Antiresonant driven systems for particle manipulation

We report on the onset of antiresonant behavior of mass transport systems driven by time-dependent forces. Antiresonances arise from the coupling of a sufficiently high number of space-time modes of the force. The presence of forces having a wide space-time spectrum, a necessary condition for the formation of an antiresonance, is typical of confined systems with uneven and deformable walls that induce entropic forces dependent on space and time. We have analyzed, in particular, the case of polymer chains confined in a flexible channel and shown how they can be sorted and trapped. The presence of resonance-antiresonance pairs found can be exploited to design protocols able to engineer optimal transport processes and to manipulate the dynamics of nano-objects.

The applications of nanopores in studies of proteins

Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.

Translocation intermediates of ubiquitin through an α-hemolysin nanopore: implications for detection of post-translational modifications

Nanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an α-hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the α-hemolysin constriction by an N-terminal β-hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the α-hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins.