title: Multistep current signal in protein translocation through graphene nanopores.
abstract: In nanopore sensing experiments, the properties of molecules are probed by the variation of ionic currents flowing through the nanopore. In this context, the electronic properties and the single-layer thickness of graphene constitute a major advantage for molecule characterization. Here we analyze the translocation pathway of the thioredoxin protein across a graphene nanopore, and the related ionic currents, by integrating two nonequilibrium molecular dynamics methods with a bioinformatic structural analysis. To obtain a qualitative picture of the translocation process and to identify salient features we performed unsupervised structural clustering on translocation conformations. This allowed us to identify some specific and robust translocation intermediates, characterized by significantly different ionic current flows. We found that the ion current strictly anticorrelates with the amount of pore occupancy by thioredoxin residues, providing a putative explanation of the multilevel current scenario observed in recently published translocation experiments.
authors: †Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Roma, Italy.
authors: Emma Letizia
authors: EL
authors: Bonome
authors: ‡Dipartimento di Fisica, Sapienza Università di Roma, 00185 Rome, Italy.
authors: Rosalba
authors: R
authors: Lepore
authors: ‡Dipartimento di Fisica, Sapienza Università di Roma, 00185 Rome, Italy.
authors: Domenico
authors: D
authors: Raimondo
authors: §CNR-Istituto dei Sistemi Complessi UoS Sapienza, Via dei Taurini 19, 00185 Roma, Italy.
authors: Fabio
authors: F
authors: Cecconi
authors: ‡Dipartimento di Fisica, Sapienza Università di Roma, 00185 Rome, Italy.|∥Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena, 291 Rome 00185, Italy.
authors: Anna
authors: A
authors: Tramontano
authors: ⊥Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Via Regina Elena 291, 00161 Roma, Italy.
authors: Mauro
authors: M
authors: Chinappi
mesh_terms: D004560:Electricity; D006108:Graphite / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D017433:Protein Structure, Secondary; D021381:Protein Transport; D013879:Thioredoxins / Q000737:chemistry*
chemical_list: D007477:Ions; D013879:Thioredoxins; D006108:Graphite