Integral membrane protein structure determination using pseudocontact shifts

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• 作者：Duncan J. Crick ; Jue X. Wang ; Bim Graham ; James D. Swarbrick…
• 关键词：Pseudocontact shift ; Lanthanide tag ; Structure determination ; Membrane proteins
• 刊名：Journal of Biomolecular NMR
• 出版年：2015
• 出版时间：April 2015
• 年：2015
• 卷：61
• 期：3-4
• 页码：197-207
• 全文大小：1,966 KB
• 参考文献：Allegrozzi M, Bertini I, Janik MBL, Lee YM, Liu G, Luchinat C (2000) Lanthanide-induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40?? from the metal ion. J Am Chem Soc 122:4154-161View Article
  Ayala I, Sounier R, Usé N, Gans P, Boisbouvier J (2009) An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein. J Biomol NMR 43:111-19View Article
  Banci L, Bertini I, Cavallaro G, Giachetti A, Luchinat C, Parigi G (2004) Paramagnetism-based restraints for Xplor-NIH. J Biomol NMR 28:249-61View Article
  Boisbouvier J, Gans P, Blackledge M, Brutscher B, Marion D (1999) Long-range structural information in NMR studies of paramagnetic molecules from electron spin-nuclear spin cross-correlated relaxation. J Am Chem Soc 121:7700-701View Article
  Bowie JU (1997) Helix packing in membrane proteins. J Mol Biol 272:780-89View Article
  Chen W-N, Loscha KV, Nitsche C, Graham B, Otting G (2014) The dengue virus NS2B-NS3 protease retains the closed conformation in the complex with BPTI. FEBS Lett 588:2206-211View Article
  Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-02View Article
  de la Cruz L, Nguyen THD, Ozawa K, Shin J, Graham B, Huber T, Otting G (2011) Binding of low molecular weight inhibitors promotes large conformational changes in the dengue virus NS2B-NS3 protease: fold analysis by pseudocontact shifts. J Am Chem Soc 133:19205-9215View Article
  de la Cruz L, Chen W-N, Graham B, Otting G (2014) Binding mode of the activity-modulating C-terminal segment of NS2B to NS3 in the dengue virus NS2B–NS3 protease. FEBS J 281:1517-533View Article
  Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, Nietlispach D (2010) Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy. Nat Struct Mol Biol 17:768-74View Article
  Godoy-Ruiz R, Guo C, Tugarinov V (2010) Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins. J Am Chem Soc 132:18340-8350View Article
  Graham B, Loh CT, Swarbrick JD, Ung P, Shin J, Yagi H, Jia X, Chhabra S, Barlow N, Pintacuda G, Huber T, Otting G (2011) DOTA-amide lanthanide tag for reliable generation of pseudocontact shifts in protein NMR spectra. Bioconjugate Chem 22:2118-125View Article
  Guan J-Y, Keizers PHJ, Liu WM, Lo F, Skinner SP, Heeneman EA, Schwalbe H, Ubbink M, Siegal G (2013) Small-molecule binding sites on proteins established by paramagnetic NMR spectroscopy. J Am Chem Soc 135:5859-868View Article
  Hass MAS, Ubbink M (2014) Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. Curr Opin Struct Biol 24:45-3View Article
  H?ussinger D, Huang JR, Grzesiek S (2009) DOTA-M8: an extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopy. J Am Chem Soc 131:14761-4767View Article
  Jia X, Maleckis A, Huber T, Otting G (2011) 4,4-dithiobisdipicolinic acid: a small and convenient lanthanide binding tag for protein NMR spectroscopy. Chemistry 17:6830-836View Article
  John M, Pintacuda G, Park AY, Dixon NE, Otting G (2006) Structure determination of protein-ligand complexes by transferred paramagnetic shifts. J Am Chem Soc 128:12910-2916View Article
  John M, Schmitz C, Park AY, Dixon NE, Huber T, Otting G (2007) Sequence-specific and stereospecific assignment of methyl groups using paramagnetic lanthanides. J Am Chem Soc 129:13749-3757View Article
  Keizers PHJ, Desreux JF, Overhand M, Ubbink M (2007) Increased paramagnetic effect of a lanthanide protein probe by two-point attachment. J Am Chem Soc 2:9292-293View Article
  Liu W-M, Keizers PHJ, Hass MA, Blok A, Timmer M, Sarris AJC, Overhand M, Ubbink M (2012) A pH-sensitive, colorful, lanthanide-chelating paramagnetic NMR probe. J Am Chem Soc 134:17306-7313View Article
  Liu W-M, Overhand M, Ubbink M (2014a) The application of paramagnetic lanthanoid ions in NMR spectroscopy on proteins. Coord Chem Rev 273-74:2-2View Article
  Liu W-M, Skinner SP, Timmer M, Blok A, Hass MAS, Filippov DV, Overhand M, Ubbink M (2014b) A two-armed lanthanoid-chelating paramagnetic nmr probe linked to proteins via thioether linkages. Chem Eur J 20:6256-258View Article
  Loh CT, Ozawa K, Tuck KL, Barlow N, Huber T, Otting G, Graham B (2013) Lanthanide tags for site-specific ligation to an unnatural amino acid and generation of pseudocontact shifts in proteins. Bioconjugate Chem 24:260-68View Article
  Man B, Su X-C, Liang H, Simonsen S, Huber T, Messerle BA, Otting G (2010) 3-Mercapto-2,6-pyridinedicarboxylic acid: a small lanthanide-binding tag for protein studies by NMR spectroscopy. Chemistry 16:3827-832View Article
  Nietlispach D, Gautier A (2011) Solution NMR studies of polytopic α-helical me
• 作者单位：Duncan J. Crick (1)
  Jue X. Wang (1)
  Bim Graham (2)
  James D. Swarbrick (2)
  Helen R. Mott (1)
  Daniel Nietlispach (1)
  
  1. Department of Biochemistry, University of Cambridge, Cambridge, UK
  2. Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
  
• 刊物类别：Physics and Astronomy
• 刊物主题：Physics
  Biophysics and Biomedical Physics
  Polymer Sciences
  Biochemistry
  
• 出版者：Springer Netherlands
• ISSN：1573-5001

文摘

Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.