Research Data Leeds Repository

Citation

Calabrese, Antonio N. and Schiffrin, Bob and Watson, Matthew and Walko, Martin and Humes, Julia R. and Karamanos, Theodoros and Horne, Jim E. and White, Paul and Kalli, Antreas and Tuma, Roman and Ashcroft, Alison E. and Brockwell, David J. and Radford, Sheena E. (2020) Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients - dataset. University of Leeds. [Dataset] https://doi.org/10.5518/701

Dataset description

SurA is the conserved major chaperone of outer membrane protein (OMP) biogenesis in the periplasm of Gram-negative bacteria, and plays a key role in cell envelope homeostasis and virulence. In E. coli, SurA comprises three domains: a core domain and two peptidyl prolyl isomerase (PPIase) domains (P1 and P2). The functional roles of these domains in chaperone activity, including their inter-subunit dynamics and interactions with substrates remain unclear. Here we have used chemical cross-linking, HDX-MS, oxidative labelling, single-molecule FRET and molecular dynamics simulations, to investigate the conformational dynamics of SurA in its apo state and to map the binding site(s) for its clients. We demonstrate that SurA predominantly samples conformations in solution in which the P2 domain is closer to the core and P1 domains than suggested by the extended conformation in its crystal structure. Using cross-linking experiments we show that SurA has multiple, yet specific, binding sites for OmpX located primarily in the core domain, and that residues spanning the whole OmpX sequence bind in these regions. HDX experiments additionally reveal that binding of OmpX, and the larger client OmpF, lead to inter-domain conformational changes between the core and P1 domains. Combining these data we generate a model for SurA OMP recognition in which unfolded OMP substrates bind in a cradle formed between the SurA domains, in a manner reminiscent of other ATP-independent chaperones. Structural flexibility between domains is likely a key feature of the SurA functional cycle, assisting in OMP recognition, binding and release of its broad range of OMP substrates for folding into the outer membrane.

Additional information:	Equipment used: 105615/Z/14/Z 208385/Z/17/Z BB/M012573/1
Keywords:	Biological science, Protein structure and dynamics
Subjects:	C000 - Biological sciences
Divisions:	Faculty of Biological Sciences > School of Molecular and Cellular Biology
Related resources:	Location Type https://doi.org/10.1101/2019.12.19.882696 Publication https://doi.org/10.1038/s41467-020-15702-1 Publication https://eprints.whiterose.ac.uk/158540/ Publication
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	09 Mar 2020 21:07
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/650
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Calabrese, Antonio N. https://orcid.org/0000-0003-2437-7761 University of Leeds https://ror.org/024mrxd33 ror Schiffrin, Bob https://orcid.org/0000-0002-1670-7356 University of Leeds https://ror.org/024mrxd33 ror Watson, Matthew https://orcid.org/0000-0003-2166-6840 University of Leeds https://ror.org/024mrxd33 ror Walko, Martin https://orcid.org/0000-0002-7160-6136 University of Leeds https://ror.org/024mrxd33 ror Humes, Julia R. https://orcid.org/0000-0002-1407-7880 University of Leeds https://ror.org/024mrxd33 ror Newcastle University https://ror.org/01kj2bm70 ror Karamanos, Theodoros https://orcid.org/0000-0003-2297-540X University of Leeds https://ror.org/024mrxd33 ror National Institutes of Health https://ror.org/01cwqze88 ror Horne, Jim E. https://orcid.org/0000-0001-5260-2634 University of Leeds https://ror.org/024mrxd33 ror White, Paul https://orcid.org/0000-0001-7536-4552 University of Leeds https://ror.org/024mrxd33 ror Kalli, Antreas https://orcid.org/0000-0001-7156-9403 University of Leeds https://ror.org/024mrxd33 ror Tuma, Roman https://orcid.org/0000-0003-0047-0013 University of Leeds https://ror.org/024mrxd33 ror Ashcroft, Alison E. https://orcid.org/0000-0002-1676-123X University of Leeds https://ror.org/024mrxd33 ror University of South Bohemia https://ror.org/033n3pw66 ror Brockwell, David J. https://orcid.org/0000-0002-0802-5937 University of Leeds https://ror.org/024mrxd33 ror Radford, Sheena E. https://orcid.org/0000-0002-3079-8039 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: BBSRC, BBSRC, BBSRC, BBSRC, EPSRC, MRC Grant numbers: BB/P000037/1, BB/N007603/1, BB/N017307/1, BB/M011151/1, EP/N035267/1, MR/P018491/ Publication date: 2020 Resource language: English Metadata language: English Research project title: Inter-domain dynamics in the chaperone SurA permit multi-site binding to its unfolded outer membrane protein clients Publisher: University of Leeds Contact email: s.e.radford@leeds.ac.uk Last Modified: 19 Dec 2024 15:00

Files

Documentation

smFRET manifest [818B] smFRET manifest [818B] smFRET manifest [818B] Security: Anyone File name: 1_smFRET.zip.manifest.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 818B

MD data.manifest [2kB] MD data.manifest [2kB] MD data.manifest [2kB] Security: Anyone File name: 2_MD_data.zip.manifest.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 2kB

Data

smFRET data [8GB] smFRET data [8GB] smFRET data [8GB] Security: Anyone File name: 1_smFRET.zip Content type: Data Description: HDF5 files of all unprocessed smFRET data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 8GB

MD data [39MB] MD data [39MB] MD data [39MB] Security: Anyone File name: 2_MD_data.zip Content type: Data Description: Extracted PDBs, final Structures, GROMACS input files, starting structures and trajectories Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 39MB