Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography

In X-ray crystallography, for the determination of the 3-D structure of macromolecules, radiation damage is still an inherent problem at modern third generation synchrotron sources, even when utilising cryo-crystallographic techniques (sample held at 100K). At doses of just several MGy, at which a t...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Radiation physics and chemistry (Oxford, England : 1993) England : 1993), 2016-11, Vol.128 (C), p.118-125
Hauptverfasser: Bury, Charles S., Carmichael, Ian, McGeehan, John E., Garman, Elspeth F.
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 125
container_issue C
container_start_page 118
container_title Radiation physics and chemistry (Oxford, England : 1993)
container_volume 128
creator Bury, Charles S.
Carmichael, Ian
McGeehan, John E.
Garman, Elspeth F.
description In X-ray crystallography, for the determination of the 3-D structure of macromolecules, radiation damage is still an inherent problem at modern third generation synchrotron sources, even when utilising cryo-crystallographic techniques (sample held at 100K). At doses of just several MGy, at which a typical diffraction dataset is collected, site-specific radiation-induced chemical changes are known to manifest within protein crystals, and a wide body of literature is now devoted to understanding the mechanisms behind such damage. Far less is known regarding radiation-induced damage to crystalline nucleic acids and the wider class of nucleoprotein complexes during macromolecular X-ray crystallography (MX) data collection. As the MX structural biology community now strives to solve structures for increasingly larger and complex macromolecular assemblies, it essential to understand how such structures are affected by the X-ray radiation used to solve them. The purpose of this review is to summarise advances in the field of specific damage to nucleoprotein complexes and to present case studies of MX damage investigations on both protein-DNA (C.Esp1396I) and protein-RNA (TRAP) complexes. To motivate further investigations into MX damage mechanisms within nucleoprotein complexes, current and emerging protocols for investigating specific damage within Fobs(n)−Fobs(1) electron density difference maps are discussed. •We review radiation damages nucleoprotein complexes during X-ray crystallography.•We detect radiation-induced chemical changes from electron density difference maps.•We use a systematic pipeline to track electron density loss with increasing dose.•Nucleic acids are radiation-insensitive compared to protein within crystals at 100K.•RNA protects key RNA-binding residues from radiation-induced decarboxylation.
doi_str_mv 10.1016/j.radphyschem.2016.05.023
format Article
fullrecord <record><control><sourceid>elsevier_osti_</sourceid><recordid>TN_cdi_osti_scitechconnect_1352289</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0969806X16301645</els_id><sourcerecordid>S0969806X16301645</sourcerecordid><originalsourceid>FETCH-LOGICAL-c399t-e02c718ba289c0443a789b5e49d1c6f7ba7da7a9a06a8eb54c3248a3acb5185f3</originalsourceid><addsrcrecordid>eNqNUN9r2zAQFmOFZmn_B3fv9iTbsqXHErZ2UBiMDfImzqdLomBbQVK2-r-fQvbQxz4dd3y_7mPsQfBKcNF9OVYB7OmwRDzQVNX5VHFZ8br5wFZC9brkSsuPbMV1p0vFu-0t-xTjkXPeK9msmPkJ1kFyfi4sTLCn4q9LBzcX8xlH8qfgE-UN_XQa6ZViEdPZOrLFsBQTYPCTHwnPI4RiWwZYCgxLTDCOfh8g57pjNzsYI93_n2v2-9vXX5vn8uXH0_fN40uJjdapJF5jL9QAtdLI27aBXulBUqutwG7XD9Bb6EED70DRIFts6lZBAzhIoeSuWbPPV10fkzMRXSI8oJ9nwmREI-ssnEH6Csq5Ywy0M6fgJgiLEdxc6jRH86ZOc6nTcGlynZm7uXIpf_HHUbiY0IxkXbh4WO_eofIPZHmHlg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography</title><source>Elsevier ScienceDirect Journals</source><creator>Bury, Charles S. ; Carmichael, Ian ; McGeehan, John E. ; Garman, Elspeth F.</creator><creatorcontrib>Bury, Charles S. ; Carmichael, Ian ; McGeehan, John E. ; Garman, Elspeth F.</creatorcontrib><description>In X-ray crystallography, for the determination of the 3-D structure of macromolecules, radiation damage is still an inherent problem at modern third generation synchrotron sources, even when utilising cryo-crystallographic techniques (sample held at 100K). At doses of just several MGy, at which a typical diffraction dataset is collected, site-specific radiation-induced chemical changes are known to manifest within protein crystals, and a wide body of literature is now devoted to understanding the mechanisms behind such damage. Far less is known regarding radiation-induced damage to crystalline nucleic acids and the wider class of nucleoprotein complexes during macromolecular X-ray crystallography (MX) data collection. As the MX structural biology community now strives to solve structures for increasingly larger and complex macromolecular assemblies, it essential to understand how such structures are affected by the X-ray radiation used to solve them. The purpose of this review is to summarise advances in the field of specific damage to nucleoprotein complexes and to present case studies of MX damage investigations on both protein-DNA (C.Esp1396I) and protein-RNA (TRAP) complexes. To motivate further investigations into MX damage mechanisms within nucleoprotein complexes, current and emerging protocols for investigating specific damage within Fobs(n)−Fobs(1) electron density difference maps are discussed. •We review radiation damages nucleoprotein complexes during X-ray crystallography.•We detect radiation-induced chemical changes from electron density difference maps.•We use a systematic pipeline to track electron density loss with increasing dose.•Nucleic acids are radiation-insensitive compared to protein within crystals at 100K.•RNA protects key RNA-binding residues from radiation-induced decarboxylation.</description><identifier>ISSN: 0969-806X</identifier><identifier>EISSN: 1879-0895</identifier><identifier>DOI: 10.1016/j.radphyschem.2016.05.023</identifier><language>eng</language><publisher>United Kingdom: Elsevier Ltd</publisher><subject>Dose ; Electron density ; Macromolecular X-ray crystallography ; Protein-nucleic acid complexes ; Radiation damage</subject><ispartof>Radiation physics and chemistry (Oxford, England : 1993), 2016-11, Vol.128 (C), p.118-125</ispartof><rights>2016 The Authors</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c399t-e02c718ba289c0443a789b5e49d1c6f7ba7da7a9a06a8eb54c3248a3acb5185f3</citedby><cites>FETCH-LOGICAL-c399t-e02c718ba289c0443a789b5e49d1c6f7ba7da7a9a06a8eb54c3248a3acb5185f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0969806X16301645$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,3536,27903,27904,65309</link.rule.ids><backlink>$$Uhttps://www.osti.gov/biblio/1352289$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Bury, Charles S.</creatorcontrib><creatorcontrib>Carmichael, Ian</creatorcontrib><creatorcontrib>McGeehan, John E.</creatorcontrib><creatorcontrib>Garman, Elspeth F.</creatorcontrib><title>Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography</title><title>Radiation physics and chemistry (Oxford, England : 1993)</title><description>In X-ray crystallography, for the determination of the 3-D structure of macromolecules, radiation damage is still an inherent problem at modern third generation synchrotron sources, even when utilising cryo-crystallographic techniques (sample held at 100K). At doses of just several MGy, at which a typical diffraction dataset is collected, site-specific radiation-induced chemical changes are known to manifest within protein crystals, and a wide body of literature is now devoted to understanding the mechanisms behind such damage. Far less is known regarding radiation-induced damage to crystalline nucleic acids and the wider class of nucleoprotein complexes during macromolecular X-ray crystallography (MX) data collection. As the MX structural biology community now strives to solve structures for increasingly larger and complex macromolecular assemblies, it essential to understand how such structures are affected by the X-ray radiation used to solve them. The purpose of this review is to summarise advances in the field of specific damage to nucleoprotein complexes and to present case studies of MX damage investigations on both protein-DNA (C.Esp1396I) and protein-RNA (TRAP) complexes. To motivate further investigations into MX damage mechanisms within nucleoprotein complexes, current and emerging protocols for investigating specific damage within Fobs(n)−Fobs(1) electron density difference maps are discussed. •We review radiation damages nucleoprotein complexes during X-ray crystallography.•We detect radiation-induced chemical changes from electron density difference maps.•We use a systematic pipeline to track electron density loss with increasing dose.•Nucleic acids are radiation-insensitive compared to protein within crystals at 100K.•RNA protects key RNA-binding residues from radiation-induced decarboxylation.</description><subject>Dose</subject><subject>Electron density</subject><subject>Macromolecular X-ray crystallography</subject><subject>Protein-nucleic acid complexes</subject><subject>Radiation damage</subject><issn>0969-806X</issn><issn>1879-0895</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><recordid>eNqNUN9r2zAQFmOFZmn_B3fv9iTbsqXHErZ2UBiMDfImzqdLomBbQVK2-r-fQvbQxz4dd3y_7mPsQfBKcNF9OVYB7OmwRDzQVNX5VHFZ8br5wFZC9brkSsuPbMV1p0vFu-0t-xTjkXPeK9msmPkJ1kFyfi4sTLCn4q9LBzcX8xlH8qfgE-UN_XQa6ZViEdPZOrLFsBQTYPCTHwnPI4RiWwZYCgxLTDCOfh8g57pjNzsYI93_n2v2-9vXX5vn8uXH0_fN40uJjdapJF5jL9QAtdLI27aBXulBUqutwG7XD9Bb6EED70DRIFts6lZBAzhIoeSuWbPPV10fkzMRXSI8oJ9nwmREI-ssnEH6Csq5Ywy0M6fgJgiLEdxc6jRH86ZOc6nTcGlynZm7uXIpf_HHUbiY0IxkXbh4WO_eofIPZHmHlg</recordid><startdate>201611</startdate><enddate>201611</enddate><creator>Bury, Charles S.</creator><creator>Carmichael, Ian</creator><creator>McGeehan, John E.</creator><creator>Garman, Elspeth F.</creator><general>Elsevier Ltd</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>OTOTI</scope></search><sort><creationdate>201611</creationdate><title>Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography</title><author>Bury, Charles S. ; Carmichael, Ian ; McGeehan, John E. ; Garman, Elspeth F.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c399t-e02c718ba289c0443a789b5e49d1c6f7ba7da7a9a06a8eb54c3248a3acb5185f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Dose</topic><topic>Electron density</topic><topic>Macromolecular X-ray crystallography</topic><topic>Protein-nucleic acid complexes</topic><topic>Radiation damage</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bury, Charles S.</creatorcontrib><creatorcontrib>Carmichael, Ian</creatorcontrib><creatorcontrib>McGeehan, John E.</creatorcontrib><creatorcontrib>Garman, Elspeth F.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>CrossRef</collection><collection>OSTI.GOV</collection><jtitle>Radiation physics and chemistry (Oxford, England : 1993)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bury, Charles S.</au><au>Carmichael, Ian</au><au>McGeehan, John E.</au><au>Garman, Elspeth F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography</atitle><jtitle>Radiation physics and chemistry (Oxford, England : 1993)</jtitle><date>2016-11</date><risdate>2016</risdate><volume>128</volume><issue>C</issue><spage>118</spage><epage>125</epage><pages>118-125</pages><issn>0969-806X</issn><eissn>1879-0895</eissn><abstract>In X-ray crystallography, for the determination of the 3-D structure of macromolecules, radiation damage is still an inherent problem at modern third generation synchrotron sources, even when utilising cryo-crystallographic techniques (sample held at 100K). At doses of just several MGy, at which a typical diffraction dataset is collected, site-specific radiation-induced chemical changes are known to manifest within protein crystals, and a wide body of literature is now devoted to understanding the mechanisms behind such damage. Far less is known regarding radiation-induced damage to crystalline nucleic acids and the wider class of nucleoprotein complexes during macromolecular X-ray crystallography (MX) data collection. As the MX structural biology community now strives to solve structures for increasingly larger and complex macromolecular assemblies, it essential to understand how such structures are affected by the X-ray radiation used to solve them. The purpose of this review is to summarise advances in the field of specific damage to nucleoprotein complexes and to present case studies of MX damage investigations on both protein-DNA (C.Esp1396I) and protein-RNA (TRAP) complexes. To motivate further investigations into MX damage mechanisms within nucleoprotein complexes, current and emerging protocols for investigating specific damage within Fobs(n)−Fobs(1) electron density difference maps are discussed. •We review radiation damages nucleoprotein complexes during X-ray crystallography.•We detect radiation-induced chemical changes from electron density difference maps.•We use a systematic pipeline to track electron density loss with increasing dose.•Nucleic acids are radiation-insensitive compared to protein within crystals at 100K.•RNA protects key RNA-binding residues from radiation-induced decarboxylation.</abstract><cop>United Kingdom</cop><pub>Elsevier Ltd</pub><doi>10.1016/j.radphyschem.2016.05.023</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0969-806X
ispartof Radiation physics and chemistry (Oxford, England : 1993), 2016-11, Vol.128 (C), p.118-125
issn 0969-806X
1879-0895
language eng
recordid cdi_osti_scitechconnect_1352289
source Elsevier ScienceDirect Journals
subjects Dose
Electron density
Macromolecular X-ray crystallography
Protein-nucleic acid complexes
Radiation damage
title Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-23T16%3A01%3A48IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-elsevier_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Radiation%20damage%20within%20nucleoprotein%20complexes%20studied%20by%20macromolecular%20X-ray%20crystallography&rft.jtitle=Radiation%20physics%20and%20chemistry%20(Oxford,%20England%20:%201993)&rft.au=Bury,%20Charles%20S.&rft.date=2016-11&rft.volume=128&rft.issue=C&rft.spage=118&rft.epage=125&rft.pages=118-125&rft.issn=0969-806X&rft.eissn=1879-0895&rft_id=info:doi/10.1016/j.radphyschem.2016.05.023&rft_dat=%3Celsevier_osti_%3ES0969806X16301645%3C/elsevier_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/&rft_els_id=S0969806X16301645&rfr_iscdi=true