Biophysical properties of the transport barrier in the nuclear pore complex

The Nuclear Pore Complex (NPC) is a large protein structure found in eukaryotic cells, perforating the nuclear envelope. It mediates bidirectional selective transport between the nucleus and the cytoplasm. The NPC contains a permeability barrier consisting of unstructured nuclear pore proteins. The structure of the permeability barrier is not well defined. As a consequence, various models have been proposed for its structure and functionality. Typically, these models consider the unstructured nuclear pore proteins as weakly or strongly interacting polymers: In the first case nuclear pore proteins protrude from the pore creating an entropic barrier; in the second case they may form a meshwork occupying the central channel, resembling a hydrogel. In this thesis, I measure the nanomechanical properties of this barrier in intact NPCs, and compare them to the properties expected for entropic brushes and gel-like materials. To this end, I carried out nanometre-scale force spectroscopy measurements using Atomic Force Microscopy (AFM). Prior to the measurements the pores were treated with reagents that activated the transport process, thus flushing out the pores to ensure that I was probing the barrier itself instead of cargo stuck in transit. I carried out Laser Scanning Confocal Microscopy experiments to verify this procedure, as well as to measure transport properties of the pores in isolated nuclei. For comparison, I also measure nanomechanical properties of artificial polymer brushes, and set the first steps towards creating protein-coated solid-state nanopores as a reductionist model system for the NPC. My results indicate that the proteins in the NPC form a condensed network, more closely resembling a hydrogel than a brush dominated by entropic interactions

Engineering monolayer poration for rapid exfoliation of microbial membranes

The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics

Single-molecule imaging to characterise the transport mechanism of the Nuclear Pore Complex

In the eukaryotic cell, a large macromolecular channel, known as the Nuclear Pore Complex (NPC), mediates all molecular transport between the nucleus and cytoplasm. In recent years, single-molecule fluorescence (SMF) imaging has emerged as a powerful tool to study the molecular mechanism of transport through the NPC. More recently, techniques such as Single-Molecule Localisation Microscopy (SMLM) have enabled the spatial and temporal distribution of cargos, transport receptors and even structural components of the NPC to be determined with nanometre accuracy. In this protocol, we describe a method to study the position and/or motion of individual molecules transiting through the NPC with high spatial and temporal precision

Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC1. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized2, 3, 4, 5, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins5, 6, and is therefore not well understood. Here, we show that stiffness topography7 with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy2, 3, 4, 5. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel

Atomic Force Microscopy with Nanoscale Cantilevers Resolves Different Structural Conformations of the DNA Double Helix

Structural variability and flexibility are crucial factors for biomolecular function. Here we have reduced the invasiness and enhanced the spatial resolution of atomic force microscopy (AFM) to visualize, for the first time, different structural conformations of the two polynucleotide strands in the DNA double helix, for single molecules under near-physiological conditions. This is achieved by identifying and tracking the anomalous resonance behavior of nanoscale AFM cantilevers in the immediate vicinity of the sample