title: Modeling of polynucleotide translocation through protein pores and nanotubes.
abstract: In an effort to understand recent experiments, we have performed Brownian dynamics simulations of polymer translocation through nanometer-scale protein pores under the influence of an external applied electric field. Multiple peaks in the translocation time distribution are observed in agreement with experiments. Under the same conditions, but replacing the protein pore with a rigid cylindrical tube of comparable size, only a single peak is observed in the translocation time distribution. These results directly show that the geometry of the protein pores is mainly responsible for multiple peaks observed in experiments. In the case of alpha-hemolysin channel, we find the vestibule, by confining many conformations of the translocating polymer, to be responsible for the second peak with longer translocation time.
authors.affiliation: Department of Polymer Science and Engineering, University of Massachusetts at Amherst, Amherst, MA 01003, USA.
authors.forename: Chung Y
authors.initials: CY
authors.lastname: Kong
authors.forename: Murugappan
authors.initials: M
authors.lastname: Muthukumar
mesh_terms: D001692:Biological Transport; D006460:Hemolysin Proteins / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism; D008567:Membranes, Artificial; D008954:Models, Biological; D008958:Models, Molecular; D010539:Permeability; D011119:Polynucleotides / Q000737:chemistry / Q000378:metabolism*; D016062:Porosity
chemical_list: D006460:Hemolysin Proteins; D026901:Membrane Transport Proteins; D008567:Membranes, Artificial; D011119:Polynucleotides