Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations.

Di Muccio G; Rossini AE; Di Marino D; Zollo G; Chinappi M

doi:10.1038/s41598-019-42867-7

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Journal article

Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations.

Di Muccio G Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via del Politecnico 1, 00133, Roma, Italy.
Rossini AE Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Università di Roma "La Sapienza", Via A. Scarpa 14-16, 00161, Rome, Italy.
Di Marino D Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology Università della Svizzera Italiana (USI), Lugano, Switzerland. daniele.di.marino@usi.ch.
Zollo G Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Università di Roma "La Sapienza", Via A. Scarpa 14-16, 00161, Rome, Italy.
Chinappi M Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via del Politecnico 1, 00133, Roma, Italy. mauro.chinappi@uniroma2.it.

2019-04-25

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Scientific reports. - 2019

English Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.

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