Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhau...
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description | Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of [almost equal to]1 Å, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 Å (1.52 ± 0.12 Å for all heavy atoms), which improved to 0.49 ± 0.05 Å (1.19 ± 0.07 Å) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 Å bbRMSD (1.06 ± 0.07 Å); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 Å; 1.29 ± 0.07 Å) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography. |
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Trent ; Wylie, Benjamin J ; Schmidt, Heather L. Frericks ; Nieuwkoop, Andrew J ; Mayrhofer, Rebecca-Maria ; Shah, Gautam J ; Graesser, Daniel T ; Rienstra, Chad M</creator><creatorcontrib>Franks, W. Trent ; Wylie, Benjamin J ; Schmidt, Heather L. Frericks ; Nieuwkoop, Andrew J ; Mayrhofer, Rebecca-Maria ; Shah, Gautam J ; Graesser, Daniel T ; Rienstra, Chad M</creatorcontrib><description>Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of [almost equal to]1 Å, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 Å (1.52 ± 0.12 Å for all heavy atoms), which improved to 0.49 ± 0.05 Å (1.19 ± 0.07 Å) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 Å bbRMSD (1.06 ± 0.07 Å); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 Å; 1.29 ± 0.07 Å) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0712393105</identifier><identifier>PMID: 18344321</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Atoms ; Atoms & subatomic particles ; Biological Sciences ; Chemical equilibrium ; Correlations ; Crystal structure ; Crystallography ; Databases, Protein ; Immunoglobulins ; Isotope Labeling ; Molecular structure ; Nanocrystals ; Nanoparticles - chemistry ; Nerve Tissue Proteins - chemistry ; Nerve Tissue Proteins - metabolism ; Nuclear magnetic resonance ; Nuclear Magnetic Resonance, Biomolecular ; Physical Sciences ; Protein Folding ; Protein Structure, Tertiary ; Proteins ; Reproducibility of Results ; Rotating bodies ; Simulated annealing ; Spectral correlation ; Spectroscopy ; Thermodynamics</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2008-03, Vol.105 (12), p.4621-4626</ispartof><rights>Copyright 2008 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Mar 25, 2008</rights><rights>2008 by The National Academy of Sciences of the USA</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c618t-ac0725d9a1afb4556678101fd297debb7628f48a7813f841864f01f998054d203</citedby><cites>FETCH-LOGICAL-c618t-ac0725d9a1afb4556678101fd297debb7628f48a7813f841864f01f998054d203</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/105/12.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25461472$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25461472$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27924,27925,53791,53793,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18344321$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Franks, W. Trent</creatorcontrib><creatorcontrib>Wylie, Benjamin J</creatorcontrib><creatorcontrib>Schmidt, Heather L. Frericks</creatorcontrib><creatorcontrib>Nieuwkoop, Andrew J</creatorcontrib><creatorcontrib>Mayrhofer, Rebecca-Maria</creatorcontrib><creatorcontrib>Shah, Gautam J</creatorcontrib><creatorcontrib>Graesser, Daniel T</creatorcontrib><creatorcontrib>Rienstra, Chad M</creatorcontrib><title>Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of [almost equal to]1 Å, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 Å (1.52 ± 0.12 Å for all heavy atoms), which improved to 0.49 ± 0.05 Å (1.19 ± 0.07 Å) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 Å bbRMSD (1.06 ± 0.07 Å); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 Å; 1.29 ± 0.07 Å) when TALOS restraints were removed before refinement. 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Trent</au><au>Wylie, Benjamin J</au><au>Schmidt, Heather L. Frericks</au><au>Nieuwkoop, Andrew J</au><au>Mayrhofer, Rebecca-Maria</au><au>Shah, Gautam J</au><au>Graesser, Daniel T</au><au>Rienstra, Chad M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2008-03-25</date><risdate>2008</risdate><volume>105</volume><issue>12</issue><spage>4621</spage><epage>4626</epage><pages>4621-4626</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><abstract>Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of [almost equal to]1 Å, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 ± 0.13 Å (1.52 ± 0.12 Å for all heavy atoms), which improved to 0.49 ± 0.05 Å (1.19 ± 0.07 Å) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 ± 0.06 Å bbRMSD (1.06 ± 0.07 Å); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 ± 0.09 Å; 1.29 ± 0.07 Å) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>18344321</pmid><doi>10.1073/pnas.0712393105</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Atoms Atoms & subatomic particles Biological Sciences Chemical equilibrium Correlations Crystal structure Crystallography Databases, Protein Immunoglobulins Isotope Labeling Molecular structure Nanocrystals Nanoparticles - chemistry Nerve Tissue Proteins - chemistry Nerve Tissue Proteins - metabolism Nuclear magnetic resonance Nuclear Magnetic Resonance, Biomolecular Physical Sciences Protein Folding Protein Structure, Tertiary Proteins Reproducibility of Results Rotating bodies Simulated annealing Spectral correlation Spectroscopy Thermodynamics |
title | Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR |
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