Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

Asandei, Alina; Dragomir, Isabela S.; Di Muccio, Giovanni; Chinappi, Mauro; Park, Yoonkyung; Luchian, Tudor

doi:10.3390/polym10080885

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Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

^1,†

^2,†,

^3,*,

^4,* and

^2,*

Interdisciplinary Research Department, Alexandru I. Cuza University, 700506 Iasi, Romania

Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania

Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy

⁴

Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju 61452, Korea

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Polymers 2018, 10(8), 885; https://doi.org/10.3390/polym10080885

Received: 6 July 2018 / Revised: 4 August 2018 / Accepted: 6 August 2018 / Published: 8 August 2018

(This article belongs to the Special Issue Polymer Translocation)

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Abstract

In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL. View Full-Text

Keywords: nanopore; peptide sensing; electrophysiology; single-molecule sequencing

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MDPI and ACS Style

Asandei, A.; Dragomir, I.S.; Di Muccio, G.; Chinappi, M.; Park, Y.; Luchian, T. Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores. Polymers 2018, 10, 885. https://doi.org/10.3390/polym10080885

AMA Style

Asandei A, Dragomir IS, Di Muccio G, Chinappi M, Park Y, Luchian T. Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores. Polymers. 2018; 10(8):885. https://doi.org/10.3390/polym10080885

Chicago/Turabian Style

Asandei, Alina, Isabela S. Dragomir, Giovanni Di Muccio, Mauro Chinappi, Yoonkyung Park, and Tudor Luchian. 2018. "Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores" Polymers 10, no. 8: 885. https://doi.org/10.3390/polym10080885

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Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

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