Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM

Runrun Wu, Jeremy W. Bakelar, Karl Lundquist, Zijian Zhang, Katie M. Kuo, David Ryoo, Yui Tik Pang, Chen Sun, Tommi White, Thomas Klose, Wen Jiang, James C. Gumbart () and Nicholas Noinaj ()
Additional contact information
Runrun Wu: Purdue University
Jeremy W. Bakelar: Purdue University
Karl Lundquist: School of Physics, Georgia Institute of Technology
Zijian Zhang: School of Physics, Georgia Institute of Technology
Katie M. Kuo: Georgia Institute of Technology
David Ryoo: Georgia Institute of Technology
Yui Tik Pang: School of Physics, Georgia Institute of Technology
Chen Sun: Purdue University
Tommi White: University of Missouri
Thomas Klose: Purdue University
Wen Jiang: Purdue University
James C. Gumbart: School of Physics, Georgia Institute of Technology
Nicholas Noinaj: Purdue University

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: Abstract In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.

Date: 2021
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DOI: 10.1038/s41467-021-27449-4

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