Abstract
Outer membrane protein biogenesis is a fundamental and essential process in all Gram-negative bacteria. The key players conducting this process are organized in the β-barrel assembly machinery (BAM) complex. This complex has recently attracted a lot of attention due to its importance in cell wall generation, maintenance, and the fascinating yet partially unknown mechanism. The currently best studied example is the BAM complex from E. coli which comprises five proteins, BamA–BamE, two of which, BamA and BamD, are essential for cell survival. Four of the complex proteins, BamB–BamE, are lipoproteins and are attached to the outer membrane via N-terminal lipid anchors. Two of them, BamB and BamD, comprise protein folds known to mediate protein–protein interactions through WD40 and TPR domains, respectively. Structures of BamB to BamE have been determined using X-ray crystallography, NMR and SAXS techniques. Details on protein preparation, crystallization, data acquisition, and determination of structures are given here along with the brief summary of the currently available structural Bam protein repertoire.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
McMorran LM, Brockwell DJ, Radford SE (2014) Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 564:265–280
Merdanovic M, Clausen T, Kaiser M et al (2011) Protein quality control in the bacterial periplasm. Annu Rev Microbiol 65:149–168
Selkrig J, Leyton DL, Webb CT et al (2014) Assembly of β-barrel proteins into bacterial outer membranes. Biochim Biophys Acta 1843:1542–1550
Albrecht R, Zeth K (2011) Structural basis of outer membrane protein biogenesis in bacteria. J Biol Chem 286:27792–27803
Kim KH, Aulakh S, Paetzel M (2011) Crystal structure of β-barrel assembly machinery BamCD protein complex. J Biol Chem 286:39116–39121
Albrecht R, Zeth K (2010) Crystallization and preliminary X-ray data collection of the Escherichia coli lipoproteins BamC, BamD and BamE. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1586–1590
Kabsch W (2010) Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D66:133–144
Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D67:235–242
Williams PA, Coates L, Mohammed F et al (2005) The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr D61:75–79
Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Cryst 30:1022–1025
Emsley P, Lohkamp B, Scott WG et al (2010) Features and development of Coot. Acta Crystallogr D66:486–501
Afonine PV, Grosse-Kunstleve RW, Echols N et al (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D68:352–367
Vonrhein C, Blanc E, Roversi P et al (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364:215–230
Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D66:479–485
Abrahams JP, Leslie AGW (1996) Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Cryst D52:30–42
Langer G, Cohen SX, Lamzin VS et al (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171–1179
Jansen KB, Baker SL, Sousa MC (2011) Crystal structure of BamB from Pseudomonas aeruginosa and functional evaluation of its conserved structural features. PLoS One 7, e49749
Noinaj N, Fairman JW, Buchanan SK (2011) The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex. J Mol Biol 407:248–260
Heuck A, Schleiffer A, Clausen T (2011) Augmenting β-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins. J Mol Biol 406:659–666
Kim KH, Paetzel M (2011) Crystal structure of Escherichia coli BamB, a lipoprotein component of the β-barrel assembly machinery complex. J Mol Biol 406:667–678
Kim KH, Aulakh S, Tan W et al (2011) Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC. Acta Crystallogr F67:1350–1358
Warner LR, Varga K, Lange OF et al (2011) Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set. J Mol Biol 411:83–95
Knowles TJ, Browning DF, Jeeves M et al (2011) Structure and function of BamE within the outer membrane and the β-barrel assembly machine. EMBO Rep 12:123–128
Kim KH, Kang HS, Okon M et al (2011) Structural characterization of Escherichia coli BamE, a lipoprotein component of the beta-barrel assembly machinery complex. Biochemistry 50:1081–1090
Acknowledgements
This work was supported by the Max Planck Society, the Ikerbasque Research Foundation and the Paul Scherrer Institute in Villigen, Switzerland. The author is grateful about the technical support at the beamlines PXI and PXII of the Swiss Light Source (SLS, Villigen, Switzerland).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Zeth, K. (2015). Structure Determination of the BAM Complex Accessory Lipoproteins BamB–E. In: Buchanan, S., Noinaj, N. (eds) The BAM Complex. Methods in Molecular Biology, vol 1329. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2871-2_15
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2871-2_15
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2870-5
Online ISBN: 978-1-4939-2871-2
eBook Packages: Springer Protocols