Loading…

Joint X-ray/NMR structure refinement of multidomain/multisubunit systems

Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is...

Full description

Saved in:
Bibliographic Details
Published in:Journal of biomolecular NMR 2019-07, Vol.73 (6-7), p.265-278
Main Authors: Carlon, Azzurra, Ravera, Enrico, Parigi, Giacomo, Murshudov, Garib N., Luchinat, Claudio
Format: Article
Language:English
Subjects:
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3
cites cdi_FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3
container_end_page 278
container_issue 6-7
container_start_page 265
container_title Journal of biomolecular NMR
container_volume 73
creator Carlon, Azzurra
Ravera, Enrico
Parigi, Giacomo
Murshudov, Garib N.
Luchinat, Claudio
description Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.
doi_str_mv 10.1007/s10858-018-0212-3
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6692505</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2119919355</sourcerecordid><originalsourceid>FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3</originalsourceid><addsrcrecordid>eNp1kUFP3DAQhS0EgoXyA7igSFx6CTtjx0l8QaoQLUVApaqVerMcxwGjJAY7rrT_vl52WaASB8uW3jfPM_MIOUI4RYBqHhBqXueA6VCkOdsiM-QVyzkAbpMZCMpzWrF6j-yH8AAAoqblLtljwBCR0hm5vHJ2nLI_uVeL-e3NzyxMPuopepN509nRDCbJrsuG2E-2dYOy4_z5HWITRztlYREmM4RPZKdTfTCH6_uA_P568ev8Mr_-8e37-ZfrXBcVTHnBG90awRRUXBXQlKoVvGgpq4EX0DWVUA0rteKshbJCpmjdIaqyEVVjmNbsgJytfB9jM5hWp_a86uWjt4PyC-mUle-V0d7LO_dXlmXaBvBk8Hlt4N1TNGGSgw3a9L0ajYtBUkQhUDC-RE_-Qx9c9GMab0nVWCCraaJwRWnvQkhb2zSDIJc5yVVOMuUklzlJlmqO306xqXgJJgF0BYQkjXfGv379ses_yAWefw</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2118141382</pqid></control><display><type>article</type><title>Joint X-ray/NMR structure refinement of multidomain/multisubunit systems</title><source>Springer Nature</source><creator>Carlon, Azzurra ; Ravera, Enrico ; Parigi, Giacomo ; Murshudov, Garib N. ; Luchinat, Claudio</creator><creatorcontrib>Carlon, Azzurra ; Ravera, Enrico ; Parigi, Giacomo ; Murshudov, Garib N. ; Luchinat, Claudio</creatorcontrib><description>Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.</description><identifier>ISSN: 0925-2738</identifier><identifier>EISSN: 1573-5001</identifier><identifier>DOI: 10.1007/s10858-018-0212-3</identifier><identifier>PMID: 30311122</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Algorithms ; Biochemistry ; Biological and Medical Physics ; Biophysics ; Couplings ; Crystallography, X-Ray ; Crystals ; Data integration ; Experimental data ; Models, Molecular ; Models, Theoretical ; NMR ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular ; Physics ; Physics and Astronomy ; Proteins ; Spectroscopy/Spectrometry ; X-ray diffraction</subject><ispartof>Journal of biomolecular NMR, 2019-07, Vol.73 (6-7), p.265-278</ispartof><rights>The Author(s) 2018. corrected publication 2019</rights><rights>Journal of Biomolecular NMR is a copyright of Springer, (2018). All Rights Reserved. © 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2018, corrected publication 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3</citedby><cites>FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3</cites><orcidid>0000-0001-6483-3587 ; 0000-0002-0806-4266 ; 0000-0001-7708-9208 ; 0000-0003-2271-8921 ; 0000-0002-1989-4644</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27898,27899</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30311122$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Carlon, Azzurra</creatorcontrib><creatorcontrib>Ravera, Enrico</creatorcontrib><creatorcontrib>Parigi, Giacomo</creatorcontrib><creatorcontrib>Murshudov, Garib N.</creatorcontrib><creatorcontrib>Luchinat, Claudio</creatorcontrib><title>Joint X-ray/NMR structure refinement of multidomain/multisubunit systems</title><title>Journal of biomolecular NMR</title><addtitle>J Biomol NMR</addtitle><addtitle>J Biomol NMR</addtitle><description>Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.</description><subject>Algorithms</subject><subject>Biochemistry</subject><subject>Biological and Medical Physics</subject><subject>Biophysics</subject><subject>Couplings</subject><subject>Crystallography, X-Ray</subject><subject>Crystals</subject><subject>Data integration</subject><subject>Experimental data</subject><subject>Models, Molecular</subject><subject>Models, Theoretical</subject><subject>NMR</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Physics</subject><subject>Physics and Astronomy</subject><subject>Proteins</subject><subject>Spectroscopy/Spectrometry</subject><subject>X-ray diffraction</subject><issn>0925-2738</issn><issn>1573-5001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp1kUFP3DAQhS0EgoXyA7igSFx6CTtjx0l8QaoQLUVApaqVerMcxwGjJAY7rrT_vl52WaASB8uW3jfPM_MIOUI4RYBqHhBqXueA6VCkOdsiM-QVyzkAbpMZCMpzWrF6j-yH8AAAoqblLtljwBCR0hm5vHJ2nLI_uVeL-e3NzyxMPuopepN509nRDCbJrsuG2E-2dYOy4_z5HWITRztlYREmM4RPZKdTfTCH6_uA_P568ev8Mr_-8e37-ZfrXBcVTHnBG90awRRUXBXQlKoVvGgpq4EX0DWVUA0rteKshbJCpmjdIaqyEVVjmNbsgJytfB9jM5hWp_a86uWjt4PyC-mUle-V0d7LO_dXlmXaBvBk8Hlt4N1TNGGSgw3a9L0ajYtBUkQhUDC-RE_-Qx9c9GMab0nVWCCraaJwRWnvQkhb2zSDIJc5yVVOMuUklzlJlmqO306xqXgJJgF0BYQkjXfGv379ses_yAWefw</recordid><startdate>20190701</startdate><enddate>20190701</enddate><creator>Carlon, Azzurra</creator><creator>Ravera, Enrico</creator><creator>Parigi, Giacomo</creator><creator>Murshudov, Garib N.</creator><creator>Luchinat, Claudio</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-6483-3587</orcidid><orcidid>https://orcid.org/0000-0002-0806-4266</orcidid><orcidid>https://orcid.org/0000-0001-7708-9208</orcidid><orcidid>https://orcid.org/0000-0003-2271-8921</orcidid><orcidid>https://orcid.org/0000-0002-1989-4644</orcidid></search><sort><creationdate>20190701</creationdate><title>Joint X-ray/NMR structure refinement of multidomain/multisubunit systems</title><author>Carlon, Azzurra ; Ravera, Enrico ; Parigi, Giacomo ; Murshudov, Garib N. ; Luchinat, Claudio</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Algorithms</topic><topic>Biochemistry</topic><topic>Biological and Medical Physics</topic><topic>Biophysics</topic><topic>Couplings</topic><topic>Crystallography, X-Ray</topic><topic>Crystals</topic><topic>Data integration</topic><topic>Experimental data</topic><topic>Models, Molecular</topic><topic>Models, Theoretical</topic><topic>NMR</topic><topic>Nuclear magnetic resonance</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Physics</topic><topic>Physics and Astronomy</topic><topic>Proteins</topic><topic>Spectroscopy/Spectrometry</topic><topic>X-ray diffraction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Carlon, Azzurra</creatorcontrib><creatorcontrib>Ravera, Enrico</creatorcontrib><creatorcontrib>Parigi, Giacomo</creatorcontrib><creatorcontrib>Murshudov, Garib N.</creatorcontrib><creatorcontrib>Luchinat, Claudio</creatorcontrib><collection>SpringerOpen</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health &amp; Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies &amp; Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Biological Sciences</collection><collection>Health &amp; Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Biological Science Database</collection><collection>Advanced Technologies &amp; Aerospace Database</collection><collection>ProQuest Advanced Technologies &amp; Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>ProQuest Health &amp; Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health &amp; Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied &amp; Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of biomolecular NMR</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Carlon, Azzurra</au><au>Ravera, Enrico</au><au>Parigi, Giacomo</au><au>Murshudov, Garib N.</au><au>Luchinat, Claudio</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Joint X-ray/NMR structure refinement of multidomain/multisubunit systems</atitle><jtitle>Journal of biomolecular NMR</jtitle><stitle>J Biomol NMR</stitle><addtitle>J Biomol NMR</addtitle><date>2019-07-01</date><risdate>2019</risdate><volume>73</volume><issue>6-7</issue><spage>265</spage><epage>278</epage><pages>265-278</pages><issn>0925-2738</issn><eissn>1573-5001</eissn><abstract>Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other’s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>30311122</pmid><doi>10.1007/s10858-018-0212-3</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0001-6483-3587</orcidid><orcidid>https://orcid.org/0000-0002-0806-4266</orcidid><orcidid>https://orcid.org/0000-0001-7708-9208</orcidid><orcidid>https://orcid.org/0000-0003-2271-8921</orcidid><orcidid>https://orcid.org/0000-0002-1989-4644</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0925-2738
ispartof Journal of biomolecular NMR, 2019-07, Vol.73 (6-7), p.265-278
issn 0925-2738
1573-5001
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6692505
source Springer Nature
subjects Algorithms
Biochemistry
Biological and Medical Physics
Biophysics
Couplings
Crystallography, X-Ray
Crystals
Data integration
Experimental data
Models, Molecular
Models, Theoretical
NMR
Nuclear magnetic resonance
Nuclear Magnetic Resonance, Biomolecular
Physics
Physics and Astronomy
Proteins
Spectroscopy/Spectrometry
X-ray diffraction
title Joint X-ray/NMR structure refinement of multidomain/multisubunit systems
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-26T15%3A21%3A33IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Joint%20X-ray/NMR%20structure%20refinement%20of%20multidomain/multisubunit%20systems&rft.jtitle=Journal%20of%20biomolecular%20NMR&rft.au=Carlon,%20Azzurra&rft.date=2019-07-01&rft.volume=73&rft.issue=6-7&rft.spage=265&rft.epage=278&rft.pages=265-278&rft.issn=0925-2738&rft.eissn=1573-5001&rft_id=info:doi/10.1007/s10858-018-0212-3&rft_dat=%3Cproquest_pubme%3E2119919355%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c470t-45bcde93a075a40b6ad954d2380540fb79ab36ca53d06713a28f11a6b97be3cc3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2118141382&rft_id=info:pmid/30311122&rfr_iscdi=true