Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification
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PT 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 3 Plasmon Nanotechnology Unit, Istituto Italiano di Tecnologia, Via Morego 30, Genova, I-16163, Italy 4 AB ANALITICA s.r.l., Via Svizzera 16, I-35127 Padova, Italy 5 Alacris Theranostics GmbH, Max-Planck-Strasse 3, D-12489 Berlin, Germany 6 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany § Andrea Spitaleri and Denis Garoli contributed equally to this work. 2
© The Author(s) 2020 Received: 2 June 2020 / Revised: 30 August 2020 / Accepted: 3 September 2020
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 nanopores, single molecule sequencing, protein sequencing, luorescence resonance energy transfer (FRET), amino-acids, fluorescence
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Introduction
The “sequence–structure–function” paradigm for proteins embodies one of the biggest scientific discoveries about the functioning of Life. The DNA sequence in each gene contains the information necessary to build proteins, via a mechanism where specific triplets of nucleic acids code for the different amino-acids. In addition to this golden rule for translation, proteins’ fundamental building blocks can be altered by alternative splicing or post-translational modifications. Mutations in specific positions can greatly
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