Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW

ARHGAP12 suppresses F-actin assembly to control epithelial tight junction mechanics and paracellular leak pathway permeability

Tight junctions (TJs) control the paracellular transport of ions, solutes, and macromolecules across epithelial barriers. There is evidence that claudin-based ion transport (the pore pathway) and the paracellular transport of macromolecules (the leak pathway) are controlled independently. However, how leak pathway flux is regulated is unclear. Here, we have identified the Cdc42/Rac GTPase-activating protein ARHGAP12 as a specific activator of the leak pathway. ARHGAP12 is recruited to TJs via an interaction between its Src homology (SH3) domain and the TJ protein ZO-2 to suppress N-WASP-mediated F-actin assembly. This dampens junctional tension and promotes the paracellular transport of macromolecules without affecting ion flux. Mechanistically, we demonstrate that the ARHGAP12 tandem WW domain interacts directly with PPxR motifs in the proline-rich domain of N-WASP and thereby attenuates SH3-domain-mediated N-WASP oligomerization and Arp2/3-driven F-actin assembly. Collectively, our data indicate that branched F-actin networks regulate junctional tension to fine-tune the TJ leak pathway.

Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs

PRPF40A plays an important role in the regulation of pre-mRNA splicing by mediating protein-protein interactions in the early steps of spliceosome assembly. By binding to proteins at the 5´ and 3´ splice sites, PRPF40A promotes spliceosome assembly by bridging the recognition of the splices. The PRPF40A WW domains are expected to recognize proline-rich sequences in SF1 and SF3A1 in the early spliceosome complexes E and A, respectively. Here, we combine NMR, SAXS and ITC to determine the structure of the PRPF40A tandem WW domains in solution and characterize the binding specificity and mechanism for proline-rich motifs recognition. Our structure of the PRPF40A WW tandem in complex with a high-affinity SF1 peptide reveals contributions of both WW domains, which also enables tryptophan sandwiching by two proline residues in the ligand. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A mediates intramolecular interactions with the WW tandem. Using NMR, ITC, mutational analysis in vitro, and immunoprecipitation experiments in cells, we show that the intramolecular interaction acts as an autoinhibitory filter for proof-reading of high-affinity proline-rich motifs in bona fide PRPF40A binding partners. We propose that similar autoinhibitory mechanisms are present in most WW tandem-containing proteins to enhance binding selectivity and regulation of WW/proline-rich peptide interaction networks.

CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering

Density-based clustering procedures are widely used in a variety of data science applications. Their advantage lies in the capability to find arbitrarily shaped and sized clusters and robustness against outliers. In particular, they proved effective in the analysis of molecular dynamics simulations, where they serve to identify relevant, low-energetic molecular conformations. As such, they can provide a convenient basis for the construction of kinetic (core-set) Markov-state models. Here we present the open-source Python project CommonNNClustering, which provides an easy-to-use and efficient reimplementation of the common-nearest-neighbor (CommonNN) method. The package provides functionalities for hierarchical clustering and an evaluation of the results. We put our emphasis on a generic API design to keep the implementation flexible and open for customization.