RNA protects a nucleoprotein complex against radiation damage
Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation cha...
| Main Authors: | , , , , , , |
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| Format: | Journal article |
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International Union of Crystallography
2016
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| _version_ | 1826270086749487104 |
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| author | Garman, E Bury, C Gerstel, M McGeehan, J Antson, A Carmichael, I Shevtsov, M |
| author_facet | Garman, E Bury, C Gerstel, M McGeehan, J Antson, A Carmichael, I Shevtsov, M |
| author_sort | Garman, E |
| collection | OXFORD |
| description | Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterised within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein T 2 complexes. Here we have developed a methodology whereby per-atom density changes can be quantified with increasing dose, over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. We determine specific damage manifestations within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, RNA is found to be far less susceptible to radiation-induced chemical changes than protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding on protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA-binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, our method enabled quantification of the reduction in radiation- induced Lys and Phe disordering upon RNA-binding, directly from the electron density. |
| first_indexed | 2024-03-06T21:35:21Z |
| format | Journal article |
| id | oxford-uuid:46111a6f-8190-4ec9-9105-c9ee80b7a96f |
| institution | University of Oxford |
| last_indexed | 2024-03-06T21:35:21Z |
| publishDate | 2016 |
| publisher | International Union of Crystallography |
| record_format | dspace |
| spelling | oxford-uuid:46111a6f-8190-4ec9-9105-c9ee80b7a96f2022-03-26T15:11:30ZRNA protects a nucleoprotein complex against radiation damageJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:46111a6f-8190-4ec9-9105-c9ee80b7a96fSymplectic Elements at OxfordInternational Union of Crystallography2016Garman, EBury, CGerstel, MMcGeehan, JAntson, ACarmichael, IShevtsov, MRadiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterised within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein T 2 complexes. Here we have developed a methodology whereby per-atom density changes can be quantified with increasing dose, over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. We determine specific damage manifestations within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, RNA is found to be far less susceptible to radiation-induced chemical changes than protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding on protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA-binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, our method enabled quantification of the reduction in radiation- induced Lys and Phe disordering upon RNA-binding, directly from the electron density. |
| spellingShingle | Garman, E Bury, C Gerstel, M McGeehan, J Antson, A Carmichael, I Shevtsov, M RNA protects a nucleoprotein complex against radiation damage |
| title | RNA protects a nucleoprotein complex against radiation damage |
| title_full | RNA protects a nucleoprotein complex against radiation damage |
| title_fullStr | RNA protects a nucleoprotein complex against radiation damage |
| title_full_unstemmed | RNA protects a nucleoprotein complex against radiation damage |
| title_short | RNA protects a nucleoprotein complex against radiation damage |
| title_sort | rna protects a nucleoprotein complex against radiation damage |
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