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The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopusoocytes and proteoliposomes showed that MFSD1–GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1–GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.

The SARS-CoV-2 pandemic has increased the demand for low-cost, portable, and rapid biosensors, driving huge research efforts toward new nanomaterial-based approaches with high sensitivity. Many of them employ antibodies as bioreceptors, which have a costly development process that requires animal facilities. Recently, sybodies emerged as a new alternative class of synthetic binders and receptors with high antigen binding efficiency, improved chemical stability, and lower production costs via animal-free methods. Their smaller size is an important asset to consider in combination with ultrasensitive field-effect transistors (FETs) as transducers, which respond more intensely when biorecognition occurs near their surface. This work demonstrates the immobilization of sybodies against the spike protein of the virus on silicon surfaces, which are often integral parts of the semiconducting channel of FETs. Immobilized sybodies maintain the capability to capture antigens, even at low concentrations in the femtomolar range, as observed by fluorescence microscopy. Finally, the first proof of concept of sybody-modified FET sensing is provided using a nanoscopic silicon net as the sensitive area where the sybodies are immobilized. The future development of further sybodies against other biomarkers and their generalization in biosensors could be critical to decrease the cost of biodetection platforms in future pandemics.

We investigated the adsorption of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the virus responsible for the current pandemic, on the surface of the model catalyst TiO2(101) using atomic force microscopy, transmission electron microscopy, fluorescence microscopy, and X-ray photoelectron spectroscopy, accompanied by density functional theory calculations. Three different methods were employed to inactivate the virus after it was loaded on the surface of TiO2(101): (i) ethanol, (ii) thermal, and (iii) UV treatments. Microscopic studies demonstrate that the denatured spike proteins and other proteins in the virus structure readsorb on the surface of TiO2under thermal and UV treatments. The interaction of the virus with the surface of TiO2was different for the thermally and UV treated samples compared to the sample inactivated via ethanol treatment. AFM and TEM results on the UV-treated sample suggested that the adsorbed viral particles undergo damage and photocatalytic oxidation at the surface of TiO2(101) which can affect the structural proteins of SARS-CoV-2 and denature the spike proteins in 30 min. The role of Pd nanoparticles (NPs) was investigated in the interaction between SARS-CoV-2 and TiO2(101). The presence of Pd NPs enhanced the adsorption of the virus due to the possible interaction of the spike protein with the NPs. This study is the first investigation of the interaction of SARS-CoV-2 with the surface of single crystalline TiO2(101) as a potential candidate for virus deactivation applications. Clarification of the interaction of the virus with the surface of semiconductor oxides will aid in obtaining a deeper understanding of the chemical processes involved in photoinactivation of microorganisms, which is important for the design of effective photocatalysts for air purification and self-cleaning materials.

Titanium dioxide (TiO2) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO2surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO2predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO2under light irradiation. Notably, in situmeasurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO2surface. The in situGISAXS measurements under an N2atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.

Members of the solute carrier 15 family (SLC15) transport di- and tripeptides as well as peptidomimetic drugs across the cell membrane. Structures of bacterial homologues have provided valuable information on the binding and transport of their natural substrates, but many do not transport medically relevant drugs. In contrast, a homologue from Escherichia coli, DtpA (dipeptide and tripeptide permease), shows a high similarity to human PepT1 (SLC15A1) in terms of ligand selectivity and transports a similar set of drugs. Here, we present the crystal structure of DtpA in ligand-free form (at 3.30 Å resolution) and in complex with the antiviral prodrug valganciclovir (at 2.65 Å resolution) supported by biochemical data. We show that valganciclovir unexpectedly binds with the ganciclovir moiety mimicking the N-terminal residue of a canonical peptide substrate. On the basis of a homology model we argue that this binding mode also applies to the human PepT1 transporter. Our results provide new insights into the binding mode of prodrugs and will assist the rational design of drugs with improved absorption rates.

Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.

A saposin protein–lipid nanoparticle system stabilizes diverse, fragile membrane proteins in a lipid environment for structural and functional studies.

Members of the major facilitator superfamily (MFS) of transport proteins are essential for the movement of a wide range of substrates across biomembranes. As this transport requires a series of conformational changes, structures of MFS transporters captured in different conformational states are needed to decipher the transport mechanism. Recently, a large number of MFS transporter structures have been determined, which has provided us with an unprecedented opportunity to understand general aspects of the transport mechanism. We propose an updated model for the conformational cycle of MFS transporters, the 'clamp-and-switch model', and discuss the role of so-called 'gating residues' and the substrate in modulating these conformational changes.

P19INK4dconsists of five ankyrin repeats and controls the human cell cycle by inhibiting the cyclin D-dependent kinases 4 and 6. Posttranslational phosphorylation of p19INK4dhas been described for Ser66 and Ser76. In the present study we show that mimicking the phosphorylation site of p19INK4dby a glutamate substitution at position 76 dramatically decreases the stability of the native but not an intermediate state. At body temperature the native conformation is completely lost and p19INK4dmolecules exhibit the intermediate state as judged by kinetic and equilibrium analysis. High resolution NMR spectroscopy verified that the three C-terminal repeats remained folded in the intermediate state, whereas all cross-peaks of the two N-terminal repeats lost their native chemical shift. Molecular dynamic simulations of p19INK4din different phosphorylation states revealed large-scale motions in phosphorylated p19INK4d, which cause destabilization of the interface between the second and third ankyrin repeat. Only doubly phosphorylated p19INK4dmimic mutants showed in vitroan increased accessibility for ubiquitination, which might be the signal for degradation in vivo.

Bin/Amphiphysin/Rvs-homology (BAR) domains generate and sense membrane curvature by binding the negatively charged membrane to their positively charged concave surfaces. N-BAR domains contain an N-terminal extension (helix-0) predicted to form an amphipathic helix upon membrane binding. We determined the NMR structure and nano-to-picosecond dynamics of helix-0 of the human Bin1/Amphiphysin II BAR domain in sodium dodecyl sulfate and dodecylphosphocholine micelles. Molecular dynamics simulations of this 34-amino acid peptide revealed electrostatic and hydrophobic interactions with the detergent molecules that induce helical structure formation from residues 8–10 toward the C-terminus. The orientation in the micelles was experimentally confirmed by backbone amide proton exchange. The simulation and the experiment indicated that the N-terminal region is disordered, and the peptide curves to adopted the micelle shape. Deletion of helix-0 reduced tubulation of liposomes by the BAR domain, whereas the helix-0 peptide itself was fusogenic. These findings support models for membrane curving by BAR domains in which helix-0 increases the binding affinity to the membrane and enhances curvature generation.

New intramolecularly coordinated organotin compounds containing the monoanionic O,C,O-coordinating ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}^– have been synthesized by substitution reactions starting from organotin halides. In view of the enhanced reactivity of the intramolecularly coordinated compounds {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}SnR2R' (2, R = Ph, R' = CH2SiMe3; 3, R = R' = Ph; 6, R = R' = Cl), cationic tin species are suggested to occur as intermediates in the formation of the heterocyclic compounds [1(Sn),3(P)-Ph2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (8), [1(Sn), 3(P)-Ph(Me3SiCH2)SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (15), and {[1(Sn),3(P)-Cl2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)]C6H2}2 (16). The latter compounds are formed by intramolecular cyclizations of pentacoordinate cationic tin species under elimination of ethyl halide. Furthermore, the synthesis of [1(Sn),3(P)-Ph2SnOP(O)(OH)-5-tert-Bu-7-P(O)(OH)2]C6H2 (13) is described. Reaction of 8 with an excess of Me3SiBr leads to the unexpected formation of {2-[P(O)(OEt)(OSiMe3)]-4-tert-Bu-6-[P(O)(OEt)2]C6H2}SnPhBr2 (9) as a result of an O–Sn bond cleavage initiated by Me3SiBr and subsequent reaction of the intermediate with further Me3SiBr under Sn–C bond cleavage. The high donor capacity and the rigidity of the new ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}^– are demonstrated by X-ray diffraction analyses of the tetraorganotin compound 2 and the monoorganotin trichloride 6. Furthermore, the molecular structures of the 2,3,1-oxaphosphastannoles 8 and 16 are discussed.

Recent results are reported on the application of the novel O,C,O-coordinating pincer ligand {2,6-[P(O)(OEt)2]2-4-tert-Bu-C6H2} (A) for the synthesis of hypercoordinate organotin(IV) compounds ASnR3(R = Ph, Cl), heteroleptic stannylenes ASnR (R = Cl, CH2SiMe3) and intramolecularly coordinated 1,2,5-oxaphosphastannolanes.

Malaria claims about half a million lives each year. Plasmodium falciparum, the causative agent of the most severe form of the disease, uses proteins that are translocated to the surface of infected erythrocytes for immune evasion. To circumvent the detection of these gene products by the immune system, the parasite evolved a complex strategy that includes gene duplications and elaborate sequence polymorphism. STEVORs are one family of these variant surface antigens and are encoded by about 40 genes. Using deep RNA sequencing of blood-stage parasites, including free merozoites, we first established stevorexpression of the cultured isolate and compared it with published transcriptomes. We reveal a biphasic expression of most stevorgenes and confirm this for individual STEVORs at the protein level. The membrane topology of a rhoptry-associated variant was experimentally elucidated and linked to host cell invasion, underlining the importance of this multifunctional protein family for parasite proliferation.