[ad_1]
Anfinsen, C. B. Ideas that govern folding of protein chains. Science 181, 223–230 (1973).
Gutte, B. An artificial 70-amino acid residue analog of ribonuclease s-protein with enzymic exercise. J. Biol. Chem. 250, 889–904 (1975).
Lear, J. D., Wasserman, Z. R. & DeGrado, W. F. Artificial amphiphilic peptide fashions for protein ion channels. Science 240, 1177–1181 (1988).
Ghadiri, M. R., Granja, J. R. & Buehler, L. Okay. Synthetic transmembrane ion channels from self-assembling peptide nanotubes. Nature 369, 301–304 (1994).
Kortemme, T. & Baker, D. Computational design of protein-protein interactions. Curr. Opin. Chem. Biol. 8, 91–97 (2004).
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).
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).
Baltzer, L., Nilsson, H. & Nilsson, J. De novo design of proteins—what are the foundations? Chem. Rev. 101, 3153–3163 (2001).
Pirro, F. et al. Allosteric cooperation in a de novo-designed two-domain protein. Proc. Natl Acad. Sci. USA 117, 33246–33253 (2020).
Polizzi, N. F. & DeGrado, W. F. An outlined structural unit permits de novo design of small-molecule-binding proteins. Science 369, 1227–1233 (2020).
Kaiser, E. T. Design and development of biologically-active peptides and proteins, together with enzymes. Biol. Chem. Hoppe-Seyler 369, 204–204 (1988).
Mutter, M. & Vuilleumier, S. A chemical method to protein design—template-assembled artificial 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).
Lu, P. L. et al. Correct computational design of multipass transmembrane proteins. Science 359, 1042–1046 (2018).
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing expertise. Developments Genet. 34, 666–681 (2018).
Shendure, J. et al. DNA sequencing at 40: previous, current and future. Nature 550, 345–353 (2017).
Mahendran, Okay. R. et al. A monodisperse transmembrane alpha-helical peptide barrel. Nat. Chem. 9, 411–419 (2017).
Krishnan, R. S. et al. Autonomously assembled artificial transmembrane peptide pore. J. Am. Chem. Soc. 141, 2949–2959 (2019).
Ying, Y. L. & Lengthy, Y. T. Nanopore-based single-biomolecule interfaces: from data to data. J. Am. Chem. Soc. 141, 15720–15729 (2019).
Varongchayakul, N., Track, J. X., Meller, A. & Grinstaff, M. W. Single-molecule protein sensing in a nanopore: a tutorial. Chem. Soc. Rev. 47, 8512–8524 (2018).
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146–1153 (2008).
Gu, L. Q., Braha, O., Conlan, S., Cheley, S. & Bayley, H. Stochastic sensing of natural analytes by a pore-forming protein containing a molecular adapter. Nature 398, 686–690 (1999).
Kawano, R. et al. Speedy detection of a cocaine-binding aptamer utilizing organic nanopores on a chip. J. Am. Chem. Soc.133, 8474–8477 (2011).
Robertson, J. W. F. et al. Single-molecule mass spectrometry in answer utilizing a solitary nanopore. Proc. Natl Acad. Sci. USA 104, 8207–8211 (2007).
Hiratani, M. & Kawano, R. DNA logic operation with nanopore decoding to acknowledge microRNA patterns in small cell lung most cancers. Anal. Chem. 90, 8531–8537 (2018).
Kawano, R. Nanopore decoding of oligonucleotides in DNA computing. Biotechnol. J. 13, 1800091 (2018).
Liu, P. & Kawano, R. Recognition of single-point mutation utilizing a organic nanopore. Small Meth. 4, 2000101 (2020).
Sutherland, T. C. et al. Construction of peptides investigated by nanopore evaluation. Nano Lett. 4, 1273–1277 (2004).
Restrepo-Perez, L., Joo, C. & Dekker, C. Paving the best way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Watanabe, H. et al. Evaluation of pore formation and protein translocation utilizing giant organic nanopores. Anal. Chem. 89, 11269–11277 (2017).
Sohma, Y., Sasaki, M., Hayashi, Y., Kimura, T. & Kiso, Y. Novel and environment friendly synthesis of inauspicious sequence-containing peptides via O–N intramolecular acyl migration response 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).
Chou, Okay. C. Prediction of beta-turns. J. Pept. Res. 49, 120–144 (1997).
Mandel-Gutfreund, Y. & Gregoret, L. M. On the importance of alternating patterns of polar and non-polar residues in beta-strands. J. Mol. Biol. 323, 453–461 (2002).
Killian, J. A. & von Heijne, G. How proteins adapt to a membrane-water interface. Developments Biochem. Sci. 25, 429–434 (2000).
Hong, H. D., Park, S., Jimenez, R. H. F., Rinehart, D. & Tamm, L. Okay. Position of fragrant facet chains within the folding and thermodynamic stability of integral membrane proteins. J. Am. Chem. Soc. 129, 8320–8327 (2007).
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).
Wang, Y. J. & Jardetzky, O. Likelihood-based protein secondary construction identification utilizing mixed NMR chemical-shift information. Protein Sci. 11, 852–861 (2002).
Kawano, R. et al. Metallic-organic cuboctahedra for artificial ion channels with a number of conductance states. Chem. 2, 393–403 (2017).
Sekiya, Y. et al. Electrophysiological evaluation of membrane disruption by bombinin and its isomer utilizing the lipid bilayer system. ACS Appl. Bio Mater. 2, 1542–1548 (2019).
Saigo, N., Izumi, Okay. & Kawano, R. Electrophysiological evaluation of antimicrobial peptides in numerous species. ACS Omega 4, 13124–13130 (2019).
Sekiya, Y., Sakashita, S., Shimizu, Okay., Usui, Okay. & Kawano, R. Channel present evaluation estimates the pore-formation and the penetration of transmembrane peptides. Analyst 143, 3540–3543 (2018).
Henrickson, S. E., Misakian, M., Robertson, B. & Kasianowicz, J. J. Pushed DNA transport into an uneven nanometer-scale pore. Phys. Rev. Lett. 85, 3057–3060 (2000).
Huang, G., Voet, A. & Maglia, G. FraC nanopores with adjustable diameter determine the mass of opposite-charge peptides with 44 dalton decision. 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).
An, N., Fleming, A. M., White, H. S. & Burrows, C. J. Nanopore detection of 8-oxoguanine within the human telomere repeat sequence. ACS Nano 9, 4296–4307 (2015).
Vorobieva, A. A. et al. De novo design of transmembrane beta barrels. Science 371, 801 (2021).
Hu, F. Z. et al. Single-molecule research of peptides with the identical amino acid composition however totally different sequences by utilizing an aerolysin nanopore. Chem. Bio. Chem. 21, 2467–2473 (2020).
Kawano, R. Artificial ion channels and DNA logic gates as elements of molecular robots. Chem. Phys. Chem. 19, 359–366 (2018).
Van Der Spoel, D. et al. GROMACS: quick, versatile, and free. J. Comput. Chem. 26, 1701–1718 (2005).
Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B. & Lindahl, E. Implementation of the CHARMM drive subject in GROMACS: evaluation of protein stability results from correction maps, digital interplay websites, and water fashions. J. Chem. Idea Comput. 6, 459–466 (2010).
Kawano, R. et al. Automated parallel recordings of topologically recognized single ion channels. Sci. Rep. 3, 1995 (2013).
Kawano, R. et al. A transportable 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).
Serra-Batiste, M. et al. Abeta42 assembles into particular beta-barrel pore-forming oligomers in membrane-mimicking environments. Proc. Natl Acad. Sci. USA 113, 10866–10871 (2016).
[ad_2]
