Detection of single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of Phi29 DNA packaging motor

Biological nanopores for sensing applications

“…In nature, diverse proteins can integrate into cell membrane and form a transmembrane pore structure, including the ion channels, 28 porins, [29][30][31] pore-forming toxin (PFT), 32 viral connectors, [33][34][35] nuclear pore complex, 36 and even the DNA helicase. 37 There are several factors that affect the sensing ability of a nanopore, such as the geometry of the pore, 38 charge distribution of the inner surface, 39,40 key amino acids in the constriction region, 41 and so on.…”

“…89,90 Recent studies reported that the connecter could be integrated into MinION™ platform for high-throughput sensing, demonstrating the huge potential of Phi29 connector in clinical diagnosis. 34,91…”

“…In addition, the large lumen is suitable for conjugating probes or adapters that enable targeted detection of specific molecules 89,90 . Recent studies reported that the connecter could be integrated into MinION™ platform for high‐throughput sensing, demonstrating the huge potential of Phi29 connector in clinical diagnosis 34,91 …”

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

“…This strategy has been adopted in efforts toward nanopore-based protein/peptide identification ( Restrepo-Pérez et al., 2019a ). Third, the emergence of commercial nanopore sequencers has enabled highly parallel nanopore analysis and high-throughput data collection on a nanopore array ( Cardozo et al., 2021 ; Zhang et al., 2021b ), which otherwise would not be realized by single-channel experiments. A large set of training data, coupled with state-of-the-art machine learning models, would boost accurate translation of complex raw signals into amino acid sequences and PTMs, analogous to the example of highly improved basecalling accuracy in nanopore DNA sequencing using deep learning ( Rang et al., 2018 ; Teng et al., 2018 ; Wick et al., 2019 ).…”

“…The study also has proposed a way toward the identification of the remaining 7 amino acids by instrumentation advances and nanopore engineering. The detection of PTMs such as phosphorylation and glycosylation, which serve as biomarkers of cell states and diseases ( Aebersold et al., 2018 ; Pagel et al., 2015 ), has also been achieved with protein nanopore sensors ( Restrepo-Pérez et al., 2019b ; Rosen et al., 2014b ; Wloka et al., 2017 ; Ying et al., 2019 ; Zhang et al., 2021b ).

Figure 2 Schematic representation of single-molecule sequencing with a nanopore In nanopore sequencing, a nanometer-sized protein pore is embedded in an insulating membrane that separates two electrolyte-filled wells.

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