Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients

• Published in: Nature communications Vol. 11; no. 1; p. 2155
• Main Authors: Calabrese, Antonio N, Schiffrin, Bob, Watson, Matthew, Karamanos, Theodoros K, Walko, Martin, Humes, Julia R, Horne, Jim E, White, Paul, Wilson, Andrew J, Kalli, Antreas C, Tuma, Roman, Ashcroft, Alison E, Brockwell, David J, Radford, Sheena E
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.05.2020; Nature Publishing Group UK; Nature Portfolio
• Subjects: Bacteria; Bacterial Outer Membrane Proteins - genetics; Bacterial Outer Membrane Proteins - metabolism; Binding Sites; Biosynthesis; Carrier Proteins - genetics; Carrier Proteins - metabolism; Computer applications; Computer simulation; Crosslinking; Crystal structure; Deuterium; Domains; E coli; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Fluorescence resonance energy transfer; Gram-negative bacteria; Hydrogen-deuterium exchange; Mass Spectrometry; Mass spectroscopy; Membrane proteins; Membranes; Molecular Chaperones - genetics; Molecular Chaperones - metabolism; Molecular dynamics; Outer membrane proteins; Peptidylprolyl isomerase; Peptidylprolyl Isomerase - genetics; Peptidylprolyl Isomerase - metabolism; Protein Binding; Proteins; Recognition; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-15702-1

The periplasmic chaperone SurA plays a key role in outer membrane protein (OMP) biogenesis. E. coli SurA comprises a core domain and two peptidylprolyl isomerase domains (P1 and P2), but its mechanisms of client binding and chaperone function have remained unclear. Here, we use chemical cross-linking, hydrogen-deuterium exchange mass spectrometry, single-molecule FRET and molecular dynamics simulations to map the client binding site(s) on SurA and interrogate the role of conformational dynamics in OMP recognition. We demonstrate that SurA samples an array of conformations in solution in which P2 primarily lies closer to the core/P1 domains than suggested in the SurA crystal structure. OMP binding sites are located primarily in the core domain, and OMP binding results in conformational changes between the core/P1 domains. Together, the results suggest that unfolded OMP substrates bind in a cradle formed between the SurA domains, with structural flexibility between domains assisting OMP recognition, binding and release.