-factor amplitudes Fobs of the original GpdQ ‘entire motion’ refinement and phenix.tls_as_xyz ensembles of various sizes. Convergence values plateau at 0.935.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528800&req=5

fig5: phenix.tls_as_xyz ensembles replicate TLS anisotropic motion. (a) GpdQ backbone with thermal ellipsoid representation of ‘entire molecule’ TLS anisotropic B factors. (b) phenix.tls_as_xyz ensemble backbones produced from ‘entire molecule’ TLS refinement. (c) Complete electron density predicted by ‘entire molecule’ TLS refinement. (d) Global correlation coefficient between experimental structure-factor amplitudes Fobs of the original GpdQ ‘entire motion’ refinement and phenix.tls_as_xyz ensembles of various sizes. Convergence values plateau at 0.935.
Mentions: We generated the ensembles produced by alternative TLS refinements of the glycerophosphodiesterase GpdQ (Jackson et al., 2007 ▸). GpdQ is found in Enterobacter aerogenes and contributes to the homeostasis of the cell membrane by hydrolyzing the 3′–5′ phosphodiester bond in glycerophos­phodiesters. Each dimer contains three distinct domains per monomer: an α/β sandwich fold containing the active site, a domain-swapped active-site cap and a novel dimerization domain comprised of dual-stranded antiparallel β-sheets connected by a small β-sheet. Owing to the high global B factors and the presence of diffuse signal (Fig. 4 ▸), Jackson et al. (2007 ▸) performed three separate TLS refinements to model the crystalline disorder: entire molecule, monomer and subdomain. All TLS refinement attempts improved the Rfree values when compared with the standard isotropic B-factor refinement; however, there was no significant difference among the final Rfree values from the various TLS runs. We hypothesized that the diffuse scattering produced by each TLS motion would contain significant differences, as diffuse signal is a direct result of correlated motion. The notion that TLS refinement produces unique diffuse signal has been suggested previously (Tickle & Moss, 1999 ▸). Physical ensembles of the TLS motion, rather than a mathematical description, were required to generate three-dimensional diffuse scattering maps from phenix.diffuse. Visual inspection confirmed that the ensembles produced by phenix.tls_as_xyz replicated the anisotropic motion predicted by TLS thermal ellipsoids (Fig. 5 ▸). Additionally, we calculated the structure factors predicted by the original TLS refinement ‘entire molecule’ and compared them with the Fmodel values (for example, as defined in Afonine et al., 2012 ▸) produced by various phenix.tls_as_xyz ensemble sizes. The structure factors converged to a global correlation value of 0.965, demonstrating that phenix.tls_as_xyz ensembles accurately represent the motions predicted by TLS refinement. Physical representation of the underlying motion also revealed that while two of the TLS refinements produced motion with small variances (a necessity within TLS theory), using each functional region as a TLS group produced fluctuations that are clearly improbable (Fig. 4 ▸). Thus, viewing TLS refinement in the form of a structural ensemble is a valuable check of the validity of the results, as matrix elements that satisfy the previously described conditions may still produce motions that are clearly implausible.

Bottom Line: 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.The description of valid underlying motions can then be output as a structural ensemble.All methods are implemented as part of the PHENIX project.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.

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.

No MeSH data available.


Related in: MedlinePlus