AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
Powered by AMiner. Clicking this button will take you away from SciOpen.
Home Nano Research Article
PDF (594.2 KB)
Cite
EndNote(RIS) BibTeX
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Research Article | Open Access

Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Andrea Spitaleri1,2,§, Denis Garoli3,4,§, Moritz Schütte5, Hans Lehrach5,6, Walter Rocchia1( ), Francesco De Angelis3( )
CONCEPT Lab, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Via Olgettina 58, Milano, I-20132, Italy
Plasmon Nanotechnology Unit, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy
AB ANALITICA s.r.l., Via Svizzera 16, I-35127 Padova, Italy
Alacris Theranostics GmbH, Max-Planck-Strasse 3, D-12489 Berlin, Germany
Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany

§ Andrea Spitaleri and Denis Garoli contributed equally to this work.

Show Author Information

Graphical Abstract

Abstract

Single molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the "shape" of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

Keywords

nanoporessingle molecule sequencingprotein sequencingluorescence resonance energy transfer (FRET)amino-acidsfluorescence

Electronic Supplementary Material

Download File(s)
12274_2020_3095_MOESM1_ESM.pdf (2.1 MB)

References

[1]
H. Steen,; M. Mann, The abc’s (and xyz’s) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 2004, 5, 699-711.
Crossref Google Scholar
[2]
Y. Shimonishi,; Y. M. Hong,; T. Kitagishi,; T. Matsuo,; H. Matsuda,; I. Katakuse, Sequencing of peptide mixtures by edman degradation and field-desorption mass spectrometry. Eur. J. Biochem. 1980, 112, 251-264.
Crossref Google Scholar
[3]
B. Domon,; R. Aebersold, Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 2010, 28, 710-721.
Crossref Google Scholar
[4]
L. Restrepo-Pérez,; C. Joo,; C. Dekker, Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 2018, 13, 786-796.
Crossref Google Scholar
[5]
A. Ameur,; W. P. Kloosterman,; M. S. Hestand, Single-molecule sequencing: Towards clinical applications. Trends Biotechnol. 2019, 37, 72-85.
Crossref Google Scholar
[6]
J. Nivala,; D. B. Marks,; M. Akeson, Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 2013, 31, 247-250.
Crossref Google Scholar
[7]
E. Kennedy,; Z. X. Dong,; C. Tennant,; G. Timp, Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore. Nat. Nanotechnol. 2016, 11, 968-976.
Crossref Google Scholar
[8]
M. Kolmogorov,; E. Kennedy,; Z. X. Dong,; G. Timp,; P. A. Pevzner, Single-molecule protein identification by sub-nanopore sensors. PLoS Comput. Biol. 2017, 13, e1005356.
Crossref Google Scholar
[9]
J. Wilson,; L. Sloman,; Z. R. He,; A. Aksimentiev, Graphene nanopores for protein sequencing. Adv. Funct. Mater. 2016, 26, 4830-4838.
Crossref Google Scholar
[10]
A. Asandei,; A. E. Rossini,; M. Chinappi,; Y. Park,; T. Luchian, Protein nanopore-based discrimination between selected neutral amino acids from polypeptides. Langmuir 2017, 33, 14451-14459.
Crossref Google Scholar
[11]
A. B. Farimani,; M. Heiranian,; N. R. Aluru, Identification of amino acids with sensitive nanoporous MoS2: Towards machine learning-based prediction. npj 2D Mater. Appl. 2018, 2, 14.
Crossref Google Scholar
[12]
S. Ohayon,; A. Girsault,; M. Nasser,; S. Shen-Orr,; A. Meller, Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput. Biol. 2019, 15, e1007067.
Crossref Google Scholar
[13]
C. B. Rosen,; D. Rodriguez-Larrea,; H. Bayley, Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat. Biotechnol. 2014, 32, 179-181.
Crossref Google Scholar
[14]
J. Van Ginkel,; M. Filius,; M. Szczepaniak,; P. Tulinski,; A. S. Meyer,; C. Joo, Single-molecule peptide fingerprinting. Proc. Natl. Acad. Sci. USA 2018, 115, 3338-3343.
Crossref Google Scholar
[15]
Y. N. Zhao,; B. Ashcroft,; P. M. Zhang,; H. Liu,; S. M. Sen,; W. S. Song,; J. Im,; B. Gyarfas,; S. Manna,; S. Biswas, et al. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. Nat. Nanotechnol. 2014, 9, 466-473.
Crossref Google Scholar
[16]
T. Ohshiro,; M. Tsutsui,; K. Yokota,; M. Furuhashi,; M. Taniguchi,; T. Kawai, Detection of post-translational modifications in single peptides using electron tunnelling currents. Nat. Nanotechnol. 2014, 9, 835-840.
Crossref Google Scholar
[17]
H. Ouldali,; K. Sarthak,; T. Ensslen,; F. Piguet,; P. Manivet,; J. Pelta,; J. C. Behrends,; A. Aksimentiev,; A. Oukhaled, Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat. Biotechnol. 2020, 38, 176-181.
Crossref Google Scholar
[18]
J. Swaminathan,; A. A. Boulgakov,; E. M. Marcotte, A theoretical justification for single molecule peptide sequencing. PLoS Comput. Biol. 2015, 11, e1004080.
Crossref Google Scholar
[19]
B. M. Venkatesan,; R. Bashir, Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 2011, 6, 615-624.
Crossref Google Scholar
[20]
R. Hu,; X. Tong,; Q. Zhao, Four aspects about solid-state nanopores for protein sensing: Fabrication, sensitivity, selectivity, and durability. Adv. Healthc Mater., in press, .
Crossref Google Scholar
[21]
J. A. Huang,; M. Z. Mousavi,; G. Giovannini,; Y. Q. Zhao,; A. Hubarevich,; M. A. Soler,; W. Rocchia,; D. Garoli,; F. De Angelis, Multiplexed discrimination of single amino acid residues in polypeptides in a single SERS hot spot. Angew. Chem., Int. Ed. 2020, 59, 11423-11431.
Crossref Google Scholar
[22]
F. B. Sheinerman,; R. Norel,; B. Honig, Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. 2000, 10, 153-159.
Crossref Google Scholar
[23]
C. Cao,; Y. T. Long, Biological nanopores: Confined spaces for electrochemical single-molecule analysis. Acc. Chem. Res. 2018, 51, 331-341.
Crossref Google Scholar
[24]
B. Lee,; F. M. Richards, The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 1971, 55, 379-400, IN3-IN4.
Crossref Google Scholar
[25]
B. Honig,; A. Nicholls, Classical electrostatics in biology and chemistry. Science 1995, 268, 1144-1149.
Crossref Google Scholar
[26]
M. P. Allen,; D. J. Tildesley, Computer Simulation of Liquids; Oxford University Press: Oxford, 2017.
Crossref
[27]
F. Angelucci,; A. E. Miele,; M. Ardini,; G. Boumis,; F. Saccoccia,; A. Bellelli, Typical 2-Cys peroxiredoxins in human parasites: Several physiological roles for a potential chemotherapy target. Mol. Biochem. Parasitol. 2016, 206, 2-12.
Crossref Google Scholar
[28]
H. Y. Wang,; Y. Li,; L. X. Qin,; A. Heyman,; O. Shoseyov,; I. Willner,; Y. T. Long,; H. Tian, Single-molecule DNA detection using a novel SP1 protein nanopore. Chem. Commun. 2013, 49, 1741-1743.
Crossref Google Scholar
[29]
Y. L. Ying,; C. Cao,; Y. T. Long, Single molecule analysis by biological nanopore sensors. Analyst 2014, 139, 3826-3835.
Crossref Google Scholar
[30]
G. Giovannini,; M. Ardini,; N. Maccaferri,; X. Zambrana-Puyalto,; G. Panella,; F. Angelucci,; R. Ippoliti,; D. Garoli,; F. De Angelis, Bio-assisted tailored synthesis of plasmonic silver nanorings and site-selective deposition on graphene arrays. Adv. Opt. Mater. 2020, 8, 1901583.
Crossref Google Scholar
[31]
A. Asandei,; M. Chinappi,; J. K. Lee,; C. H. Seo,; L. Mereuta,; Y. Park,; T. Luchian, Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores. Sci. Rep. 2015, 5, 10419.
Crossref Google Scholar
[32]
L. Restrepo-Pérez,; S. John,; A. Aksimentiev,; C. Joo,; C. Dekker, SDS-assisted protein transport through solid-state nanopores. Nanoscale 2017, 9, 11685-11693.
Crossref Google Scholar
[33]
B. Cressiot,; E. Braselmann,; A. Oukhaled,; A. H. Elcock,; J. Pelta,; P. L. Clark, Dynamics and energy contributions for transport of unfolded pertactin through a protein nanopore. ACS Nano 2015, 9, 9050-9061.
Crossref Google Scholar
[34]
M. Chinappi,; T. Luchian,; F. Cecconi, Nanopore tweezers: Voltage-controlled trapping and releasing of analytes. Phys. Rev. E 2015, 92, 032714.
Crossref Google Scholar
[35]
M. Pastoriza-Gallego,; M. F. Breton,; F. Discala,; L. Auvray,; J. M. Betton,; J. Pelta, Evidence of unfolded protein translocation through a protein nanopore. ACS Nano 2014, 8, 11350-11360.
Crossref Google Scholar
[36]
H. J. Kim,; U. J. Choi,; H. Kim,; K. Lee,; K. B. Park,; H. M. Kim,; S. W. Chi,; J. S. Lee,; K. B. Kim, Translocation of DNA and protein through a sequentially polymerized polyurea nanopore. Nanoscale 2019, 11, 444-453.
Crossref Google Scholar
[37]
L. Mereuta,; M. Roy,; A. Asandei,; J. K. Lee,; Y. Park,; I. Andricioaei,; T. Luchian, Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation. Sci. Rep. 2014, 4, 3885.
Crossref Google Scholar
[38]
C. Plesa,; S. W. Kowalczyk,; R. Zinsmeester,; A. Y. Grosberg,; Y. Rabin,; C. Dekker, Fast translocation of proteins through solid state nanopores. Nano Lett. 2013, 13, 658-663.
Crossref Google Scholar
[39]
D. Rodriguez-Larrea,; H. Bayley, Multistep protein unfolding during nanopore translocation. Nat. Nanotechnol. 2013, 8, 288-295.
Crossref Google Scholar
[40]
M. Ayub,; H. Bayley, Engineered transmembrane pores. Curr. Opin. Chem. Biol. 2016, 34, 117-126.
Crossref Google Scholar
[41]
R. Roy,; S. Hohng,; T. Ha, A practical guide to single-molecule FRET. Nat. Methods 2008, 5, 507-516.
Crossref Google Scholar
[42]
M. Dimura,; T. O. Peulen,; C. A. Hanke,; A. Prakash,; H. Gohlke,; C. A. M. Seidel, Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr. Opin. Struct. Biol. 2016, 40, 163-185.
Crossref Google Scholar
[43]
M. Hoefling,; H. Grubmüller, In silico FRET from simulated dye dynamics. Comput. Phys. Commun. 2013, 184, 841-852.
Crossref Google Scholar
Nano Research
Volume 14 Issue 1,
January 2021
Pages 328-333
DOI: 10.1007/s12274-020-3095-z
Cite this article:
Spitaleri A, Garoli D, Schütte M, et al. Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification. Nano Research, 2021, 14(1): 328-333. https://doi.org/10.1007/s12274-020-3095-z
Topics:
Mass spectrometryMolecular dynamicsNanoporesPeptides

958

Views

28

Downloads

10

Crossref

0

Web of Science

13

Scopus

0

CSCD

Altmetrics
Received: 02 June 2020
Revised: 30 August 2020
Accepted: 03 September 2020
Published: 05 January 2021
© The Author(s) 2021

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Return