Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy
NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows expone...
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creator | Shchukina, Alexandra Małecki, Paweł Mateos, Borja Nowakowski, Michał Urbańczyk, Mateusz Kontaxis, Georg Kasprzak, Paweł Conrad‐Billroth, Clara Konrat, Robert Kazimierczuk, Krzysztof |
description | NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature‐dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature‐swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non‐linearities effectively. Non‐linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.
Time‐saving processing: The rates of temperature‐dependent chemical shift changes help in protein structure analysis. Three‐dimensional experiments to reveal these changes are often lengthy to the extent of being barely feasible. Two specially tailored data processing techniques yield temperature coefficients and their non‐linearities to overcome this limitation. |
doi_str_mv | 10.1002/chem.202003678 |
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Time‐saving processing: The rates of temperature‐dependent chemical shift changes help in protein structure analysis. Three‐dimensional experiments to reveal these changes are often lengthy to the extent of being barely feasible. Two specially tailored data processing techniques yield temperature coefficients and their non‐linearities to overcome this limitation.</description><identifier>ISSN: 0947-6539</identifier><identifier>EISSN: 1521-3765</identifier><identifier>DOI: 10.1002/chem.202003678</identifier><identifier>PMID: 32985764</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Biomedical materials ; CD44 antigen ; Chemistry ; Data acquisition ; Data processing ; Dynamic structural analysis ; Information processing ; Magnetic resonance spectroscopy ; multidimensional spectroscopy ; NMR ; NMR spectroscopy ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular - methods ; Osteopontin ; protein dynamics ; protein structures ; Proteins ; Proteins - chemistry ; Radon ; Radon transformation ; Signal processing ; Spectra ; Spectroscopy ; Spectrum analysis ; structure elucidation ; Temperature ; Temperature dependence</subject><ispartof>Chemistry : a European journal, 2021-01, Vol.27 (5), p.1753-1767</ispartof><rights>2020 Wiley‐VCH GmbH</rights><rights>2020 Wiley-VCH GmbH.</rights><rights>2021 Wiley‐VCH GmbH</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4108-d2c4f98475daded553c39ddfb7530112226f0e390cc45e3424f14a2a4e06c25b3</citedby><cites>FETCH-LOGICAL-c4108-d2c4f98475daded553c39ddfb7530112226f0e390cc45e3424f14a2a4e06c25b3</cites><orcidid>0000-0001-6489-4080 ; 0000-0001-6085-1593 ; 0000-0001-7118-137X ; 0000-0002-0310-4943 ; 0000-0001-7387-4284 ; 0000-0001-9585-1737 ; 0000-0002-1356-0301 ; 0000-0001-7273-217X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fchem.202003678$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fchem.202003678$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32985764$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shchukina, Alexandra</creatorcontrib><creatorcontrib>Małecki, Paweł</creatorcontrib><creatorcontrib>Mateos, Borja</creatorcontrib><creatorcontrib>Nowakowski, Michał</creatorcontrib><creatorcontrib>Urbańczyk, Mateusz</creatorcontrib><creatorcontrib>Kontaxis, Georg</creatorcontrib><creatorcontrib>Kasprzak, Paweł</creatorcontrib><creatorcontrib>Conrad‐Billroth, Clara</creatorcontrib><creatorcontrib>Konrat, Robert</creatorcontrib><creatorcontrib>Kazimierczuk, Krzysztof</creatorcontrib><title>Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy</title><title>Chemistry : a European journal</title><addtitle>Chemistry</addtitle><description>NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature‐dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature‐swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non‐linearities effectively. Non‐linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.
Time‐saving processing: The rates of temperature‐dependent chemical shift changes help in protein structure analysis. Three‐dimensional experiments to reveal these changes are often lengthy to the extent of being barely feasible. Two specially tailored data processing techniques yield temperature coefficients and their non‐linearities to overcome this limitation.</description><subject>Biomedical materials</subject><subject>CD44 antigen</subject><subject>Chemistry</subject><subject>Data acquisition</subject><subject>Data processing</subject><subject>Dynamic structural analysis</subject><subject>Information processing</subject><subject>Magnetic resonance spectroscopy</subject><subject>multidimensional spectroscopy</subject><subject>NMR</subject><subject>NMR spectroscopy</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular - methods</subject><subject>Osteopontin</subject><subject>protein dynamics</subject><subject>protein structures</subject><subject>Proteins</subject><subject>Proteins - chemistry</subject><subject>Radon</subject><subject>Radon transformation</subject><subject>Signal processing</subject><subject>Spectra</subject><subject>Spectroscopy</subject><subject>Spectrum analysis</subject><subject>structure elucidation</subject><subject>Temperature</subject><subject>Temperature dependence</subject><issn>0947-6539</issn><issn>1521-3765</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkEtLw0AURgdRbK1uXcqAGzep805mKbVaoa2idR2mkxtMycuZBO2_N6UPwY2rC_ee-8F3ELqkZEgJYbf2A4ohI4wQrsLoCPWpZDTgoZLHqE-0CAMlue6hM-9XhBCtOD9FPc50JEMl-mi-gKIGZ5rWATYemxKPvxtn8H1WQOmzqsRZiWdt3mTJfmNy_OKqBrrDfPaK32qwjau8rer1OTpJTe7hYjcH6P1hvBhNgunz49PobhpYQUkUJMyKVEcilIlJIJGSW66TJF2GkhNKGWMqJcA1sVZI4IKJlArDjACiLJNLPkA329zaVZ8t-CYuMm8hz00JVetjJoTSUaSk6NDrP-iqal1XYkOFWnDGRdRRwy1luybeQRrXLiuMW8eUxBvT8cZ0fDDdPVztYttlAckB36vtAL0FvrIc1v_ExaPJePYb_gNuSYmH</recordid><startdate>20210121</startdate><enddate>20210121</enddate><creator>Shchukina, Alexandra</creator><creator>Małecki, Paweł</creator><creator>Mateos, Borja</creator><creator>Nowakowski, Michał</creator><creator>Urbańczyk, Mateusz</creator><creator>Kontaxis, Georg</creator><creator>Kasprzak, Paweł</creator><creator>Conrad‐Billroth, Clara</creator><creator>Konrat, Robert</creator><creator>Kazimierczuk, Krzysztof</creator><general>Wiley Subscription Services, Inc</general><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>7SR</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>K9.</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-6489-4080</orcidid><orcidid>https://orcid.org/0000-0001-6085-1593</orcidid><orcidid>https://orcid.org/0000-0001-7118-137X</orcidid><orcidid>https://orcid.org/0000-0002-0310-4943</orcidid><orcidid>https://orcid.org/0000-0001-7387-4284</orcidid><orcidid>https://orcid.org/0000-0001-9585-1737</orcidid><orcidid>https://orcid.org/0000-0002-1356-0301</orcidid><orcidid>https://orcid.org/0000-0001-7273-217X</orcidid></search><sort><creationdate>20210121</creationdate><title>Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy</title><author>Shchukina, Alexandra ; Małecki, Paweł ; Mateos, Borja ; Nowakowski, Michał ; Urbańczyk, Mateusz ; Kontaxis, Georg ; Kasprzak, Paweł ; Conrad‐Billroth, Clara ; Konrat, Robert ; Kazimierczuk, Krzysztof</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4108-d2c4f98475daded553c39ddfb7530112226f0e390cc45e3424f14a2a4e06c25b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biomedical materials</topic><topic>CD44 antigen</topic><topic>Chemistry</topic><topic>Data acquisition</topic><topic>Data processing</topic><topic>Dynamic structural analysis</topic><topic>Information processing</topic><topic>Magnetic resonance spectroscopy</topic><topic>multidimensional spectroscopy</topic><topic>NMR</topic><topic>NMR spectroscopy</topic><topic>Nuclear magnetic resonance</topic><topic>Nuclear Magnetic Resonance, Biomolecular - methods</topic><topic>Osteopontin</topic><topic>protein dynamics</topic><topic>protein structures</topic><topic>Proteins</topic><topic>Proteins - chemistry</topic><topic>Radon</topic><topic>Radon transformation</topic><topic>Signal processing</topic><topic>Spectra</topic><topic>Spectroscopy</topic><topic>Spectrum analysis</topic><topic>structure elucidation</topic><topic>Temperature</topic><topic>Temperature dependence</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shchukina, Alexandra</creatorcontrib><creatorcontrib>Małecki, Paweł</creatorcontrib><creatorcontrib>Mateos, Borja</creatorcontrib><creatorcontrib>Nowakowski, Michał</creatorcontrib><creatorcontrib>Urbańczyk, Mateusz</creatorcontrib><creatorcontrib>Kontaxis, Georg</creatorcontrib><creatorcontrib>Kasprzak, Paweł</creatorcontrib><creatorcontrib>Conrad‐Billroth, Clara</creatorcontrib><creatorcontrib>Konrat, Robert</creatorcontrib><creatorcontrib>Kazimierczuk, Krzysztof</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><jtitle>Chemistry : a European journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shchukina, Alexandra</au><au>Małecki, Paweł</au><au>Mateos, Borja</au><au>Nowakowski, Michał</au><au>Urbańczyk, Mateusz</au><au>Kontaxis, Georg</au><au>Kasprzak, Paweł</au><au>Conrad‐Billroth, Clara</au><au>Konrat, Robert</au><au>Kazimierczuk, Krzysztof</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy</atitle><jtitle>Chemistry : a European journal</jtitle><addtitle>Chemistry</addtitle><date>2021-01-21</date><risdate>2021</risdate><volume>27</volume><issue>5</issue><spage>1753</spage><epage>1767</epage><pages>1753-1767</pages><issn>0947-6539</issn><eissn>1521-3765</eissn><abstract>NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature‐dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature‐swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non‐linearities effectively. Non‐linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided.
Time‐saving processing: The rates of temperature‐dependent chemical shift changes help in protein structure analysis. Three‐dimensional experiments to reveal these changes are often lengthy to the extent of being barely feasible. Two specially tailored data processing techniques yield temperature coefficients and their non‐linearities to overcome this limitation.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>32985764</pmid><doi>10.1002/chem.202003678</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0001-6489-4080</orcidid><orcidid>https://orcid.org/0000-0001-6085-1593</orcidid><orcidid>https://orcid.org/0000-0001-7118-137X</orcidid><orcidid>https://orcid.org/0000-0002-0310-4943</orcidid><orcidid>https://orcid.org/0000-0001-7387-4284</orcidid><orcidid>https://orcid.org/0000-0001-9585-1737</orcidid><orcidid>https://orcid.org/0000-0002-1356-0301</orcidid><orcidid>https://orcid.org/0000-0001-7273-217X</orcidid></addata></record> |
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subjects | Biomedical materials CD44 antigen Chemistry Data acquisition Data processing Dynamic structural analysis Information processing Magnetic resonance spectroscopy multidimensional spectroscopy NMR NMR spectroscopy Nuclear magnetic resonance Nuclear Magnetic Resonance, Biomolecular - methods Osteopontin protein dynamics protein structures Proteins Proteins - chemistry Radon Radon transformation Signal processing Spectra Spectroscopy Spectrum analysis structure elucidation Temperature Temperature dependence |
title | Temperature as an Extra Dimension in Multidimensional Protein NMR Spectroscopy |
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