An Engineered OmpG Nanopore with Displayed Peptide Motifs for Single-Molecule Multiplex Protein Detection
Joshua C. Foster
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorBach Pham
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Current address: Department of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
Search for more papers by this authorRyan Pham
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorMinji Kim
Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorProf. Matthew D. Moore
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorCorresponding Author
Prof. Min Chen
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorJoshua C. Foster
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorBach Pham
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Current address: Department of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
Search for more papers by this authorRyan Pham
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorMinji Kim
Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorProf. Matthew D. Moore
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorCorresponding Author
Prof. Min Chen
Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003 USA
Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003 USA
Search for more papers by this authorAbstract
Molecular detection via nanopore, achieved by monitoring changes in ionic current arising from analyte interaction with the sensor pore, is a promising technology for multiplex sensing development. Outer Membrane Protein G (OmpG), a monomeric porin possessing seven functionalizable loops, has been reported as an effective sensing platform for selective protein detection. Using flow cytometry to screen unfavorable constructs, we identified two OmpG nanopores with unique peptide motifs displayed in either loop 3 or 6, which also exhibited distinct analyte signals in single-channel current recordings. We exploited these motif-displaying loops concurrently to facilitate single-molecule multiplex protein detection in a mixture. We additionally report a strategy to increase sensor sensitivity via avidity motif display. These sensing schemes may be expanded to more sophisticated designs utilizing additional loops to increase multiplicity and sensitivity.
Conflict of interest
The authors declare no conflict of interest.
Open Research
Data Availability Statement
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Supporting Information
As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
| Filename | Description |
|---|---|
| ange202214566-sup-0001-misc_information.pdf2.8 MB | Supporting Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- 1
- 1aR. M. Califf, Exp. Biol. Med. 2018, 243, 213–221;
- 1bL. Cohen, D. R. Walt, Chem. Rev. 2019, 119, 293–321;
- 1cS. B. Nimse, M. D. Sonawane, K. S. Song, T. Kim, Analyst 2016, 141, 740–755.
- 2J. Leva-Bueno, S. A. Peyman, P. A. Millner, Med. Microbiol. Immunol. 2020, 209, 343–362.
- 3J. E. Reiner, A. Balijepalli, J. W. Robertson, J. Campbell, J. Suehle, J. J. Kasianowicz, Chem. Rev. 2012, 112, 6431–6451.
- 4
- 4aY. Wang, Y. Zhao, A. Bollas, Y. Wang, K. F. Au, Nat. Biotechnol. 2021, 39, 1348–1365;
- 4bS. K. Tabatabaei, B. Pham, C. Pan, J. Liu, S. Chandak, S. A. Shorkey, A. G. Hernandez, A. Aksimentiev, M. Chen, C. M. Schroeder, O. Milenkovic, Nano Lett. 2022, 22, 1905–1914.
- 5
- 5aG. Huang, K. Willems, M. Soskine, C. Wloka, G. Maglia, Nat. Commun. 2017, 8, 935;
- 5bH. J. Hwang, J. S. Kim, J. Lee, J. S. Min, K. B. Jeong, E. Kim, M. K. Lee, S. W. Chi, Anal. Chem. 2022, 94, 7449–7454;
- 5cS. Yan, J. Zhang, Y. Wang, W. Guo, S. Zhang, Y. Liu, J. Cao, Y. Wang, L. Wang, F. Ma, P. Zhang, H. Y. Chen, S. Huang, Nano Lett. 2021, 21, 6703–6710;
- 5dH. Brinkerhoff, A. S. W. Kang, J. Liu, A. Aksimentiev, C. Dekker, Science 2021, 374, 1509–1513.
- 6
- 6aH. Ouldali, K. Sarthak, T. Ensslen, F. Piguet, P. Manivet, J. Pelta, J. C. Behrends, A. Aksimentiev, A. Oukhaled, Nat. Biotechnol. 2020, 38, 176–181;
- 6bL. Restrepo-Pérez, G. Huang, P. R. Bohländer, N. Worp, R. Eelkema, G. Maglia, C. Joo, C. Dekker, ACS Nano 2019, 13, 13668–13676;
- 6cL. Restrepo-Pérez, C. H. Wong, G. Maglia, C. Dekker, C. Joo, Nano Lett. 2019, 19, 7957–7964.
- 7
- 7aF. L. R. Lucas, R. C. A. Versloot, L. Yakovlieva, M. T. C. Walvoort, G. Maglia, Nat. Commun. 2021, 12, 5795;
- 7bS. Zhang, G. Huang, R. C. A. Versloot, B. M. H. Bruininks, P. C. T. de Souza, S. J. Marrink, G. Maglia, Nat. Chem. 2021, 13, 1192–1199.
- 8
- 8aL. Duan, L. Yobas, ACS Nano 2018, 12, 7892–7900;
- 8bL. He, P. Karau, V. Tabard-Cossa, Nanoscale 2019, 11, 16342–16350;
- 8cZ. Zhang, X. Wang, X. Wei, S. W. Zheng, B. J. Lenhart, P. Xu, J. Li, J. Pan, H. Albrecht, C. Liu, Biosens. Bioelectron. 2021, 181, 113134;
- 8dS. Wei, Z. R. Weiss, Z. Williams, G3 2018, 8, 1649–1657;
- 8eS. Huang, M. Romero-Ruiz, O. K. Castell, H. Bayley, M. I. Wallace, Nat. Nanotechnol. 2015, 10, 986–991;
- 8fN. Cardozo, K. Zhang, K. Doroschak, A. Nguyen, Z. Siddiqui, N. Bogard, K. Strauss, L. Ceze, J. Nivala, Nat. Biotechnol. 2022, 40, 42–46;
- 8gM. Palla, S. Punthambaker, B. Stranges, F. Vigneault, J. Nivala, D. Wiegand, A. Ayer, T. Craig, D. Gremyachinskiy, H. Franklin, S. Sun, J. Pollard, A. Trans, C. Arnold, C. Schwab, C. McGaw, P. Sarvabhowman, D. Dalal, E. Thai, E. Amato, I. Lederman, M. Taing, S. Kelley, A. Qwan, C. W. Fuller, S. Roever, G. M. Church, ACS Nano 2021, 15, 489–502;
- 8hN. A. Bell, U. F. Keyser, Nat. Nanotechnol. 2016, 11, 645–651;
- 8iU. F. Keyser, Nat. Nanotechnol. 2016, 11, 106–108;
- 8jL. Liu, T. Li, S. Zhang, P. Song, B. Guo, Y. Zhao, H. C. Wu, Angew. Chem. Int. Ed. 2018, 57, 11882–11887; Angew. Chem. 2018, 130, 12058–12063.
- 9
- 9aM. A. Fahie, B. Yang, M. Mullis, M. A. Holden, M. Chen, Anal. Chem. 2015, 87, 11143–11149;
- 9bK. Chuah, Y. Wu, S. R. C. Vivekchand, K. Gaus, P. J. Reece, A. P. Micolich, J. J. Gooding, Nat. Commun. 2019, 10, 2109.
- 10
- 10aS. Conlan, Y. Zhang, S. Cheley, H. Bayley, Biochemistry 2000, 39, 11845–11854;
- 10bB. Liang, L. K. Tamm, Proc. Natl. Acad. Sci. USA 2007, 104, 16140–16145;
- 10cJ. S. Retel, A. J. Nieuwkoop, M. Hiller, V. A. Higman, E. Barbet-Massin, J. Stanek, L. B. Andreas, W. T. Franks, B. J. van Rossum, K. R. Vinothkumar, L. Handel, G. G. de Palma, B. Bardiaux, G. Pintacuda, L. Emsley, W. Kühlbrandt, H. Oschkinat, Nat. Commun. 2017, 8, 2073.
- 11
- 11aG. Bainbridge, I. Gokce, J. H. Lakey, FEBS Lett. 1998, 431, 305–308;
- 11bO. Beckstein, P. C. Biggin, P. Bond, J. N. Bright, C. Domene, A. Grottesi, J. Holyoake, M. S. Sansom, FEBS Lett. 2003, 555, 85–90;
- 11cO. Yildiz, K. R. Vinothkumar, P. Goswami, W. Kühlbrandt, EMBO J. 2006, 25, 3702–3713;
- 11dT. Zhuang, C. Chisholm, M. Chen, L. K. Tamm, J. Am. Chem. Soc. 2013, 135, 15101–15113;
- 11eT. Zhuang, L. K. Tamm, Angew. Chem. Int. Ed. 2014, 53, 5897–5902; Angew. Chem. 2014, 126, 6007–6012;
- 11fA. Perez-Rathke, M. A. Fahie, C. Chisholm, J. Liang, M. Chen, J. Am. Chem. Soc. 2018, 140, 1105–1115;
- 11gB. Pham, C. M. Chisholm, J. Foster, E. Friis, M. A. Fahie, M. Chen, Biochim. Biophys. Acta Biomembr. 2021, 1863, 183485.
- 12
- 12aS. Zernia, N. J. van der Heide, N. S. Galenkamp, G. Gouridis, G. Maglia, ACS Nano 2020, 14, 2296–2307;
- 12bD. Kozak, W. Anderson, R. Vogel, M. Trau, Nano Today 2011, 6, 531–545.
- 13
- 13aM. A. Fahie, M. Chen, J. Phys. Chem. B 2015, 119, 10198–10206;
- 13bM. A. Fahie, B. Yang, B. Pham, M. Chen, ACS Sens. 2016, 1, 614–622.
- 14
- 14aB. Pham, S. J. Eron, M. E. Hill, X. Li, M. A. Fahie, J. A. Hardy, M. Chen, Biophys. J. 2019, 117, 844–855;
- 14bM. A. Fahie, J. Candido, G. Andree, M. Chen, ACS Sens. 2021, 6, 1286–1294.
- 15
- 15aV. Visudtiphole, D. A. Chalton, Q. Hong, J. H. Lakey, Biochem. Biophys. Res. Commun. 2006, 351, 113–117;
- 15bG. S. Verhoeven, S. Alexeeva, M. Dogterom, T. den Blaauwen, PLoS One 2009, 4, e6739.
- 16S. E. Rollauer, M. A. Sooreshjani, N. Noinaj, S. K. Buchanan, Philos. Trans. R. Soc. B 2015, 370, 20150023.
- 17A. Balijepalli, J. Ettedgui, A. T. Cornio, J. W. Robertson, K. P. Cheung, J. J. Kasianowicz, C. Vaz, ACS Nano 2014, 8, 1547–1553.
- 18
- 18aT. Lamla, V. A. Erdmann, Protein Expression Purif. 2004, 33, 39–47;
- 18bP. H. Bessette, J. J. Rice, P. S. Daugherty, Protein Eng. Des. Sel. 2004, 17, 731–739.
- 19M. Chen, S. Khalid, M. S. Sansom, H. Bayley, Proc. Natl. Acad. Sci. USA 2008, 105, 6272–6277.
- 20J. Kong, N. A. Bell, U. F. Keyser, Nano Lett. 2016, 16, 3557–3562.
- 21M. Ayub, H. Bayley, Curr. Opin. Chem. Biol. 2016, 34, 117–126.
- 22G. Wang, L. Wang, Y. Han, S. Zhou, X. Guan, Acc. Chem. Res. 2013, 46, 2867–2877.
This is the
German version
of Angewandte Chemie.
Note for articles published since 1962:
Do not cite this version alone.
Take me to the International Edition version with citable page numbers, DOI, and citation export.
We apologize for the inconvenience.
