All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

Abstract

Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

Nanopore‐Based Protein Sequencing Using Biopores: Current Achievements and Open Challenges

“…Molecular dynamics (MD) simulations have proved a useful computational tool to investigate transport phenomena in biological nanopore sensing systems and to interpret experimental data. Examples are the estimation of α-HL ionic conductance and electro-osmotic flow, [120,131,132] investigation of singlestranded DNA molecules inside α-HL, [133] the cotranslocational unfolding of thioredoxin, [134] and DNA base distinguishability in MspA. [135] A core question in nanopore protein sequencing is the capability to distinguish among the 20 amino acids.…”

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

“…To overcome this difficulties, other approaches, such as dielectrophoretic trapping 20–24 and electro-osmotic flow 6,7,25,26 have been proposed. In addition, the complex interplay between unfolding, capture and translocation typically results in a non-homogeneous multistep co-translocational unfolding process 18,27–32 .…”

Vibration assisted electron tunneling through nano-gaps in graphene nano-ribbons for amino-acid and peptide bond recognition

“…[1][2][3][4][5] Proteins are challenging and the setup of newly conceived methods for fast and reliable amino-acid recognition is highly desirable to face the huge size of the human proteome. [3][4][5][6][7][8][9][10][11][12] Compared to other schemes, the measurement of the transversal tunneling current across a gap seems to be particularly promising and suitable. Amino-acid (AA) recognition can be attained, at least in principle, by measuring the tunneling current owing through the gap during peptide translocation, provided a bias is applied between the electrodes: 11,13 indeed, the tunneling current measured should reect the chemical and physical nature of the piece of molecule that occupies the nano-gap.…”