Gap Size Dependence of Atomistic-Resolved Peptide Bond Signals by Tunneling Current Across Nano-Gaps of Graphene Nano-Ribbons

Tommaso Civitarese,Giuseppe Zollo

doi:10.3390/computation8020029

Abstract

According to the recent literature, it has been demonstrated that the atomistic scale recognition of amino acids and peptide-bonds in polypeptides and proteins is in principle possible by measuring the tunneling current flowing across a narrow nano-gap in graphene nano ribbons during the peptide translocation. In this paper, we concentrate on the tunneling current signal properties measured for nano-gaps of different sizes. Using the non equilibrium Green function method based on the density functional theory, we have studied the tunneling current for larger gap sizes that can be actually realized according to the present state of the art sub-nanometer nano-pore and nano-gap technology. Also in these cases the peptide bond can be still recognized, the obtained signal being well within the measurable range of the current. The signal shapes undergo a change from a double peak feature per peptide bond for narrow gaps to a structured single peak signal per peptide bond for wider gaps. The reason is related to the different orbital overlap range of the two contributions giving rise to the original double peak signal for narrow gaps.

Highlights

The importance of identifying the sequence and the 3-D structure of proteins is crucial to understand their function and behavior within living organisms; for instance, mis-folding of proteins is believed to be related to neurodegenerative diseases such as Parkinson’s and Alzheimer
The translocating molecule is a peptide composed by five amino acids but only the central three are taken into account for the present results: the first and the fifth amino acids of the peptide chain are adjacent to the C and the N-terminal groups whose lone pairs could affect the measured current
We have studied the gap size dependence of the tunneling current signal obtained during a Gly homopeptide translocation across the two semi-infinite hydrogenated graphene nano ribbons electrodes

Summary

Introduction

The importance of identifying the sequence and the 3-D structure of proteins is crucial to understand their function and behavior within living organisms; for instance, mis-folding of proteins is believed to be related to neurodegenerative diseases such as Parkinson’s and Alzheimer. Current methods require long sequencing times that represent a serious bottleneck for the needs of the rising importance of proteomics. Fast and efficient techniques (especially for large protein chains) are required and solid-state nanopores and nanogaps are emerging as promising tools for single molecule analysis [1,2,3]. In this framework, a new sequencer consisting of arrays of nano-gaps between graphene nano-ribbons has recently been proposed [4], as schematically represented, exploiting the ideal 2D structure of the leads that allows an atomistic resolution sensing. The collected signal could be processed and employed to obtain the primary structure of a peptide or a protein

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Conclusion