Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles
Abstract
Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validationmore »
- Authors:
-
- Univ. of California San Francisco, San Francisco, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Australian National Univ., Canberra, ACT (Australia)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California Berkeley, Berkeley, CA (United States)
- Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch (France); Univ. de Lorraine, Vandoeuvre-les-Nancy (France)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1214720
- Alternate Identifier(s):
- OSTI ID: 1225739
- Report Number(s):
- LA-UR-14-28191
Journal ID: ISSN 1399-0047; ABCRE6; PII: S1399004715007415
- Grant/Contract Number:
- AC52-06NA25396
- 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:
- 59 BASIC BIOLOGICAL SCIENCES; diffuse scattering; TLS; correlated motion; structural ensemble; structure refinement
Citation Formats
Van Benschoten, Andrew H., Afonine, Pavel V., Terwilliger, Thomas C., Wall, Michael E., Jackson, Colin J., Sauter, Nicholas K., Adams, Paul D., Urzhumtsev, Alexandre, and Fraser, James S. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles. United States: N. p., 2015.
Web. doi:10.1107/S1399004715007415.
Van Benschoten, Andrew H., Afonine, Pavel V., Terwilliger, Thomas C., Wall, Michael E., Jackson, Colin J., Sauter, Nicholas K., Adams, Paul D., Urzhumtsev, Alexandre, & Fraser, James S. Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles. United States. https://doi.org/10.1107/S1399004715007415
Van Benschoten, Andrew H., Afonine, Pavel V., Terwilliger, Thomas C., Wall, Michael E., Jackson, Colin J., Sauter, Nicholas K., Adams, Paul D., Urzhumtsev, Alexandre, and Fraser, James S. Tue .
"Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles". United States. https://doi.org/10.1107/S1399004715007415. https://www.osti.gov/servlets/purl/1214720.
@article{osti_1214720,
title = {Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles},
author = {Van Benschoten, Andrew H. and Afonine, Pavel V. and Terwilliger, Thomas C. and Wall, Michael E. and Jackson, Colin J. and Sauter, Nicholas K. and Adams, Paul D. and Urzhumtsev, Alexandre and Fraser, James S.},
abstractNote = {Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.},
doi = {10.1107/S1399004715007415},
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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