Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case
Density Functional Theory (B3LYP/6-31G(d,p)) calculations of (15)N amide and (13)C carbonyl NMR chemical shielding tensors have been performed on WALP23trans-membrane alpha-helix peptide and compared to solid state NMR experiment performed on [(13)C(1)-Ala(13), (15)N-Leu(14)] specifically labelled p...
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description | Density Functional Theory (B3LYP/6-31G(d,p)) calculations of (15)N amide and (13)C carbonyl NMR chemical shielding tensors have been performed on WALP23trans-membrane alpha-helix peptide and compared to solid state NMR experiment performed on [(13)C(1)-Ala(13), (15)N-Leu(14)] specifically labelled peptide powder sample. Using either theoretical results obtained on the whole peptide or experimental data as reference, several simplest chemical models have been explored in order to reduce the computational cost while maintaining good theoretical accuracy. From this study, it appears that the hydrogen bond (N-H...O=C) network that exists in the alpha-helix has a major influence on the chemical shielding tensor and more specifically on the carbonyl (13)C sigma(22) eigenvalue. We show that a small truncated WALP_7 model is not adequate for (13)C(1) NMR description. The application of an external electric field in order to model the hydrogen bond network allows calculating chemical shielding tensors with accurate eigenvalues while the associated eigenvectors are largely modified. Finally, a 23 residues polyglycine peptide that includes the Alanine and Leucine residues for which NMR parameters must be calculated is proposed as the chemical model. This model is sufficient to mostly reproduce the calculation performed on WALP23 with major gain in computational time. Moreover, the application of a low intensity external electric field allows reaching the experimental accuracy for the determination of the eigenvalues. |
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GIAO-DFT study of WALP23 transmembrane α-helix as a test case</title><source>MEDLINE</source><source>Royal Society Of Chemistry Journals 2008-</source><source>Alma/SFX Local Collection</source><creator>ROUGIER, Léa ; MILON, Alain ; REAT, Valérie ; JOLIBOIS, Franck</creator><creatorcontrib>ROUGIER, Léa ; MILON, Alain ; REAT, Valérie ; JOLIBOIS, Franck</creatorcontrib><description>Density Functional Theory (B3LYP/6-31G(d,p)) calculations of (15)N amide and (13)C carbonyl NMR chemical shielding tensors have been performed on WALP23trans-membrane alpha-helix peptide and compared to solid state NMR experiment performed on [(13)C(1)-Ala(13), (15)N-Leu(14)] specifically labelled peptide powder sample. Using either theoretical results obtained on the whole peptide or experimental data as reference, several simplest chemical models have been explored in order to reduce the computational cost while maintaining good theoretical accuracy. From this study, it appears that the hydrogen bond (N-H...O=C) network that exists in the alpha-helix has a major influence on the chemical shielding tensor and more specifically on the carbonyl (13)C sigma(22) eigenvalue. We show that a small truncated WALP_7 model is not adequate for (13)C(1) NMR description. The application of an external electric field in order to model the hydrogen bond network allows calculating chemical shielding tensors with accurate eigenvalues while the associated eigenvectors are largely modified. Finally, a 23 residues polyglycine peptide that includes the Alanine and Leucine residues for which NMR parameters must be calculated is proposed as the chemical model. This model is sufficient to mostly reproduce the calculation performed on WALP23 with major gain in computational time. Moreover, the application of a low intensity external electric field allows reaching the experimental accuracy for the determination of the eigenvalues.</description><identifier>ISSN: 1463-9076</identifier><identifier>EISSN: 1463-9084</identifier><identifier>DOI: 10.1039/b923883b</identifier><identifier>PMID: 20464012</identifier><language>eng</language><publisher>Cambridge: Royal Society of Chemistry</publisher><subject>Alanine - chemistry ; Amino Acid Sequence ; Carbon Isotopes - chemistry ; Chemical Sciences ; Chemistry ; Colloidal state and disperse state ; Exact sciences and technology ; General and physical chemistry ; Hydrogen Bonding ; Leucine - chemistry ; Magnetic Resonance Spectroscopy ; Membranes ; Nitrogen Isotopes - chemistry ; Peptides - chemistry ; Protein Structure, Secondary ; Quantum Theory</subject><ispartof>Physical chemistry chemical physics : PCCP, 2010-07, Vol.12 (26), p.6999-7008</ispartof><rights>2015 INIST-CNRS</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c380t-203249e2e9c6cfed7389eb9ccaa9cd5091c86a61476346f298b0cd6ad3e5e0d63</citedby><cites>FETCH-LOGICAL-c380t-203249e2e9c6cfed7389eb9ccaa9cd5091c86a61476346f298b0cd6ad3e5e0d63</cites><orcidid>0000-0001-5692-8201 ; 0000-0002-3581-590X ; 0000-0002-2174-4039</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23029490$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20464012$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-02131847$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>ROUGIER, Léa</creatorcontrib><creatorcontrib>MILON, Alain</creatorcontrib><creatorcontrib>REAT, Valérie</creatorcontrib><creatorcontrib>JOLIBOIS, Franck</creatorcontrib><title>Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case</title><title>Physical chemistry chemical physics : PCCP</title><addtitle>Phys Chem Chem Phys</addtitle><description>Density Functional Theory (B3LYP/6-31G(d,p)) calculations of (15)N amide and (13)C carbonyl NMR chemical shielding tensors have been performed on WALP23trans-membrane alpha-helix peptide and compared to solid state NMR experiment performed on [(13)C(1)-Ala(13), (15)N-Leu(14)] specifically labelled peptide powder sample. Using either theoretical results obtained on the whole peptide or experimental data as reference, several simplest chemical models have been explored in order to reduce the computational cost while maintaining good theoretical accuracy. From this study, it appears that the hydrogen bond (N-H...O=C) network that exists in the alpha-helix has a major influence on the chemical shielding tensor and more specifically on the carbonyl (13)C sigma(22) eigenvalue. We show that a small truncated WALP_7 model is not adequate for (13)C(1) NMR description. The application of an external electric field in order to model the hydrogen bond network allows calculating chemical shielding tensors with accurate eigenvalues while the associated eigenvectors are largely modified. Finally, a 23 residues polyglycine peptide that includes the Alanine and Leucine residues for which NMR parameters must be calculated is proposed as the chemical model. This model is sufficient to mostly reproduce the calculation performed on WALP23 with major gain in computational time. Moreover, the application of a low intensity external electric field allows reaching the experimental accuracy for the determination of the eigenvalues.</description><subject>Alanine - chemistry</subject><subject>Amino Acid Sequence</subject><subject>Carbon Isotopes - chemistry</subject><subject>Chemical Sciences</subject><subject>Chemistry</subject><subject>Colloidal state and disperse state</subject><subject>Exact sciences and technology</subject><subject>General and physical chemistry</subject><subject>Hydrogen Bonding</subject><subject>Leucine - chemistry</subject><subject>Magnetic Resonance Spectroscopy</subject><subject>Membranes</subject><subject>Nitrogen Isotopes - chemistry</subject><subject>Peptides - chemistry</subject><subject>Protein Structure, Secondary</subject><subject>Quantum Theory</subject><issn>1463-9076</issn><issn>1463-9084</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpFkctu1DAUhi0EoqUg8QTIGwQsUnwbx16OCr1IU5VFEcvIsU8aQ2IPdgLMq_AWvAjPhIeZTlfHsj5_8vl_hF5SckoJ1-9bzbhSvH2EjqmQvNJEiceHcy2P0LOcvxJC6ILyp-iIESEFoewY_b6ODobBhzs89YB96IYZggUcO9xvXIp3EHAbg8MBpp8xfcMxYNvD6K0ZcO49DO7_Ywg5powdZJv8evIxnOKLq-VN9eH8Fudpdput8sty9YlxPCUT8ghjWybgv3-qHgb_C5uMTTHlCVuT4Tl60pkhw4v9PEGfzz_enl1Wq5uLq7PlqrJckalihDOhgYG20nbgaq40tNpaY7R1C6KpVdJIKmrJheyYVi2xThrHYQHESX6C3u28vRmadfKjSZsmGt9cLlfN9o4wyqkS9Q9a2Dc7dp3i97n8tBl9tiXAskecc1NzLghRqi7k2x1pU8w5QXdQU9JsS2vuSyvoq710bkdwB_C-pQK83gMml9i7kpr1-YHjhGmhCf8HMbafgg</recordid><startdate>20100714</startdate><enddate>20100714</enddate><creator>ROUGIER, Léa</creator><creator>MILON, Alain</creator><creator>REAT, Valérie</creator><creator>JOLIBOIS, Franck</creator><general>Royal Society of Chemistry</general><scope>IQODW</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>7X8</scope><scope>1XC</scope><scope>VOOES</scope><orcidid>https://orcid.org/0000-0001-5692-8201</orcidid><orcidid>https://orcid.org/0000-0002-3581-590X</orcidid><orcidid>https://orcid.org/0000-0002-2174-4039</orcidid></search><sort><creationdate>20100714</creationdate><title>Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case</title><author>ROUGIER, Léa ; MILON, Alain ; REAT, Valérie ; JOLIBOIS, Franck</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c380t-203249e2e9c6cfed7389eb9ccaa9cd5091c86a61476346f298b0cd6ad3e5e0d63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Alanine - chemistry</topic><topic>Amino Acid Sequence</topic><topic>Carbon Isotopes - chemistry</topic><topic>Chemical Sciences</topic><topic>Chemistry</topic><topic>Colloidal state and disperse state</topic><topic>Exact sciences and technology</topic><topic>General and physical chemistry</topic><topic>Hydrogen Bonding</topic><topic>Leucine - chemistry</topic><topic>Magnetic Resonance Spectroscopy</topic><topic>Membranes</topic><topic>Nitrogen Isotopes - chemistry</topic><topic>Peptides - chemistry</topic><topic>Protein Structure, Secondary</topic><topic>Quantum Theory</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>ROUGIER, Léa</creatorcontrib><creatorcontrib>MILON, Alain</creatorcontrib><creatorcontrib>REAT, Valérie</creatorcontrib><creatorcontrib>JOLIBOIS, Franck</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>Physical chemistry chemical physics : PCCP</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>ROUGIER, Léa</au><au>MILON, Alain</au><au>REAT, Valérie</au><au>JOLIBOIS, Franck</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case</atitle><jtitle>Physical chemistry chemical physics : PCCP</jtitle><addtitle>Phys Chem Chem Phys</addtitle><date>2010-07-14</date><risdate>2010</risdate><volume>12</volume><issue>26</issue><spage>6999</spage><epage>7008</epage><pages>6999-7008</pages><issn>1463-9076</issn><eissn>1463-9084</eissn><abstract>Density Functional Theory (B3LYP/6-31G(d,p)) calculations of (15)N amide and (13)C carbonyl NMR chemical shielding tensors have been performed on WALP23trans-membrane alpha-helix peptide and compared to solid state NMR experiment performed on [(13)C(1)-Ala(13), (15)N-Leu(14)] specifically labelled peptide powder sample. Using either theoretical results obtained on the whole peptide or experimental data as reference, several simplest chemical models have been explored in order to reduce the computational cost while maintaining good theoretical accuracy. From this study, it appears that the hydrogen bond (N-H...O=C) network that exists in the alpha-helix has a major influence on the chemical shielding tensor and more specifically on the carbonyl (13)C sigma(22) eigenvalue. We show that a small truncated WALP_7 model is not adequate for (13)C(1) NMR description. The application of an external electric field in order to model the hydrogen bond network allows calculating chemical shielding tensors with accurate eigenvalues while the associated eigenvectors are largely modified. Finally, a 23 residues polyglycine peptide that includes the Alanine and Leucine residues for which NMR parameters must be calculated is proposed as the chemical model. This model is sufficient to mostly reproduce the calculation performed on WALP23 with major gain in computational time. Moreover, the application of a low intensity external electric field allows reaching the experimental accuracy for the determination of the eigenvalues.</abstract><cop>Cambridge</cop><pub>Royal Society of Chemistry</pub><pmid>20464012</pmid><doi>10.1039/b923883b</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-5692-8201</orcidid><orcidid>https://orcid.org/0000-0002-3581-590X</orcidid><orcidid>https://orcid.org/0000-0002-2174-4039</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Alanine - chemistry Amino Acid Sequence Carbon Isotopes - chemistry Chemical Sciences Chemistry Colloidal state and disperse state Exact sciences and technology General and physical chemistry Hydrogen Bonding Leucine - chemistry Magnetic Resonance Spectroscopy Membranes Nitrogen Isotopes - chemistry Peptides - chemistry Protein Structure, Secondary Quantum Theory |
title | Modelling the influence of hydrogen bond network on chemical shielding tensors description. GIAO-DFT study of WALP23 transmembrane α-helix as a test case |
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