Anfinsen, C. B. Principles that govern folding of protein chains. Science 181, 223–230 (1973).
Google Scholar
Gutte, B. A synthetic 70-amino acid residue analog of ribonuclease s-protein with enzymic activity. J. Biol. Chem. 250, 889–904 (1975).
Google Scholar
Lear, J. D., Wasserman, Z. R. & DeGrado, W. F. Synthetic amphiphilic peptide models for protein ion channels. Science 240, 1177–1181 (1988).
Google Scholar
Ghadiri, M. R., Granja, J. R. & Buehler, L. K. Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature 369, 301–304 (1994).
Google Scholar
Kortemme, T. & Baker, D. Computational design of protein-protein interactions. Curr. Opin. Chem. Biol. 8, 91–97 (2004).
Google Scholar
Korendovych, I. V. & DeGrado, W. F. De novo protein design, a retrospective. Q. Rev. Biophys. https://doi.org/10.1017/s0033583519000131 (2020).
Bolon, D. N., Voigt, C. A. & Mayo, S. L. De novo design of biocatalysts. Curr. Opin. Chem. Biol. 6, 125–129 (2002).
Google Scholar
Beesley, J. L. & Woolfson, D. N. The de novo design of alpha-helical peptides for supramolecular self-assembly. Curr. Opin. Biotechnol. 58, 175–182 (2019).
Google Scholar
Baltzer, L., Nilsson, H. & Nilsson, J. De novo design of proteins—what are the rules? Chem. Rev. 101, 3153–3163 (2001).
Google Scholar
Pirro, F. et al. Allosteric cooperation in a de novo-designed two-domain protein. Proc. Natl Acad. Sci. USA 117, 33246–33253 (2020).
Google Scholar
Polizzi, N. F. & DeGrado, W. F. A defined structural unit enables de novo design of small-molecule-binding proteins. Science 369, 1227–1233 (2020).
Google Scholar
Kaiser, E. T. Design and construction of biologically-active peptides and proteins, including enzymes. Biol. Chem. Hoppe-Seyler 369, 204–204 (1988).
Mutter, M. & Vuilleumier, S. A chemical approach to protein design—template-assembled synthetic proteins (TASP). Angew. Chem. -Int. Ed. 28, 535–554 (1989).
Dou, J. Y. et al. De novo design of a fluorescence-activating beta-barrel. Nature 561, 485–491 (2018).
Google Scholar
Lu, P. L. et al. Accurate computational design of multipass transmembrane proteins. Science 359, 1042–1046 (2018).
Google Scholar
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing technology. Trends Genet. 34, 666–681 (2018).
Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 345–353 (2017).
Google Scholar
Mahendran, K. R. et al. A monodisperse transmembrane alpha-helical peptide barrel. Nat. Chem. 9, 411–419 (2017).
Google Scholar
Krishnan, R. S. et al. Autonomously assembled synthetic transmembrane peptide pore. J. Am. Chem. Soc. 141, 2949–2959 (2019).
Ying, Y. L. & Long, Y. T. Nanopore-based single-biomolecule interfaces: from information to knowledge. J. Am. Chem. Soc. 141, 15720–15729 (2019).
Google Scholar
Varongchayakul, N., Song, J. X., Meller, A. & Grinstaff, M. W. Single-molecule protein sensing in a nanopore: a tutorial. Chem. Soc. Rev. 47, 8512–8524 (2018).
Google Scholar
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).
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
Kawano, R. et al. Rapid detection of a cocaine-binding aptamer using biological nanopores on a chip. J. Am. Chem. Soc.133, 8474–8477 (2011).
Google Scholar
Robertson, J. W. F. et al. Single-molecule mass spectrometry in solution using a solitary nanopore. Proc. Natl Acad. Sci. USA 104, 8207–8211 (2007).
Google Scholar
Hiratani, M. & Kawano, R. DNA logic operation with nanopore decoding to recognize microRNA patterns in small cell lung cancer. Anal. Chem. 90, 8531–8537 (2018).
Google Scholar
Kawano, R. Nanopore decoding of oligonucleotides in DNA computing. Biotechnol. J. 13, 1800091 (2018).
Liu, P. & Kawano, R. Recognition of single-point mutation using a biological nanopore. Small Meth. 4, 2000101 (2020).
Google Scholar
Sutherland, T. C. et al. Structure of peptides investigated by nanopore analysis. Nano Lett. 4, 1273–1277 (2004).
Google Scholar
Restrepo-Perez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Google Scholar
Watanabe, H. et al. Analysis of pore formation and protein translocation using large biological nanopores. Anal. Chem. 89, 11269–11277 (2017).
Google Scholar
Sohma, Y., Sasaki, M., Hayashi, Y., Kimura, T. & Kiso, Y. Novel and efficient synthesis of difficult sequence-containing peptides through O–N intramolecular acyl migration reaction of O-acyl isopeptides. Chem. Commun. 2004, 124–125 (2004).
Wimley, W. C. The versatile beta-barrel membrane protein. Curr. Opin. Struct. Biol. 13, 404–411 (2003).
Google Scholar
Chou, K. C. Prediction of beta-turns. J. Pept. Res. 49, 120–144 (1997).
Google Scholar
Mandel-Gutfreund, Y. & Gregoret, L. M. On the significance of alternating patterns of polar and non-polar residues in beta-strands. J. Mol. Biol. 323, 453–461 (2002).
Google Scholar
Killian, J. A. & von Heijne, G. How proteins adapt to a membrane-water interface. Trends Biochem. Sci. 25, 429–434 (2000).
Google Scholar
Hong, H. D., Park, S., Jimenez, R. H. F., Rinehart, D. & Tamm, L. K. Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins. J. Am. Chem. Soc. 129, 8320–8327 (2007).
Google Scholar
Cao, B. Q., Porollo, A., Adamczak, R., Jarrell, M. & Meller, J. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics 22, 303–309 (2006).
Google Scholar
Wang, Y. J. & Jardetzky, O. Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci. 11, 852–861 (2002).
Google Scholar
Kawano, R. et al. Metal-organic cuboctahedra for synthetic ion channels with multiple conductance states. Chem. 2, 393–403 (2017).
Google Scholar
Sekiya, Y. et al. Electrophysiological analysis of membrane disruption by bombinin and its isomer using the lipid bilayer system. ACS Appl. Bio Mater. 2, 1542–1548 (2019).
Google Scholar
Saigo, N., Izumi, K. & Kawano, R. Electrophysiological analysis of antimicrobial peptides in diverse species. ACS Omega 4, 13124–13130 (2019).
Google Scholar
Sekiya, Y., Sakashita, S., Shimizu, K., Usui, K. & Kawano, R. Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides. Analyst 143, 3540–3543 (2018).
Google Scholar
Henrickson, S. E., Misakian, M., Robertson, B. & Kasianowicz, J. J. Driven DNA transport into an asymmetric nanometer-scale pore. Phys. Rev. Lett. 85, 3057–3060 (2000).
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, 835 (2019).
An, N., Fleming, A. M., Middleton, E. G. & Burrows, C. J. Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity. Proc. Natl Acad. Sci. USA 111, 14325–14331 (2014).
Google Scholar
An, N., Fleming, A. M., White, H. S. & Burrows, C. J. Nanopore detection of 8-oxoguanine in the human telomere repeat sequence. ACS Nano 9, 4296–4307 (2015).
Google Scholar
Vorobieva, A. A. et al. De novo design of transmembrane beta barrels. Science 371, 801 (2021).
Hu, F. Z. et al. Single-molecule study of peptides with the same amino acid composition but different sequences by using an aerolysin nanopore. Chem. Bio. Chem. 21, 2467–2473 (2020).
Google Scholar
Kawano, R. Synthetic ion channels and DNA logic gates as components of molecular robots. Chem. Phys. Chem. 19, 359–366 (2018).
Google Scholar
Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005).
Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E. Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models. J. Chem. Theory Comput. 6, 459–466 (2010).
Google Scholar
Kawano, R. et al. Automated parallel recordings of topologically identified single ion channels. Sci. Rep. 3, 1995 (2013).
Kawano, R. et al. A portable lipid bilayer system for environmental sensing with a transmembrane protein. PLoS ONE 9, e102427 (2014).
Ohara, M., Takinoue, M. & Kawano, R. Nanopore logic operation with DNA to RNA transcription in a droplet system. ACS Synth. Biol. 6, 1427–1432 (2017).
Google Scholar
Serra-Batiste, M. et al. Abeta42 assembles into specific beta-barrel pore-forming oligomers in membrane-mimicking environments. Proc. Natl Acad. Sci. USA 113, 10866–10871 (2016).
Google Scholar
