Abstract
The structure determination of membrane protein in lipid environment can be carried out using cryo-electron microscopy combined with the recent development of data collection and image processing. We describe a protocol to study assemblies or stacks of membrane protein reconstituted into a lipid membrane using both cryo-electron tomography and single particle analysis, which is an alternative approach to electron crystallography for solving 3D structure. We show the organization of the successive layers of OprM molecules revealing the protein–protein interactions between OprM molecules of two successive lipid bilayers.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Cheong GW, Young HS, Ogawa H, Toyoshima C, Stokes DL (1996) Lamellar stacking in three-dimensional crystals of Ca(2+)-ATPase from sarcoplasmic reticulum. Biophys J 70:1689–1699
Shi D, Lewis MR, Young HS, Stokes DL (1998) Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum: merging electron diffraction tilt series and imaging the (h, k, 0) projection. J Mol Biol 284:1547–1564
Rubinstein JL (2007) Structural analysis of membrane protein complexes by single particle electron microscopy. Methods 41:409–416
Gregorini M, Wang J, Xie XS, Milligan RA, Engel A (2007) Three-dimensional reconstruction of bovine brain V-ATPase by cryo-electron microscopy and single particle analysis. J Struct Biol 158:445–454
Nakagawa T, Cheng Y, Ramm E, Sheng M, Walz T (2005) Structure and different conformational states of native AMPA receptor complexes. Nature 433:545–549
McDevitt CA, Collins RF, Conway M, Modok S, Storm J, Kerr ID, Ford RC, Callaghan R (2006) Purification and 3D structural analysis of oligomeric human multidrug transporter ABCG2. Structure 14:1623–1632
Chami M, Steinfels E, Orelle C, Jault JM, Di Pietro A, Rigaud J-L, Marco S (2002) Three-dimensional structure by cryo-electron microscopy of YvcC, an homodimeric ATP-binding cassette transporter from Bacillus subtilis. J Mol Biol 315:1075–1085
Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr Opin Struct Biol 12:679–684
Shuttleworth CA, Kielty CM (2001) The supramolecular organization of fibrillin-rich microfibrils. J Cell Biol 152:1045–1056
Holmes DF, Gilpin CJ, Baldock C, Ziese U, Koster AJ, Kadler KE (2001) Corneal collagen fibril structure in three dimensions: structural insights into fibril assembly, mechanical properties, and tissue organization. Proc Natl Acad Sci 98:7307–7312
Bohm J, Lambert O, Frangakis AS, Letellier L, Baumeister W, Rigaud JL (2001) FhuA-mediated phage genome transfer into liposomes: a cryo-electron tomography study. Curr Biol 11:1168–1175
Winkler H, Taylor KA (1999) Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle. Ultramicroscopy 77:141–152
Chen LF, Blanc E, Chapman MS, Taylor KA (2001) Real space refinement of acto-myosin structures from sectioned muscle. J Struct Biol 133:221–232
Förster F, Medalia O, Zauberman N, Baumeister W, Fass D (2005) Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc Natl Acad Sci USA 102:4729–4734
Bostina M, Bubeck D, Schwartz C, Nicastro D, Filman DJ, Hogle JM (2007) Single particle cryoelectron tomography characterization of the structure and structural variability of poliovirus-receptor-membrane complex at 30 Å resolution. J Struct Biol 160:200–210
Zanetti G, Briggs JA, Grünewald K, Sattentau QJ, Fuller SD (2006) Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. PLoS Pathog 2:e83
Zhu P, Liu J, Bess J Jr, Chertova E, Lifson JD, Grisé H, Ofek GA, Taylor KA, Roux KH (2006) Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature 441:847–852
Strauss M, Hofhaus G, Schröder RR, Kühlbrandt W (2008) Dimer ribbons of ATP synthase shape the inner mitochondrial membrane. EMBO J 7:1154–1160
Al-Amoudi A, Díez DC, Betts MJ, Frangakis AS (2007) The molecular architecture of cadherins in native epidermal desmosomes. Nature 450:832–837
Akama H, Kanemaki M, Yoshimura M, Tsukihara T, Kashiwagi T, Yoneyama H, Narita S, Nakagawa A, Nakae T (2004) Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end. J Biol Chem 279:52816–52819
Lambert O, Benabdelhak H, Chami M, Jouan L, Nouaille E, Ducruix A, Brisson A (2005) Trimeric structure of OprN and OprM efflux proteins from Pseudomonas aeruginosa, by 2D electron crystallography. J Struct Biol 150:50–57
Zheng QS, Braunfeld MB, Sedat JW, Agard DA (2004) An improved strategy for automated electron microscopic tomography. J Struct Biol 147:91–101
Rigaud J-L, Mosser G, Lacapere J-J, Olofsson A, Levy D, Ranck J-L (2005) Bio-Beads: an efficient strategy for two-dimensional crystallization of membrane proteins. J Struct Biol 118:226–235
Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, Mc Dowall AW, Schultz P (1988) Cryo-electron microscopy of vitrified specimens. Q Rev Biophys 21:129–228
Mastronarde DN (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol 120:343–352
Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 116:190–199
Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A (2004) XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol 148:194–204
Förster F, Pruggnaller S, Seybert A, Frangakis AS (2008) Classification of cryo-electron sub-tomograms using constrained correlation. J Struct Biol 161:276–286
Schmid MF, Booth CR (2008) Methods for aligning and for averaging 3D volumes with missing data. J Struct Biol 161:243–248
Acknowledgments
We would like to thank Dr. Achilleas Frangakis for fruitful discussions and for giving us access to the EM facilities of EMBL (Heidelberg) and Pr. A. Ducruix for providing purified membrane protein samples. S. Trépout is recipient of PhD fellowship from French Ministry of Education and Research and Technology (MENRT). This work has been supported in part by Agence Nationale de la Recherche (ANR-06-PCV1-001) and by Conseil Régional d’Aquitaine (20071302007) grants.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Trépout, S., Taveau, JC., Lambert, O. (2010). Structure Determination of Membrane Protein by Both Cryo-Electron Tomography and Single Particle Analysis. In: Lacapère, JJ. (eds) Membrane Protein Structure Determination. Methods in Molecular Biology, vol 654. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-762-4_11
Download citation
DOI: https://doi.org/10.1007/978-1-60761-762-4_11
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-761-7
Online ISBN: 978-1-60761-762-4
eBook Packages: Springer Protocols