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Survivin’s dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein–protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin’s nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine., Survivin’s dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. Here authors report a strategy addressing its dimer interface overlapping with the nuclear export signal, the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine.

We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2 × 2 origami structure with increasing level of detail ranging from the mean-field level to an all-atom representation of the DNA structure. We observe a consistent pore conductivity as a function of salt concentration for all four models. However, a comparison of our data to recent experimental investigations on similar systems displays significant deviations. We discuss possible reasons for the discrepancies and propose extensions to our models for future investigations.

We report the first supramolecular stabilizers of the interaction between 14-3-3ζ and two of its effectors, Tau and C-Raf, which are involved in neurodegenerative diseases and proliferative signal transduction, respectively. These supramolecular ligands open up an opportunity to modulate functions of 14-3-3 with these effectors.

Many biologically important ligands of proteins are large, flexible, and in many cases charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods such as docking or molecular dynamics (MD) simulation. The alternative approach proposed here is scanning of a spatial and angular grid around the protein with smaller fragments of the large ligand. Energy values for complete grids can be computed efficiently with a well-known fast Fourier transform-accelerated algorithm and a physically meaningful interaction model. We show that the approach can readily incorporate flexibility of the protein and ligand. The energy grids (EGs) resulting from the ligand fragment scans can be transformed into probability distributions and then directly compared to probability distributions estimated from MD simulations and experimental structural data. We test the approach on a diverse set of complexes between proteins and large, flexible ligands, including a complex of sonic hedgehog protein and heparin, three heparin sulfate substrates or nonsubstrates of an epimerase, a multibranched supramolecular ligand that stabilizes a protein-peptide complex, a flexible zwitterionic ligand that binds to a surface basin of a Kringle domain, and binding of ATP to a flexible site of an ion channel. In all cases, the EG approach gives results that are in good agreement with experimental data or MD simulations.

Self-cleavage of proteins is an important natural process that is difficult to control externally. Recently a new mechanism for the accelerated autolysis of trypsin was discovered involving polyanionic template polymers; however it relies on unspecific interactions and is inactive at elevated salt loads. We have now developed affinity copolymers that bind to the surface of proteases by specific recognition of selected amino acid residues. These are highly efficient trypsin inhibitors with low nanomolar IC50 levels and operate at physiological conditions. In this manuscript we show how these affinity copolymers employ the new mechanism of polymer-assisted self-digest (PAS) and act as a template for multiple protease molecules. Their elevated local concentration leads to accelerated autolysis on the accessible surface area and shields complexed areas. The resulting extremely efficient trypsin inhibition was studied by SDS-PAGE, gel filtration, CD, CZE and ESI-MS. We also present a simple theoretical model that simulates most experimental findings and confirms them as a result of multivalency and efficient reversible templating. For the first time, mass spectrometric kinetic analysis of the released peptide fragments gives deeper insight into the underlying mechanism and reveals that polymer-bound trypsin cleaves much more rapidly with low specificity at predominantly uncomplexed surface areas. CA Schrader

14-3-3 Proteins play a central role in signalling pathways in cells: they interact as gatekeeper proteins with a huge number of binding partners. Their function as hub for intracellular communication can explain why these adapter proteins are associated with a wide range of diseases. How they control the various cellular mechanisms is still unclear, but it is assumed that the dimeric nature of the 14-3-3 proteins plays a key role in their activity. Here, we present, to the best of our knowledge, the first example of a small molecule binding to the 14-3-3ζ dimerisation interface. This compound was designed by rational in silico optimisation of a peptidic ligand identified from biochemical screening of a peptidic library, and the binding was characterised by UV/Vis spectroscopy, microscale thermophoresis, multiscale simulations, and X-ray crystallography.