Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11.

The formation of complexes between Rab11 and its effectors regulates multiple aspects of membrane trafficking, including recycling and ciliogenesis. WD repeat-containing protein 44 (WDR44) is a structurally uncharacterized Rab11 effector that regulates ciliogenesis by competing with prociliogenesis factors for Rab11 binding. Here, we present a detailed biochemical and biophysical characterization of the WDR44-Rab11 complex and define specific residues mediating binding. Using AlphaFold2 modeling and hydrogen/deuterium exchange mass spectrometry, we generated a molecular model of the Rab11-WDR44 complex. The Rab11-binding domain of WDR44 interacts with switch I, switch II, and the interswitch region of Rab11. Extensive mutagenesis of evolutionarily conserved residues in WDR44 at the interface identified numerous complex-disrupting mutations. Using hydrogen/deuterium exchange mass spectrometry, we found that the dynamics of the WDR44-Rab11 interface are distinct from the Rab11 effector FIP3, with WDR44 forming a more extensive interface with the switch II helix of Rab11 compared with FIP3. The WDR44 interaction was specific to Rab11 over evolutionarily similar Rabs, with mutations defining the molecular basis of Rab11 specificity. Finally, WDR44 can be phosphorylated by Sgk3, with this leading to reorganization of the Rab11-binding surface on WDR44. Overall, our results provide molecular detail on how WDR44 interacts with Rab11 and how Rab11 can form distinct effector complexes that regulate membrane trafficking events.

In vitro reconstitution of Sgk3 activation by phosphatidylinositol 3-phosphate.

Serum- and glucocorticoid-regulated kinase 3 (Sgk3) is a serine/threonine protein kinase activated by the phospholipid phosphatidylinositol 3-phosphate (PI3P) downstream of growth factor signaling via class I phosphatidylinositol 3-kinase (PI3K) signaling and by class III PI3K/Vps34-mediated PI3P production on endosomes. Upregulation of Sgk3 activity has recently been linked to a number of human cancers; however, the precise mechanism of activation of Sgk3 is unknown. Here, we use a wide range of cell biological, biochemical, and biophysical techniques, including hydrogen-deuterium exchange mass spectrometry, to investigate the mechanism of activation of Sgk3 by PI3P. We show that Sgk3 is regulated by a combination of phosphorylation and allosteric activation. We demonstrate that binding of Sgk3 to PI3P via its regulatory phox homology (PX) domain induces large conformational changes in Sgk3 associated with its activation and that the PI3P-binding pocket of the PX domain of Sgk3 is sequestered in its inactive conformation. Finally, we reconstitute Sgk3 activation via Vps34-mediated PI3P synthesis on phosphatidylinositol liposomes in vitro. In addition to identifying the mechanism of Sgk3 activation by PI3P, our findings open up potential therapeutic avenues in allosteric inhibitor development to target Sgk3 in cancer.

Deposition of MoSe2 flakes using cyclic selenides.

The currently limited portfolio of volatile organoselenium compounds used for atomic layer deposition (ALD) has been extended by designing and preparing a series of four-, five- and six-membered cyclic silylselenides. Their fundamental properties were tailored by alternating the ring size, the number of embedded Se atoms and the used peripheral alkyl chains. In contrast to former preparations based on formation of sodium or lithium selenides, the newly developed synthetic method utilizes a direct and easy reaction of elemental selenium with chlorosilanes. Novel 2,2,4,4-tetraisopropyl-1,3,2,4-diselenadisiletane, which features good trade-off between chemical/thermal stability and reactivity, has been successfully used for gas-to-solid phase reaction with MoCl5 affording MoSe2. A thorough characterization of the as-deposited 2D MoSe2 flakes revealed its out-of-plane orientation and high purity. Hence, the developed four-membered cyclic silylselenide turned out to be well-suited Se-precursor for ALD of MoSe2.

Towards Volatile Organoselenium Compounds with Cost-Effective Synthesis.

The current portfolio of organoselenium compounds applicable as volatile precursors for atomic layer deposition can be denoted as very limited. Hence, we report herein facile and cost-effective preparation of two bis(trialkylstannyl)selenides as well as one selenole and three bis(trialkylsilyl)selenides. Their syntheses have been optimized to: (i) use readily available and inexpensive starting materials, (ii) involve operationally simple methodology (heating in a pressure vessel), (iii) use a minimum amount of additives and catalysts, and (iv) either exclude additional purification or involve only simple distillation. The chemical structure of prepared Se derivatives was confirmed by multinuclear NMR and GC/MS. Their fundamental thermal properties were investigated by differential scanning calorimetry (DSC) and TGA methods that revealed thermal stability within the range of 160-300 °C.

Cyclic Silylselenides: Convenient Selenium Precursors for Atomic Layer Deposition.

Three cyclic silylselenides were prepared in a straightforward manner. Property tuning has been achieved by varying the ring size and the number of embedded selenium atoms. All silylselenides possess improved resistance towards moisture and oxidation as well as high thermal robustness and sufficient volatility with almost zero residues. The six-membered diselenide proved to be particularly superior Se precursors for atomic layer deposition and allowed facile preparation of MoSe2 layers. Their structure and composition have been investigated by Raman and X-ray photoelectron spectroscopy as well as scanning electron microscopy revealing vertically aligned flaky shaped nanosheets.

Reductant-Induced Free Radical Fluoroalkylation of Nitrogen Heterocycles and Innate Aromatic Amino Acid Residues in Peptides and Proteins.

A series of fluoroalkylated cyclic λ3 -iodanes and their hydrochloride salts was prepared and used in a combination with sodium ascorbate in buffer or aqueous methanol mixtures for radical fluoroalkylation of a range of substituted indoles, pyrroles, tryptophan or its derivatives, and Trp residues in peptides. As demonstrated on several peptides, the aromatic amino acid residues of Trp, Tyr, Phe, and His are targeted with high selectivity to Trp. The functionalization method is biocompatible, mild, rapid, and transition-metal-free. The proteins myoglobin, ubiquitin, and human carbonic anhydrase I were also successfully functionalized.

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.

The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology and function and links out to a large range of domain-specific resources that hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance to the FAIR data principles by providing complex-specific, stable identifiers that include versioning. Protein complexes are now available from 20 species for download in standards-compliant formats such as PSI-XML, MI-JSON and ComplexTAB or can be accessed via an improved REST API. A component-based JS front-end framework has been implemented to drive a new website and this has allowed the use of APIs from linked services to import and visualize information such as the 3D structure of protein complexes, its role in reactions and pathways and the co-expression of complex components in the tissues of multi-cellular organisms. A first draft of the complete complexome of Saccharomyces cerevisiae is now available to browse and download.