High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data View Full Text


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Article Info

DATE

2011-09-22

AUTHORS

Ming Tang, Lindsay J. Sperling, Deborah A. Berthold, Charles D. Schwieters, Anna E. Nesbitt, Andrew J. Nieuwkoop, Robert B. Gennis, Chad M. Rienstra

ABSTRACT

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals. More... »

PAGES

227

References to SciGraph publications

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  • 2010-01-27. Structure of a bacterial homologue of vitamin K epoxide reductase in NATURE
  • 2009-02-08. Nanomole-scale protein solid-state NMR by breaking intrinsic 1H T1 boundaries in NATURE METHODS
  • 2007-11-16. Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints in JOURNAL OF BIOMOLECULAR NMR
  • 2010-04-07. Super-resolution biomolecular crystallography with low-resolution data in NATURE
  • 2008-08-01. A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints in JOURNAL OF BIOMOLECULAR NMR
  • 2010-05-30. Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2008-09-12. Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data in JOURNAL OF BIOMOLECULAR NMR
  • 2009-05-20. Biophysical dissection of membrane proteins in NATURE
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    http://scigraph.springernature.com/pub.10.1007/s10858-011-9565-6

    DOI

    http://dx.doi.org/10.1007/s10858-011-9565-6

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21938394


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    32 schema:description X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.
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    42 X-ray experimental data
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    59 high resolution
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    61 joint calculation
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    65 membrane protein structures
    66 membrane proteins
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    70 nuclear magnetic resonance spectroscopy
    71 overall quality
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    73 protein
    74 protein structure
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    78 reflection
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    81 resonance spectroscopy
    82 restraint
    83 solid-state NMR restraints
    84 solid-state nuclear magnetic resonance spectroscopy
    85 solution nuclear magnetic resonance spectroscopy
    86 space
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