1H, 13C and 15N Resonance assignments for YdbL from Escherichia coli in both its apo state and in complex with the C-terminus of YnbE

Abstract The interaction between AsmA-like protein YdbH and YnbE constitutes one of the main putative phospholipid transport systems driving outer membrane (OM) biogenesis in Escherichia coli . YdbH is anchored to the IM via its N-terminus and extends into a long, periplasmic domain composed of stacked β-sheets which generates a hydrophobic groove to shield phospholipids from the aqueous periplasm. It forms a continuous cell-envelope spanning complex via its interaction with OM lipoprotein YnbE. YnbE is highly self-multimeric and forms complexes with YdbH of unknown stoichiometry. YdbL, encoded within the same operon as YdbH and YnbE, is a soluble periplasmic protein that acts in a chaperone-like role to modulate YnbE multimerisation and mediate efficient YdbH-YnbE complex assembly. NMR revealed a direct and highly conserved interaction interface between YdbL and the C-terminus of YnbE, supporting the hypothesis that YdbL can directly tune YnbE behaviour. In this report, we present the 1 H, 13 C and 15 N resonance assignments for YdbL in both its apo state and in complex with a peptide derived from the C-terminus of YnbE. Analysis of the chemical shift data reveals the interaction interface for YdbL with YnbE does not result in significant changes in secondary structure but does appear to increase stabilisation of interacting α-helices. Overall, chemical shift changes observed for YdbL upon complex formation are reflective of side chain rearrangements in the peptide binding site and the interaction is confirmed with direct peptide-YdbL NOEs. Peptide-peptide short and medium range NOEs, and analysis of Hα chemical shifts, provide evidence that the bound YnbE peptide adopts an α-helical fold as predicted by in silico modelling of the interaction of full-length YnbE with YdbL. Together, these results strengthen directly related work underpinning YdbL function in controlling YnbE multimerisation to ensure correct complex formation with YdbH.