title: Journey of poly-nucleotides through OmpF porin.
abstract: OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.
authors.affiliation: Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
authors.forename: Hamid
authors.initials: H
authors.lastname: Hadi-Alijanvand
authors.affiliation: Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Rouhani
mesh_terms: D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism*; D018272:Porins / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D009711:Nucleotides; C109237:OmpF protein; D018272:Porins