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Structural insight into the biogenesis of β-barrel membrane proteins

Nature volume 501, pages 385–390 (2013)Cite this article

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Abstract

β-barrel membrane proteins are essential for nutrient import, signalling, motility and survival. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex is responsible for the biogenesis of β-barrel membrane proteins, with homologous complexes found in mitochondria and chloroplasts. Here we describe the structure of BamA, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain. Three structural features shed light on the mechanism by which BamA catalyses β-barrel assembly. First, the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the β-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. And third, the β-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane.

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Figure 1: The structure of BamA from the BAM complex.
Figure 2: HdBamA and NgBamA crystal structures reveal conformational changes.
Figure 3: Mutational analysis of E.coli BamA.
Figure 4: BamA primes the membrane for OMP insertion.

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Accession codes

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors for HdBamAΔ3 and NgBamA are deposited in the Protein Data Bank under accession codes 4K3C and 4K3B, respectively.

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Acknowledgements

We thank H. Bernstein and R. Ieva for providing JCM-166 cells, J. Beckwith and R. Misra for providing antibodies, and A. M. Stanley and T. Barnard for discussions and comments on the manuscript. N.N., A.J.K., N.C.E., H.C. and S.K.B. are supported by the Intramural Research Program of the National Institutes of Health (NIH), National Institute of Diabetes and Digestive and Kidney Diseases. J.C.G. acknowledges support from the NIH under grants K22-AI100927 and R01-GM67887. P.L. is supported by a postdoctoral fellowship through the Diamond Light Source. T.L. is an Australian Research Council (ARC) Federation Fellow and acknowledges support from ARC Discovery Project (DP120101878) and ARC Linkage International Grant (LX0776170). We thank the respective staffs at the Southeast Regional Collaborative Access Team (SER-CAT) and General Medicine and Cancer Institute’s Collaborative Access Team (GM/CA-CAT) beamlines at the Advanced Photon Source, Argonne National Laboratory and the Diamond Light Source for their assistance during data collection. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract no. W-31-109-Eng-38 (SER-CAT), and by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no. DE-AC02-06CH11357 (GM/CA-CAT). Anton computer time was provided by the National Resource for Biomedical Supercomputing and the Pittsburgh Supercomputing Center through Grant RC2GM093307 from the NIH, using a machine donated by DE Shaw Research.

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Authors and Affiliations

  1. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Nicholas Noinaj, Adam J. Kuszak, Hoshing Chang, Nicole C. Easley & Susan K. Buchanan

  2. School of Physics, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA

    James C. Gumbart

  3. Diamond Light Source Ltd, Oxfordshire OX11 0DE, UK,

    Petra Lukacik

  4. Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia,

    Trevor Lithgow

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Contributions

N.N., H.C., N.C.E. and S.K.B. cloned, expressed and purified HdBamAΔ3 and NgBamA. P.L. performed data collection for experimental phasing. N.N. crystallized and solved the HdBamAΔ3 and NgBamA crystal structures. N.N. and A.J.K. performed the homology modelling and functional assays. J.C.G. designed, conducted and analysed the molecular dynamics simulations. N.N., A.J.K. and S.K.B. analysed and discussed all data. T.L. and S.K.B. conceived and designed the original project. N.N., A.J.K., T.L. and S.K.B. wrote the manuscript.

Corresponding author

Correspondence to Susan K. Buchanan.

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Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-2, Supplementary Figures 1-18, Supplementary Models 1-2, details of Supplementary Videos 1-2 and additional references. (PDF 4312 kb)

Supplementary Data

This file contains the data for Supplementary Models 1-2. (ZIP 169 kb)

Molecular dynamics (MD) simulations of FhaC and NgBamA

MD simulations were used to probe the stability of the barrel domains of FhaC and NgBamA. This video illustrates the changes that occur within the barrel domain (opening and closing) in NgBamA as the simulation progresses (see also Figure 4 and Supplementary Figure 16). (MOV 10499 kb)

Proposed mechanisms for the role of BamA in the biogenesis of β-barrel membrane proteins.

Animated video summarizing the two proposed mechanisms believed to be involved in recognizing, folding, and inserting β-barrel membrane proteins into the outer membrane. These mechanisms are based on studies (structural biology, computational, and functional) reported here, as well as, previously reported studies about the function of BamA. (MOV 5810 kb)

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Noinaj, N., Kuszak, A., Gumbart, J. et al. Structural insight into the biogenesis of β-barrel membrane proteins. Nature 501, 385–390 (2013). https://doi.org/10.1038/nature12521

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