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

Antonio N. Calabrese; Bob Schiffrin; Matthew Watson; Theodoros K. Karamanos; Martin Walko; Julia R. Humes; Jim E. Horne; Paul White; Andrew J. Wilson; Antreas C. Kalli; Roman Tuma; Alison E. Ashcroft; David J. Brockwell; Sheena E. Radford

doi:10.1038/s41467-020-15702-1

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

Antonio N. Calabrese
, Bob Schiffrin
, Matthew Watson
, Theodoros K. Karamanos
, Martin Walko
, Julia R. Humes
, Jim E. Horne
, Paul White
, Andrew J. Wilson
, Antreas C. Kalli
, Roman Tuma
, Alison E. Ashcroft
, David J. Brockwell
, Sheena E. Radford^*

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

37 Citations (Scopus)

Abstract

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.

Original language	English
Article number	2155
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-15702-1
Publication status	Published - 1 Dec 2020

Bibliographical note

Funding Information:
We thank members of the Radford and Brockwell laboratories for helpful discussions, along with Nasir Khan and James Ault for excellent technical support and Tomas Fessl for advice on FRET data analysis. The plasmid containing the mature sequence of SurA was kindly provided by D. Kahne (Harvard). A.N.C. (BB/P000037/1), B.S. (BB/N007603/ 1, BB/T000635/1), M.W. (BB/N017307/1) and J.E.H. (BB/M011151/1) acknowledge funding from the BBSRC. M.W. was funded by the EPSRC (EP/N035267/1), J.R.H. was funded by the US National Institutes of Health (GM102829) and PW acknowledges funding from the MRC (MR/P018491/1). The Monolith NT.115 MST instrument was purchased with funding from the Wellcome Trust (105615/Z/14/Z). Funding from the Wellcome Trust (208385/Z/17/Z) and BBSRC (BB/M012573/1) enabled the purchase of mass spectrometry equipment.

Publisher Copyright:
© 2020, The Author(s).

ASJC Scopus subject areas

General Chemistry
General Biochemistry,Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-020-15702-1

Cite this

Calabrese, A. N., Schiffrin, B., Watson, M., Karamanos, T. K., Walko, M., Humes, J. R., Horne, J. E., White, P., Wilson, A. J., Kalli, A. C., Tuma, R., Ashcroft, A. E., Brockwell, D. J., & Radford, S. E. (2020). Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Nature Communications, 11(1), Article 2155. https://doi.org/10.1038/s41467-020-15702-1

@article{091b7ff348884ef382343c250bd68e45,

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

abstract = "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.",

author = "Calabrese, \{Antonio N.\} and Bob Schiffrin and Matthew Watson and Karamanos, \{Theodoros K.\} and Martin Walko and Humes, \{Julia R.\} and Horne, \{Jim E.\} and Paul White and Wilson, \{Andrew J.\} and Kalli, \{Antreas C.\} and Roman Tuma and Ashcroft, \{Alison E.\} and Brockwell, \{David J.\} and Radford, \{Sheena E.\}",

note = "Funding Information: We thank members of the Radford and Brockwell laboratories for helpful discussions, along with Nasir Khan and James Ault for excellent technical support and Tomas Fessl for advice on FRET data analysis. The plasmid containing the mature sequence of SurA was kindly provided by D. Kahne (Harvard). A.N.C. (BB/P000037/1), B.S. (BB/N007603/ 1, BB/T000635/1), M.W. (BB/N017307/1) and J.E.H. (BB/M011151/1) acknowledge funding from the BBSRC. M.W. was funded by the EPSRC (EP/N035267/1), J.R.H. was funded by the US National Institutes of Health (GM102829) and PW acknowledges funding from the MRC (MR/P018491/1). The Monolith NT.115 MST instrument was purchased with funding from the Wellcome Trust (105615/Z/14/Z). Funding from the Wellcome Trust (208385/Z/17/Z) and BBSRC (BB/M012573/1) enabled the purchase of mass spectrometry equipment. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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Calabrese, AN, Schiffrin, B, Watson, M, Karamanos, TK, Walko, M, Humes, JR, Horne, JE, White, P, Wilson, AJ, Kalli, AC, Tuma, R, Ashcroft, AE, Brockwell, DJ & Radford, SE 2020, 'Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients', Nature Communications, vol. 11, no. 1, 2155. https://doi.org/10.1038/s41467-020-15702-1

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T1 - Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients

AU - Calabrese, Antonio N.

AU - Schiffrin, Bob

AU - Watson, Matthew

AU - Karamanos, Theodoros K.

AU - Walko, Martin

AU - Humes, Julia R.

AU - Horne, Jim E.

AU - White, Paul

AU - Wilson, Andrew J.

AU - Kalli, Antreas C.

AU - Tuma, Roman

AU - Ashcroft, Alison E.

AU - Brockwell, David J.

AU - Radford, Sheena E.

N1 - Funding Information: We thank members of the Radford and Brockwell laboratories for helpful discussions, along with Nasir Khan and James Ault for excellent technical support and Tomas Fessl for advice on FRET data analysis. The plasmid containing the mature sequence of SurA was kindly provided by D. Kahne (Harvard). A.N.C. (BB/P000037/1), B.S. (BB/N007603/ 1, BB/T000635/1), M.W. (BB/N017307/1) and J.E.H. (BB/M011151/1) acknowledge funding from the BBSRC. M.W. was funded by the EPSRC (EP/N035267/1), J.R.H. was funded by the US National Institutes of Health (GM102829) and PW acknowledges funding from the MRC (MR/P018491/1). The Monolith NT.115 MST instrument was purchased with funding from the Wellcome Trust (105615/Z/14/Z). Funding from the Wellcome Trust (208385/Z/17/Z) and BBSRC (BB/M012573/1) enabled the purchase of mass spectrometry equipment. Publisher Copyright: © 2020, The Author(s).

PY - 2020/12/1

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N2 - 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.

AB - 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.

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DO - 10.1038/s41467-020-15702-1

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SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2155

ER -

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

Abstract

Bibliographical note

ASJC Scopus subject areas

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