Dual client binding sites in the ATP-independent chaperone SurA
Jazyk angličtina Země Velká Británie, Anglie Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
094232/Z/10/Z
Wellcome Trust (Wellcome)
222373/Z/21/Z
Wellcome Trust - United Kingdom
BB/T000635/1
RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
220628/Z/20/Z
Wellcome Trust - United Kingdom
105615/Z/14/Z
Wellcome Trust (Wellcome)
220628
Wellcome Trust - United Kingdom
PubMed
39277579
PubMed Central
PMC11401910
DOI
10.1038/s41467-024-52021-1
PII: 10.1038/s41467-024-52021-1
Knihovny.cz E-zdroje
- MeSH
- ABC transportéry metabolismus chemie genetika MeSH
- adenosintrifosfát metabolismus MeSH
- Escherichia coli * metabolismus genetika MeSH
- molekulární chaperony * metabolismus MeSH
- molekulární modely MeSH
- peptidylprolylisomerasa * metabolismus genetika MeSH
- proteinové domény MeSH
- proteiny vnější bakteriální membrány metabolismus genetika chemie MeSH
- proteiny z Escherichia coli * metabolismus genetika chemie MeSH
- rezonanční přenos fluorescenční energie MeSH
- sbalování proteinů MeSH
- transportní proteiny * metabolismus MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- ABC transportéry MeSH
- adenosintrifosfát MeSH
- molekulární chaperony * MeSH
- peptidylprolylisomerasa * MeSH
- proteiny vnější bakteriální membrány MeSH
- proteiny z Escherichia coli * MeSH
- SurA protein, E coli MeSH Prohlížeč
- transportní proteiny * MeSH
The ATP-independent chaperone SurA protects unfolded outer membrane proteins (OMPs) from aggregation in the periplasm of Gram-negative bacteria, and delivers them to the β-barrel assembly machinery (BAM) for folding into the outer membrane (OM). Precisely how SurA recognises and binds its different OMP clients remains unclear. Escherichia coli SurA comprises three domains: a core and two PPIase domains (P1 and P2). Here, by combining methyl-TROSY NMR, single-molecule Förster resonance energy transfer (smFRET), and bioinformatics analyses we show that SurA client binding is mediated by two binding hotspots in the core and P1 domains. These interactions are driven by aromatic-rich motifs in the client proteins, leading to SurA core/P1 domain rearrangements and expansion of clients from collapsed, non-native states. We demonstrate that the core domain is key to OMP expansion by SurA, and uncover a role for SurA PPIase domains in limiting the extent of expansion. The results reveal insights into SurA-OMP recognition and the mechanism of activation for an ATP-independent chaperone, and suggest a route to targeting the functions of a chaperone key to bacterial virulence and OM integrity.
Astbury Centre for Structural Molecular Biology School of Chemistry University of Leeds Leeds UK
Faculty of Science University of South Bohemia České Budějovice Czech Republic
School of Chemistry University of Birmingham Edgbaston Birmingham UK
Zobrazit více v PubMed
Nikaido, H. Molecular basis of bacterial outer membrane permeability revisited. Microbiol. Mol. Biol. Rev.67, 593–656 (2003). 10.1128/MMBR.67.4.593-656.2003 PubMed DOI PMC
Rojas, E. R. et al. The outer membrane is an essential load-bearing element in Gram-negative bacteria. Nature559, 617–621 (2018). 10.1038/s41586-018-0344-3 PubMed DOI PMC
Jarosławski, S., Duquesne, K., Sturgis, J. N. & Scheuring, S. High‐resolution architecture of the outer membrane of the Gram‐negative bacteria Roseobacter denitrificans. Mol. Microbiol.74, 1211–1222 (2009). 10.1111/j.1365-2958.2009.06926.x PubMed DOI
Benn, G. et al. Phase separation in the outer membrane of Escherichia coli. Proc. Natl Acad. Sci. USA118, e2112237118 (2021). 10.1073/pnas.2112237118 PubMed DOI PMC
Webby, M. N. et al. Lipids mediate supramolecular outer membrane protein assembly in bacteria. Sci. Adv.8, eadc9566 (2022). 10.1126/sciadv.adc9566 PubMed DOI PMC
Koebnik, R., Locher, K. P. & Van Gelder, P. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol. Microbiol.37, 239–253 (2000). 10.1046/j.1365-2958.2000.01983.x PubMed DOI
Schiffrin, B., Brockwell, D. J. & Radford, S. E. Outer membrane protein folding from an energy landscape perspective. BMC Biol.15, 123 (2017). 10.1186/s12915-017-0464-5 PubMed DOI PMC
Horne, J. E., Brockwell, D. J. & Radford, S. E. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J. Biol. Chem.295, 10340–10367 (2020). 10.1074/jbc.REV120.011473 PubMed DOI PMC
Hagan, C. L., Silhavy, T. J. & Kahne, D. β-Barrel membrane protein assembly by the Bam complex. Annu. Rev. Biochem.80, 189–210 (2011). 10.1146/annurev-biochem-061408-144611 PubMed DOI
Goemans, C., Denoncin, K. & Collet, J. F. Folding mechanisms of periplasmic proteins. Biochim. Biophys. Acta Mol. Cell Res.1843, 1517–1528 (2014).10.1016/j.bbamcr.2013.10.014 PubMed DOI
He, W. et al. Chaperone Spy protects outer membrane proteins from folding stress via dynamic complex formation. mBio12, e0213021 (2021). 10.1128/mBio.02130-21 PubMed DOI PMC
Plummer, A. M. & Fleming, K. G. From chaperones to the membrane with a BAM! Trends Biochem. Sci.41, 872–882 (2016). 10.1016/j.tibs.2016.06.005 PubMed DOI PMC
Konovalova, A., Kahne, D. E. & Silhavy, T. J. Outer membrane biogenesis. Annu. Rev. Microbiol.71, 539–556 (2017). 10.1146/annurev-micro-090816-093754 PubMed DOI PMC
Wu, R., Stephenson, R., Gichaba, A. & Noinaj, N. The big BAM theory: an open and closed case? Biochim. Biophys. Acta Biomembr.1862, 183062 (2020). 10.1016/j.bbamem.2019.183062 PubMed DOI PMC
Bakelar, J., Buchanan, S. K. & Noinaj, N. The structure of the β-barrel assembly machinery complex. Science351, 180–186 (2016). 10.1126/science.aad3460 PubMed DOI PMC
Gu, Y. et al. Structural basis of outer membrane protein insertion by the BAM complex. Nature531, 64–69 (2016). 10.1038/nature17199 PubMed DOI
Han, L. et al. Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins. Nat. Struct. Mol. Biol.23, 192–196 (2016). 10.1038/nsmb.3181 PubMed DOI
Iadanza, M. G. et al. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM. Nat. Commun.7, 12865 (2016). 10.1038/ncomms12865 PubMed DOI PMC
Doyle, M. T. & Bernstein, H. D. Bacterial outer membrane proteins assemble via asymmetric interactions with the BamA β-barrel. Nat. Commun.10, 3358 (2019). 10.1038/s41467-019-11230-9 PubMed DOI PMC
Tomasek, D. et al. Structure of a nascent membrane protein as it folds on the BAM complex. Nature583, 473–478 (2020). 10.1038/s41586-020-2370-1 PubMed DOI PMC
Wu, R. et al. Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM. Nat. Commun.12, 7131 (2021). 10.1038/s41467-021-27449-4 PubMed DOI PMC
Doyle, M. T. et al. Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding. Cell185, 1105–1260 (2022).10.1016/j.cell.2022.02.016 PubMed DOI PMC
Struyvé, M., Moons, M. & Tommassen, J. Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. J. Mol. Biol.218, 141–148 (1991). 10.1016/0022-2836(91)90880-F PubMed DOI
Wang, X., Peterson, J. H. & Bernstein, H. D. Bacterial outer membrane proteins are targeted to the Bam complex by two parallel mechanisms. mBio12, 10–1128 (2021). PubMed PMC
Robert, V. et al. Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. PLoS Biol.4, e377 (2006). 10.1371/journal.pbio.0040377 PubMed DOI PMC
Gessmann, D. et al. Outer membrane β-barrel protein folding is physically controlled by periplasmic lipid head groups and BamA. Proc. Natl Acad. Sci. USA111, 5878–5883 (2014). 10.1073/pnas.1322473111 PubMed DOI PMC
Imai, Y. et al. A new antibiotic selectively kills Gram-negative pathogens. Nature576, 459–464 (2019). 10.1038/s41586-019-1791-1 PubMed DOI PMC
Kaur, H. et al. The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature593, 125–129 (2021). 10.1038/s41586-021-03455-w PubMed DOI
Haysom, S. F. et al. Darobactin B stabilises a lateral-closed conformation of the BAM complex in E. coli cells. Angew. Chem. Int. Ed. Engl.62, e202218783 (2023). 10.1002/anie.202218783 PubMed DOI PMC
Rizzitello, A. E., Harper, J. R. & Silhavy, T. J. Genetic evidence for parallel pathways of chaperone activity in the periplasm of Escherichia coli. J. Bacteriol.183, 6794–6800 (2001). 10.1128/JB.183.23.6794-6800.2001 PubMed DOI PMC
Sklar, J. G., Wu, T., Kahne, D. & Silhavy, T. J. Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. Genes Dev.21, 2473–2484 (2007). 10.1101/gad.1581007 PubMed DOI PMC
Missiakas, D., Betton, J.-M. & Raina, S. New components of protein folding in extracytoplasmic compartments of Escherichia coli SurA, FkpA and Skp/OmpH. Mol. Microbiol.21, 871–884 (1996). 10.1046/j.1365-2958.1996.561412.x PubMed DOI
Lazar, S. W. & Kolter, R. SurA assists the folding of Escherichia coli outer membrane proteins. J. Bacteriol.178, 1770–1773 (1996). 10.1128/jb.178.6.1770-1773.1996 PubMed DOI PMC
Rouvière, P. E. & Gross, C. A. SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins. Genes Dev.10, 3170–3182 (1996). 10.1101/gad.10.24.3170 PubMed DOI
Behrens, S., Maier, R., de Cock, H., Schmid, F. X. & Gross, C. A. The SurA periplasmic PPIase lacking its parvulin domains functions in vivo and has chaperone activity. EMBO J.20, 285–294 (2001). 10.1093/emboj/20.1.285 PubMed DOI PMC
Vertommen, D., Ruiz, N., Leverrier, P., Silhavy, T. J. & Collet, J. F. Characterization of the role of the Escherichia coli periplasmic chaperone SurA using differential proteomics. Proteomics9, 2432–2443 (2009). 10.1002/pmic.200800794 PubMed DOI PMC
Obi, I. R. & Francis, M. S. Demarcating SurA activities required for outer membrane targeting of Yersinia pseudotuberculosis adhesins. Infect. Immun.81, 2296–2308 (2013). 10.1128/IAI.01208-12 PubMed DOI PMC
Justice, S. S. et al. Periplasmic peptidyl prolyl cis-trans isomerases are not essential for viability, but SurA is required for pilus biogenesis in Escherichia coli. J. Bacteriol.187, 7680–7686 (2005). 10.1128/JB.187.22.7680-7686.2005 PubMed DOI PMC
Justice, S. S., Lauer, S. R., Hultgren, S. J. & Hunstad, D. A. Maturation of intracellular Escherichia coli communities requires SurA. Infect. Immun.74, 4793–4800 (2006). 10.1128/IAI.00355-06 PubMed DOI PMC
Palomino, C., Marín, E. & Fernández, L. Á. The fimbrial usher FimD follows the SurA-BamB pathway for its assembly in the outer membrane of Escherichia coli. J. Bacteriol.193, 5222–5230 (2011). 10.1128/JB.05585-11 PubMed DOI PMC
Watts, K. M. & Hunstad, D. A. Components of SurA required for outer membrane biogenesis in uropathogenic Escherichia coli. PLoS ONE3, e3359 (2008). 10.1371/journal.pone.0003359 PubMed DOI PMC
Purdy, G. E., Fisher, C. R. & Payne, S. M. IcsA surface presentation in Shigella flexneri requires the periplasmic chaperones DegP, Skp, and SurA. J. Bacteriol.189, 5566–5573 (2007). 10.1128/JB.00483-07 PubMed DOI PMC
Ieva, R. & Bernstein, H. D. Interaction of an autotransporter passenger domain with BamA during its translocation across the bacterial outer membrane. Proc. Natl Acad. Sci. USA106, 19120–19125 (2009). 10.1073/pnas.0907912106 PubMed DOI PMC
Ruiz-Perez, F. et al. Roles of periplasmic chaperone proteins in the biogenesis of serine protease autotransporters of Enterobacteriaceae. J. Bacteriol.191, 6571–6583 (2009). 10.1128/JB.00754-09 PubMed DOI PMC
Sauri, A. et al. The Bam (Omp85) complex is involved in secretion of the autotransporter haemoglobin protease. Microbiology155, 3982–3991 (2009). 10.1099/mic.0.034991-0 PubMed DOI
Oberhettinger, P., Leo, J. C., Linke, D., Autenrieth, I. B. & Schütz, M. S. The inverse autotransporter intimin exports its passenger domain via a hairpin intermediate. J. Biol. Chem.290, 1837–1849 (2015). 10.1074/jbc.M114.604769 PubMed DOI PMC
Klein, K. et al. Deprivation of the periplasmic chaperone SurA reduces virulence and restores antibiotic susceptibility of multidrug-resistant Pseudomonas aeruginosa. Front. Microbiol.10, 100 (2019). 10.3389/fmicb.2019.00100 PubMed DOI PMC
Bitto, E. & McKay, D. B. Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins. Structure10, 1489–1498 (2002). 10.1016/S0969-2126(02)00877-8 PubMed DOI
Humes, J. R. et al. The role of SurA PPIase domains in preventing aggregation of the outer-membrane proteins tOmpA and OmpT. J. Mol. Biol.431, 1267–1283 (2019). 10.1016/j.jmb.2019.01.032 PubMed DOI
Schiffrin, B. et al. Dynamic interplay between the periplasmic chaperone SurA and the BAM complex in outer membrane protein folding. Commun. Biol.5, 560 (2022). 10.1038/s42003-022-03502-w PubMed DOI PMC
Ricci, D. P., Schwalm, J., Gonzales-Cope, M. & Silhavy, T. J. The activity and specificity of the outer membrane protein chaperone SurA are modulated by a proline isomerase domain. mBio4, e00540–13 (2013). 10.1128/mBio.00540-13 PubMed DOI PMC
Soltes, G. R., Schwalm, J., Ricci, D. P. & Silhavy, T. J. The activity of Escherichia coli chaperone SurA is regulated by conformational changes involving a parvulin domain. J. Bacteriol.198, 921–929 (2016). 10.1128/JB.00889-15 PubMed DOI PMC
Marx, D. C., Leblanc, M. J., Plummer, A. M., Krueger, S. & Fleming, K. G. Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA. Protein Sci.29, 2043–2053 (2020). 10.1002/pro.3924 PubMed DOI PMC
Marx, D. C. et al. SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins. Proc. Natl Acad. Sci. USA117, 28026–28035 (2020). 10.1073/pnas.2008175117 PubMed DOI PMC
Jia, M. et al. Conformational dynamics of the periplasmic chaperone SurA. Biochemistry59, 3235–3246 (2020). 10.1021/acs.biochem.0c00507 PubMed DOI
Calabrese, A. N. et al. Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients. Nat. Commun.11, 2155 (2020). 10.1038/s41467-020-15702-1 PubMed DOI PMC
Hennecke, G., Nolte, J., Volkmer-Engert, R., Schneider-Mergener, J. & Behrens, S. The periplasmic chaperone SurA exploits two features characteristic of integral outer membrane proteins for selective substrate recognition. J. Biol. Chem.280, 23540–23548 (2005). 10.1074/jbc.M413742200 PubMed DOI
Bitto, E. & McKay, D. B. The periplasmic molecular chaperone protein SurA binds a peptide motif that is characteristic of integral outer membrane proteins. J. Biol. Chem.278, 49316–49322 (2003). 10.1074/jbc.M308853200 PubMed DOI
Xu, X., Wang, S., Hu, Y. X. & McKay, D. B. The periplasmic bacterial molecular chaperone SurA adapts its structure to bind peptides in different conformations to assert a sequence preference for aromatic residues. J. Mol. Biol.373, 367–381 (2007). 10.1016/j.jmb.2007.07.069 PubMed DOI PMC
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature596, 583–589 (2021). 10.1038/s41586-021-03819-2 PubMed DOI PMC
Varadi, M. et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res.50, D439–D444 (2021).10.1093/nar/gkab1061 PubMed DOI PMC
Li, G. et al. Single-molecule detection reveals different roles of Skp and SurA as chaperones. ACS Chem. Biol.13, 1082–1089 (2018). 10.1021/acschembio.8b00097 PubMed DOI
Chamachi, N. et al. Chaperones Skp and SurA dynamically expand unfolded OmpX and synergistically disassemble oligomeric aggregates. Proc. Natl Acad. Sci. USA119, e2118919119 (2022). 10.1073/pnas.2118919119 PubMed DOI PMC
Vogt, J. & Schulz, G. E. The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure7, 1301–1309 (1999). 10.1016/S0969-2126(00)80063-5 PubMed DOI
Burmann, B. M., Wang, C. & Hiller, S. Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes OmpX-Skp and tOmpA-Skp. Nat. Struct. Mol. Biol.20, 1265–1272 (2013). 10.1038/nsmb.2677 PubMed DOI
Krainer, G. et al. Slow interconversion in a heterogeneous unfolded-state ensemble of outer-membrane phospholipase A. Biophys. J.113, 1280–1289 (2017). 10.1016/j.bpj.2017.05.037 PubMed DOI PMC
Devlin, T., Fleming, P. J., Loza, N. & Fleming, K. G. Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties. Eur. Biophys. J.52, 415–425 (2023). PubMed
Torella, J. P., Holden, S. J., Santoso, Y., Hohlbein, J. & Kapanidis, A. N. Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophys. J.100, 1568–1577 (2011). 10.1016/j.bpj.2011.01.066 PubMed DOI PMC
Kalinin, S., Valeri, A., Antonik, M., Felekyan, S. & Seidel, C. A. Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states. J. Phys. Chem. B114, 7983–7995 (2010). 10.1021/jp102156t PubMed DOI
Tugarinov, V., Hwang, P. M., Ollerenshaw, J. E. & Kay, L. E. Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J. Am. Chem. Soc.125, 10420–10428 (2003). 10.1021/ja030153x PubMed DOI
Schütz, S. & Sprangers, R. Methyl TROSY spectroscopy: a versatile NMR approach to study challenging biological systems. Prog. Nucl. Magn.116, 56–84 (2020).10.1016/j.pnmrs.2019.09.004 PubMed DOI
Kleckner, I. R. & Foster, M. P. An introduction to NMR-based approaches for measuring protein dynamics. Biochim. Biophys. Acta Protein Proteom.1814, 942–968 (2011).10.1016/j.bbapap.2010.10.012 PubMed DOI PMC
Williamson, M. P. Using chemical shift perturbation to characterise ligand binding. Prog. Nucl. Magn. Reson. Spectrosc.73, 1–16 (2013). 10.1016/j.pnmrs.2013.02.001 PubMed DOI
Ruschak, A. M. & Kay, L. E. Methyl groups as probes of supra-molecular structure, dynamics and function. J. Biomol. NMR46, 75–87 (2010). 10.1007/s10858-009-9376-1 PubMed DOI
Ebie Tan, A., Burgess, N. K., DeAndrade, D. S., Marold, J. D. & Fleming, K. G. Self-association of unfolded outer membrane proteins. Macromol. Biosci.10, 763 (2010). 10.1002/mabi.200900479 PubMed DOI PMC
Weinhäupl, K. et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell175, 1365–1379.e25 (2018). 10.1016/j.cell.2018.10.039 PubMed DOI PMC
Sučec, I. et al. Structural basis of client specificity in mitochondrial membrane-protein chaperones. Sci. Adv.6, eabd0263 (2020). 10.1126/sciadv.abd0263 PubMed DOI PMC
Burmann, B. M. et al. Regulation of α-synuclein by chaperones in mammalian cells. Nature577, 127–132 (2020). 10.1038/s41586-019-1808-9 PubMed DOI PMC
Foster, M. P., McElroy, C. A. & Amero, C. D. Solution NMR of large molecules and assemblies. Biochemistry46, 331–340 (2007). 10.1021/bi0621314 PubMed DOI PMC
Bhattacharya, S. et al. NMR-guided directed evolution. Nature610, 389–393 (2022). 10.1038/s41586-022-05278-9 PubMed DOI PMC
Bitto, E. & McKay, D. B. Binding of phage-display-selected peptides to the periplasmic chaperone protein SurA mimics binding of unfolded outer membrane proteins. FEBS Lett.568, 94–98 (2004). 10.1016/j.febslet.2004.05.014 PubMed DOI
Vorobieva, A. A. et al. De novo design of transmembrane β barrels. Science371, eabc8182 (2021). 10.1126/science.abc8182 PubMed DOI PMC
Behrens-Kneip, S. The role of SurA factor in outer membrane protein transport and virulence. Int. J. Med. Microbiol.300, 421–428 (2010). 10.1016/j.ijmm.2010.04.012 PubMed DOI
Gao, M., Nakajima An, D. & Skolnick, J. Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria. eLife11, e82885 (2022). 10.7554/eLife.82885 PubMed DOI PMC
Schiffrin, B., Radford, S. E., Brockwell, D. J. & Calabrese, A. N. PyXlinkViewer: a flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system. Protein Sci.29, 1851–1857 (2020). 10.1002/pro.3902 PubMed DOI PMC
Moon, C. P., Zaccai, N. R., Fleming, P. J., Gessmann, D. & Fleming, K. G. Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm. Proc. Natl Acad. Sci. USA110, 4285–4290 (2013). 10.1073/pnas.1212527110 PubMed DOI PMC
Quan, S. et al. Super Spy variants implicate flexibility in chaperone action. eLife3, e01584 (2014). 10.7554/eLife.01584 PubMed DOI PMC
Stirling, P. C., Bakhoum, S. F., Feigl, A. B. & Leroux, M. R. Convergent evolution of clamp-like binding sites in diverse chaperones. Nat. Struct. Mol. Biol.13, 865–870 (2006). 10.1038/nsmb1153 PubMed DOI
Schiffrin, B. et al. Skp is a multivalent chaperone of outer-membrane proteins. Nat. Struct. Mol. Biol.23, 786–793 (2016). 10.1038/nsmb.3266 PubMed DOI PMC
Suss, O. & Reichmann, D. Protein plasticity underlines activation and function of ATP-independent chaperones. Front Mol. Biosci.2, 43 (2015). 10.3389/fmolb.2015.00043 PubMed DOI PMC
Mitra, R., Wu, K., Lee, C. & Bardwell, J. C. ATP-independent chaperones. Annu. Rev. Biophys.51, 409–429 (2022). 10.1146/annurev-biophys-090121-082906 PubMed DOI
Burmann, B. M. & Hiller, S. Chaperones and chaperone–substrate complexes: dynamic playgrounds for NMR spectroscopists. Prog. Nucl. Magn.86, 41–64 (2015).10.1016/j.pnmrs.2015.02.004 PubMed DOI
Karamanos, T. K. & Clore, G. M. Large chaperone complexes through the lens of nuclear magnetic resonance spectroscopy. Ann. Rev. Biophys.51, 223–246 (2022). 10.1146/annurev-biophys-090921-120150 PubMed DOI PMC
Cock, P. J. A. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics25, 1422–1423 (2009). 10.1093/bioinformatics/btp163 PubMed DOI PMC
Hamelryck, T. & Manderick, B. PDB file parser and structure class implemented in Python. Bioinformatics19, 2308–2310 (2003). 10.1093/bioinformatics/btg299 PubMed DOI
Paysan-Lafosse, T. et al. InterPro in 2022. Nucleic Acids Res.51, D418–D427 (2022).10.1093/nar/gkac993 PubMed DOI PMC
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics28, 3150–3152 (2012). 10.1093/bioinformatics/bts565 PubMed DOI PMC
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol.7, 539 (2011). 10.1038/msb.2011.75 PubMed DOI PMC
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics25, 1189–1191 (2009). 10.1093/bioinformatics/btp033 PubMed DOI PMC
Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res.44, W344–W350 (2016). 10.1093/nar/gkw408 PubMed DOI PMC
Landau, M. et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res.33, W299–W302 (2005). 10.1093/nar/gki370 PubMed DOI PMC
Hagan, C. L., Kim, S. & Kahne, D. Reconstitution of outer membrane protein assembly from purified components. Science328, 890–892 (2010). 10.1126/science.1188919 PubMed DOI PMC
Burgess, N. K., Dao, T. P., Stanley, A. M. & Fleming, K. G. Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro. J. Biol. Chem.283, 26748–26758 (2008). 10.1074/jbc.M802754200 PubMed DOI PMC
Cordes, T., Vogelsang, J. & Tinnefeld, P. On the mechanism of trolox as antiblinking and antibleaching reagent. J. Am. Chem. Soc.131, 5018–5019 (2009). 10.1021/ja809117z PubMed DOI
Ingargiola, A., Lerner, E., Chung, S., Weiss, S. & Michalet, X. FRETBursts: an open source toolkit for analysis of freely-diffusing single-molecule FRET. PLoS ONE11, e0160716 (2016). 10.1371/journal.pone.0160716 PubMed DOI PMC
Lee, N. K. et al. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys. J.88, 2939–2953 (2005). 10.1529/biophysj.104.054114 PubMed DOI PMC
Tomov, T. E. et al. Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis. Biophys. J.102, 1163–1173 (2012). 10.1016/j.bpj.2011.11.4025 PubMed DOI PMC
Hartmann, A., Krainer, G., Keller, S. & Schlierf, M. Quantification of millisecond protein-folding dynamics in membrane-mimetic environments by single-molecule förster resonance energy transfer spectroscopy. Anal. Chem.87, 11224–11232 (2015). 10.1021/acs.analchem.5b03207 PubMed DOI
Kalinin, S., Valeri, A., Antonik, M., Felekyan, S. & Seidel, C. A. M. Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states.J. Phys. Chem. B114, 7983–7995 (2010). 10.1021/jp102156t PubMed DOI
Azatian, S. B., Kaur, N. & Latham, M. P. Increasing the buffering capacity of minimal media leads to higher protein yield. J. Biomol. NMR73, 11–17 (2019). 10.1007/s10858-018-00222-4 PubMed DOI PMC
McMorran, L. M., Bartlett, A. I., Huysmans, G. H., Radford, S. E. & Brockwell, D. J. Dissecting the effects of periplasmic chaperones on the in vitro folding of the outer membrane protein PagP. J. Mol. Biol.425, 3178–3191 (2013). 10.1016/j.jmb.2013.06.017 PubMed DOI PMC
Schanda, P. & Brutscher, B. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J. Am. Chem. Soc.127, 8014–8015 (2005). 10.1021/ja051306e PubMed DOI
Favier, A. & Brutscher, B. NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers. J. Biomol. NMR73, 199–211 (2019). 10.1007/s10858-019-00249-1 PubMed DOI
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR6, 277–293 (1995). 10.1007/BF00197809 PubMed DOI
Vranken, W. F. et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins59, 687–696 (2005). 10.1002/prot.20449 PubMed DOI
Hunter, J. D. Matplotlib: a 2D graphics environment. Comput. Sci. Eng.9, 90–95 (2007).10.1109/MCSE.2007.55 DOI
Harris, C.R. et al. Array programming with NumPy. Nature585, 357–362 (2020). 10.1038/s41586-020-2649-2 PubMed DOI PMC
Helmus, J. J. & Jaroniec, C. P. Nmrglue an open source Python package for the analysis of multidimensional NMR data. J. Biomol. NMR55, 355–367 (2013). 10.1007/s10858-013-9718-x PubMed DOI PMC
Eswar, N. et al. Comparative protein structure modeling using Modeller. Curr. Protoc. Bioinform.54, 5–6 (2006). PubMed PMC