Bayley, H. Nanopore sequencing: from imagination to reality. Clin. Chem. 61, 25–31 (2014).
Google Scholar
Kang, X. F., Cheley, S., Guan, X. & Bayley, H. Stochastic detection of enantiomers. J. Am. Chem. Soc. 128, 10684–10685 (2006).
Google Scholar
Huang, G., Voet, A. & Maglia, G. FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution. Nat. Commun. 10, 1–10 (2019).
Google Scholar
Huang, G., Willems, K., Soskine, M., Wloka, C. & Maglia, G. Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores. Nat. Commun. 8, 935 (2017).
Restrepo-Pérez, L., Wong, C. H., Maglia, G., Dekker, C. & Joo, C. Label-free detection of post-translational modifications with a nanopore. Nano Lett. 19, 7957–7964 (2019).
Google Scholar
Ouldali, H. et al. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat. Biotechnol. 38, 176–181 (2020).
Google Scholar
Hu, Z.-L., Huo, M.-Z., Ying, Y.-L. & Long, Y.-T. Biological nanopore approach for single‐molecule protein sequencing. Angew. Chemie 60, 14738–14749 (2020).
Google Scholar
Nivala, J., Mulroney, L., Li, G., Schreiber, J. & Akeson, M. Discrimination among protein variants using an unfoldase-coupled nanopore. ACS Nano 8, 12365–12375 (2014).
Google Scholar
Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).
Google Scholar
Xu, C. et al. Computational design of transmembrane pores. Nature 585, 129–134 (2020).
Google Scholar
Joh, N. H. et al. De novo design of a transmembrane Zn2+-transporting four-helix bundle. Science 346, 1520–1520 (2014).
Google Scholar
Lu, P. et al. Accurate computational design of multipass transmembrane proteins. Science 359, 1042–1046 (2018).
Google Scholar
Scott, A. et al. Constructing ion channels from water-soluble α-helical barrels. Nat. Chem. 13, 643–650 (2021).
Spruijt, E., Tusk, S. E. & Bayley, H. DNA scaffolds support stable and uniform peptide nanopores. Nat. Nanotechnol. 13, 739–745 (2018).
Google Scholar
Seemüller, E. et al. Proteasome from Thermoplasma acidophilum: a threonine protease. Science 268, 579–582 (1995).
Google Scholar
Löwe, J. et al. Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268, 533–539 (1995).
Google Scholar
Sugiyama, M. et al. Spatial arrangement and functional role of α subunits of proteasome activator PA28 in hetero-oligomeric form. Biochem. Biophys. Res. Commun. 432, 141–145 (2013).
Google Scholar
Förster, A., Masters, E. I., Whitby, F. G., Robinson, H. & Hill, C. P. The 1.9 Å structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. Mol. Cell 18, 589–599 (2005).
Google Scholar
Jiang, J., Pentelute, B. L., Collier, R. J. & Hong Zhou, Z. Atomic structure of anthrax protective antigen pore elucidates toxin translocation. Nature 521, 545–549 (2015).
Google Scholar
Cheley, S., Braha, O., Lu, X., Conlan, S. & Bayley, H. A functional protein pore with a “retro” transmembrane domain. Protein Sci. 8, 1257–1267 (1999).
Google Scholar
Gu, L. Q. et al. Reversal of charge selectivity in transmembrane protein pores by using noncovalent molecular adapters. Proc. Natl Acad. Sci. USA 97, 3959–3964 (2000).
Google Scholar
Maglia, G., Restrepo, M. R., Mikhailova, E. & Bayley, H. Enhanced translocation of single DNA molecules through α-hemolysin nanopores by manipulation of internal charge. Proc. Natl Acad. Sci. USA 105, 19720–19725 (2008).
Google Scholar
Chen, B. et al. Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase. Structure 18, 1420–1430 (2010).
Google Scholar
Gu, L. Q., Braha, O., Conlan, S., Cheley, S. & Bayley, H. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter. Nature 398, 686–690 (1999).
Google Scholar
Yannakopoulou, K. et al. Symmetry requirements for effective blocking of pore-forming toxins: comparative study with α-, β-, and γ-cyclodextrin derivatives. Antimicrob. Agents Chemother. 55, 3594–3597 (2011).
Google Scholar
Förster, A. & Hill, C. P. Proteasome activators. Protein Degrad. 2, 89–110 (2007).
Google Scholar
Huber, E. M. & Groll, M. The mammalian proteasome activator PA28 forms an asymmetric α4β3 complex. Structure 25, 1473–1480.e3 (2017).
Google Scholar
Kuehn, L. & Dahlmann, B. Proteasome activator PA28 and its interaction with 20S proteasomes. Arch. Biochem. Biophys. 329, 87–96 (1996).
Google Scholar
Benaroudj, N., Zwickl, P., Seemüller, E., Baumeister, W. & Goldberg, A. L. ATP hydrolysis by the proteasome regulatory complex PAN serves multiple functions in protein degradation. Mol. Cell 11, 69–78 (2003).
Google Scholar
Huang, R. et al. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study. Proc. Natl Acad. Sci. USA 113, E4090–W4199 (2016).
Ripstein, Z. A., Huang, R., Augustyniak, R., Kay, L. E. & Rubinstein, J. L. Structure of a AAA+ unfoldase in the process of unfolding substrate. eLife 6, 1–14 (2017).
Google Scholar
Gerega, A. et al. VAT, the Thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase. J. Biol. Chem. 280, 42856–42862 (2005).
Google Scholar
Akopian, T. N., Kisselev, A. F. & Goldberg, A. L. Processive degradation of proteins and other catalytic properties of the proteasome from Thermoplasma acidophilum. J. Biol. Chem. 272, 1791–1798 (1997).
Google Scholar
Pédelacq, J. D., Cabantous, S., Tran, T., Terwilliger, T. C. & Waldo, G. S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2006).
Google Scholar
Ward, W. W., Prentice, H. J., Roth, A. F., Cody, C. W. & Reeves, S. C. Spectral perturbations of the aequorea green-fluorescent protein. Photochem. Photobiol. 35, 803–808 (1982).
Google Scholar
Hsu, S.-T. D., Blaser, G. & Jackson, S. E. The folding, stability and conformational dynamics of β-barrel fluorescent proteins. Chem. Soc. Rev. 38, 2951–2965 (2009).
Google Scholar
Kisselev, A. F., Songyang, Z. & Goldberg, A. L. Why does threonine, and not serine, function as the active site nucleophile in proteasomes? J. Biol. Chem. 275, 14831–14837 (2000).
Google Scholar
Biesemans, A., Soskine, M. & Maglia, G. A protein rotaxane controls the translocation of proteins across a ClyA nanopore. Nano Lett. 15, 6076–6081 (2015).
Google Scholar
Majumder, P. et al. Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Proc. Natl Acad. Sci. USA 116, 534–539 (2019).
Google Scholar
Kisselev, A. F., Akopian, T. N. & Goldberg, A. L. Range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes. J. Biol. Chem. 273, 1982–1989 (1998).
Google Scholar
Maglia, G., Heron, A. J. J., Stoddart, D., Japrung, D. & Bayley, H. Analysis of single nucleic acid molecules with protein nanopores. Methods Enzym. 475, 591–623 (2010).
Google Scholar
