title: Introducing an artificial photo-switch into a biological pore: A model study of an engineered α-hemolysin.
abstract: In recent years, engineered biological pores responsive to external stimuli have been fruitfully used for various biotechnological applications. Moreover, the strategy of tethering photo-switchable moieties into biomolecules has provided an unprecedented temporal control of purposely designed nanodevices, as demonstrated, for example, by the light-mediated regulation of the activity of enzymes and biochannels. Inspired by these advancements, we propose here a de novo designed nanodevice featuring the α-hemolysin (αHL) membrane channel purposely functionalized by an artificial "on/off" molecular switch. The switch, which is based on the photo-isomerization of the azobenzene moiety, introduces a smart nano-valve into the natural non-gated pore to confer tunable transport properties. We validated through molecular dynamics simulations and free energy calculations the effective inter-conversion of the engineered αHL pore between two configurations corresponding to an "open" and a "closed" form. The reported switchable translocation of a single-stranded DNA fragment under applied voltage supports the promising capabilities of this nanopore prototype in view of molecular sensing, detection and delivery applications at single-molecule level.
authors.affiliation: Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. Electronic address: bala.chandramouli@sns.it.
authors.forename: Balasubramanian
authors.initials: B
authors.lastname: Chandramouli
authors.affiliation: Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy.
authors.forename: Danilo
authors.initials: D
authors.lastname: Di Maio
authors.affiliation: Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy.
authors.forename: Giordano
authors.initials: G
authors.lastname: Mancini
authors.affiliation: Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy. Electronic address: giuseppe.brancato@sns.it.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Brancato
mesh_terms: D015374:Biosensing Techniques; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000302:isolation & purification; D006460:Hemolysin Proteins / Q000737:chemistry* / Q000235:genetics; D008027:Light; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D016062:Porosity; D015202:Protein Engineering
chemical_list: D004277:DNA, Single-Stranded; D006460:Hemolysin Proteins
keywords: DNA detection; Engineered protein; Light-activated channel gating; Molecular dynamics simulations; Nanopore analytics; α-Hemolysin membrane channel