Biology subjects

De Feyter, S.

Publications and source records attributed to De Feyter, S..

4 recordsLinked to original sources

bioRxiv2026

Design and characterization of SAKe, a new building block for protein self-assembly

The nanofabrication of functional protein-based surfaces is challenging due to the chemical complexity of proteins and their unpredictable behavior at the solid-liquid interface. Many proteins of interest -such as antibodies or large enzymatic complexes - lack strong and dynamic protein-protein and protein-surface interactions necessary to drive self-assembly of stable arrays with high surface coverage. Additionally, adsorption-induced conformational changes at the solid-liquid interface could lead to a loss of activity and increase the risk of undesirable interfacial processes. Here we introduce SAKe, a kelch-like designer protein, as a versatile platform to address these challenges. Ancestral sequence reconstruction led to high thermal stability, and the high symmetry allowed modularity of the proteins core. Rational engineering of the bottom side allowed SAKe to form large (up to 5 micrometers in length), well-defined and pH-dependent two-dimensional assemblies while maintaining structural integrity, which is key for further development of functional materials. SAKe self-assembly was investigated through in-liquid atomic force microscopy on muscovite mica. High resolution imaging confirmed the integrity of the SAKe protein upon adsorption on the solid-liquid interface. These results showcase the SAKe protein as a platform for the further engineering of functional protein-based two-dimensional materials.

bioengineering↗

bioRxiv2024

Extended Plasmonic Nanostructures Templated by Tobacco Mosaic Virus Coat Protein

Optical and magnetic metamaterials possess interesting properties that cannot be achieved with conventional materials. However, there is currently no synthetic method offering both scalability and nanometer spatial precision. Biotemplating is a promising technique that has the potential to organize nanoscale components with high precision while being scalable and low-cost. Here we demonstrate a versatile template using hexahistidine-tagged tobacco mosaic virus coat protein. The protein self-assembles into disks which further assemble into extended nanostructures under mild conditions. Large sheets with either hexagonal or square packing and core-shell nanorods were formed, and gold nanoparticles were attached to the disks within each nanostructure to form assemblies of nanoparticle rings.

biochemistry↗

bioRxiv2024

HIV integrase compacts viral DNA into biphasic condensates

The human immunodeficiency virus (HIV) infects non-dividing cells and its genome must be compacted to enter the cell nucleus. Here, we show that the viral enzyme integrase (IN) compacts HIV DNA mimetics in vitro. Under physiological conditions, IN-compacted genomes are consistent in size with those found for pre-integration complexes in infected cells. Compaction occurs in two stages: first IN tetramers bridge DNA strands and assemble into "rosette" structures that consist of a nucleo-protein core and extruding bare DNA. In a second stage, the extruding DNA loops condense onto the rosette core to form a disordered and viscoelastic outer layer. Notably, the core complex is susceptible towards IN inhibitors, whereas the diffuse outer layer is not. Together, our data suggest that IN has a structural role in viral DNA compaction and raise the possibility to develop inhibitors that target IN-DNA interactions in disordered condensates. TeaserSingle-molecule studies demonstrate the mechanism, dynamics, and drug-susceptibility of viral genome compaction by HIV integrase.

biophysics↗

bioRxiv2020

High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced transient nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ~10,000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but unlike to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes, likely due to their shorter N-terminal -helix. Finally, our results reconcile previously conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability.

biophysics↗