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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.

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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

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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

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

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