All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore.
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.
†Dipartimento di Fisica, Sapienza Università di Roma, P.le A. Moro, 5, 00185 Rome, Italy.
Daniele
D
Di Marino
‡Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Via Eudossiana 18, 00184 Rome, Italy.
Emma Letizia
EL
Bonome
†Dipartimento di Fisica, Sapienza Università di Roma, P.le A. Moro, 5, 00185 Rome, Italy.|§Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Viale Regina Elena 291, 00161 Rome, Italy.
Anna
A
Tramontano
∥Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Via Regina Elena 291, 00161, Roma, Italia.
Mauro
M
Chinappi
D006460:Hemolysin Proteins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D021381:Protein Transport; D058767:Protein Unfolding; D013879:Thioredoxins / Q000737:chemistry / Q000378:metabolism
D006460:Hemolysin Proteins; D013879:Thioredoxins
molecular dynamics; nanopore sensing; protein translocation