Translocation of linearized full-length proteins through an engineered nanopore under opposing electrophoretic force

Gu, L.-Q., Cheley, S. & Bayley, H. Electroosmotic enhancement of the binding of a neutral molecule to a transmembrane pore. Proc. Natl. Acad. Sci. USA100, 15498–15503 (2003).

Article 
CAS 
PubMed 
PubMed Central 

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).

Article 
PubMed 
PubMed Central 

Google Scholar 

Huang, G. et al. Electro-osmotic vortices promote the capture of folded proteins by PlyAB nanopores. Nano Lett.20, 3819–3827 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Asandei, A. et al. Electroosmotic trap against the electrophoretic force near a protein nanopore reveals peptide dynamics during capture and translocation. ACS Appl. Mater. Interfaces8, 13166–13179 (2016).

Article 
CAS 
PubMed 

Google Scholar 

Willems, K. et al. Engineering and modeling the electrophoretic trapping of a single protein inside a nanopore. ACS Nano13, 9980–9992 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Gubbiotti, A. et al. Electroosmosis in nanopores: computational methods and technological applications. Adv. Phys. X7, 2036638 (2022).

Google Scholar 

Brinkerhoff, H., Kang, A. S. W., Liu, J., Aksimentiev, A. & Dekker, C. Multiple rereads of single proteins at single–amino acid resolution using nanopores. Science374, 1509–1513 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Yan, S. et al. Single molecule ratcheting motion of peptides in a Mycobacterium smegmatis porin A (MspA) nanopore. Nano Lett.21, 6703–6710 (2021).

Article 
CAS 
PubMed 

Google Scholar 

Chen, Z. et al. Controlled movement of ssDNA conjugated peptide through Mycobacterium smegmatis porin A (MspA) pore by a helicase motor for peptide sequencing application. Chem. Sci.12, 15750–15756 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Rosen, C. B., Rodriguez-Larrea, D. & Bayley, H. Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat. Biotechnol.32, 179–181 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Yu, L. et al. Unidirectional single-file transport of full-length proteins through a nanopore. Nat. Biotechnol.41,1130–1139 (2023).

Article 
CAS 
PubMed 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Aksimentiev, A. & Schulten, K. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys. J.88, 3745–3761 (2005).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Bonome, E. L., Cecconi, F. & Chinappi, M. Electroosmotic flow through an α-hemolysin nanopore. Microfluid. Nanofluid.21,96 (2017).

Article 

Google Scholar 

Bétermier, F. et al. Single-sulfur atom discrimination of polysulfides with a protein nanopore for improved batteries. Commun. Mater.1, 59 (2020).

Article 

Google Scholar 

Di Muccio, G., Morozzo della Rocca, B. & Chinappi, M. Geometrically induced selectivity and unidirectional electroosmosis in uncharged nanopores. ACS Nano16, 8716–8728 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar 

Raffy, S., Sassoon, N., Hofnung, M. & Betton, J.-M. Tertiary structure-dependence of misfolding substitutions in loops of the maltose-binding protein. Protein Sci.7, 2136–2142 (1998).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Fonin, A. V. et al. Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors. PeerJ2, e275 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar 

Ohmae, E., Sasaki, Y. & Gekko, K. Effects of five-tryptophan mutations on structure, stability and function of Escherichia coli dihydrofolate reductase. J. Biochem.130, 439–447 (2001).

Article 
CAS 
PubMed 

Google Scholar 

Japrung, D., Henricus, M., Li, Q. H., Maglia, G. & Bayley, H. Urea facilitates the translocation of single-stranded DNA and RNA through the α-hemolysin nanopore. Biophys. J.98, 1856–1863 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Pastoriza-Gallego, M. et al. Evidence of unfolded protein translocation through a protein nanopore. ACS Nano8, 11350–11360 (2014).

Article 
CAS 
PubMed 

Google Scholar 

Oukhaled, G. et al. Unfolding of proteins and long transient conformations detected by single nanopore recording. Phys. Rev. Lett. 98, 158101 (2007).

Pastoriza-Gallego, M. et al. Dynamics of unfolded protein transport through an aerolysin pore. J. Am. Chem. Soc.133, 2923–2931 (2011).

Article 
CAS 
PubMed 

Google Scholar 

Rodriguez-Larrea, D. & Bayley, H. Multistep protein unfolding during nanopore translocation. Nat. Nanotechnol.8, 288–295 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph.14, 33–38 (1996).

Article 
CAS 
PubMed 

Google Scholar 

Bitinaite, J. et al. USER friendly DNA engineering and cloning method by uracil excision. Nucleic Acids Res.35, 1992–2002 (2007).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Cavaleiro, A. M., Kim, S. H., Seppälä, S., Nielsen, M. T. & Nørholm, M. H. H. Accurate DNA assembly and genome engineering with optimized uracil excision cloning. ACS Synth. Biol.4, 1042–1046 (2015).

Article 
CAS 
PubMed 

Google Scholar 

Nørholm, M. H. A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering. BMC Biotechnol.10, 21 (2010).

Article 
PubMed 
PubMed Central 

Google Scholar 

Zhang, S. et al. Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins. Nat. Chem.13, 1192–1199 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Maglia, G., Heron, A. J. J. A. J., Stoddart, D., Japrung, D. & Bayley, H. Analysis of single nucleic acid molecules with protein nanopores. Methods Enzymol.475, 591–623 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res.46, W296–W303 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Tanaka, Y. et al. 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal α-hemolysin into heptameric pore structure. Protein Sci.20, 448–456 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Lambey, P. et al. Structural insights into recognition of chemokine receptors by Staphylococcus aureus leukotoxins. eLife11, e72555 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Nocadello, S. et al. Crystal structures of the components of the Staphylococcus aureus leukotoxin ED. Acta Crystallogr. Sect. D Struct. Biol.72, 113–120 (2016).

Article 
CAS 

Google Scholar 

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature596, 583–589 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Pettersen, E. F. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem.25, 1605–12 (2004).

Article 
CAS 
PubMed 

Google Scholar 

Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem.26, 1781–1802 (2005).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Best, R. B. et al. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J. Chem. Theory Comput.8, 3257–3273 (2012).

Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys.79, 926–935 (1983).

Article 
CAS 

Google Scholar 

Yoo, J. & Aksimentiev, A. Improved parametrization of Li+, Na+, K+, and Mg2+ Ions for all-atom molecular dynamics simulations of nucleic acid systems. J. Phys. Chem. Lett.3, 45–50 (2012).

Article 
CAS 

Google Scholar 

Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys.103, 8577–8593 (1995).

Article 
CAS 

Google Scholar 

Miyamoto, S. & Kollman, P. A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem.13, 952–962 (1992).

Article 
CAS 

Google Scholar 

Andersen, H. C. Rattle: a ‘velocity’ version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys.52, 24–34 (1983).

Article 
CAS 

Google Scholar 

Martyna, G. J., Tobias, D. J. & Klein, M. L. Constant pressure molecular dynamics algorithms. J. Chem. Phys.101, 4177–4189 (1994).

Article 
CAS 

Google Scholar 

Gumbart, J., Khalili-Araghi, F., Sotomayor, M. & Roux, B. Constant electric field simulations of the membrane potential illustrated with simple systems. Biochim. Biophys. Acta1818, 294–302 (2012).

Article 
CAS 
PubMed 

Google Scholar 

Crozier, P. S., Henderson, D., Rowley, R. L. & Busath, D. D. Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics. Biophys. J.81, 3077–3089 (2001).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

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