The HOPS Proteins hVps41 and hVps39 Are Required for Homotypic and Heterotypic Late Endosome Fusion

The homotypic fusion and protein sorting (HOPS) complex is a multisubunit tethering complex that in yeast regulates membrane fusion events with the vacuole, the yeast lysosome. Mammalian homologs of all HOPS components have been found, but little is known about their function. Here, we studied the role of hVps41 and hVps39, two components of the putative human HOPS complex, in the endo‐lysosomal pathway of human cells. By expressing hemagglutinin (HA)‐tagged constructs, we show by immunoelectron microscopy (immunoEM) that both hVps41 and hVps39 associate with the limiting membrane of late endosomes as well as lysosomes. Small interference RNA (siRNA)‐mediated knockdown of hVps41 or hVps39 resulted in an accumulation of late endosomes, a depletion in the number of lysosomes and a block in the degradation of endocytosed cargo. Lysosomal pH and cathepsin B activity remained unaltered in these conditions. By immunoEM we found that hVps41 or hVps39 knockdown impairs homotypic fusion between late endosomes as well as heterotypic fusion between late endosomes and lysosomes. Thus, our data show that both hVps41 and hVps39 are required for late endosomal–lysosomal fusion events and the delivery of endocytic cargo to lysosomes in human cells.     

Length–weight relationships of nine freshwater fishes from six rivers of the Western Ghats of India

Length–weight relationships (LWRs) were estimated for nine freshwater fish species collected three times using a scoop net (mesh size 0.3–0.5 cm), cast net (mesh size 1–1.5 cm) and gillnet (mesh size 2.5–4.5 cm) from six rivers of the Western Ghats of India during August 2017–October 2018. The b values for LWRs varied from 2.862 to 3.656 (R² > 0.916 and p < 0.0001 for all species).     

Der p 5 Crystal Structure Provides Insight into the Group 5 Dust Mite Allergens

Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK. The crystallographic asymmetric unit contains three dimers of Der p 5 that are not exactly alike. Solution scattering techniques were used to assess the multimeric state of Der p 5 in vitro and showed that the predominant state was monomeric, similar to Blo t 5, but larger multimeric species are also present. In the crystal, the formation of the Der p 5 dimer creates a large hydrophobic cavity of ∼3000 ų that could be a ligand-binding site. Many allergens are known to bind hydrophobic ligands, which are thought to stimulate the innate immune system and have adjuvant-like effects on IgE-mediated inflammatory responses.     

Exploring the effects of sparse restraints on protein structure prediction

One of the main barriers to accurate computational protein structure prediction is searching the vast space of protein conformations. Distance restraints or inter‐residue contacts have been used to reduce this search space, easing the discovery of the correct folded state. It has been suggested that about 1 contact for every 12 residues may be sufficient to predict structure at fold level accuracy. Here, we use coarse‐grained structure‐based models in conjunction with molecular dynamics simulations to examine this empirical prediction. We generate sparse contact maps for 15 proteins of varying sequence lengths and topologies and find that given perfect secondary‐structural information, a small fraction of the native contact map (5%‐10%) suffices to fold proteins to their correct native states. We also find that different sparse maps are not equivalent and we make several observations about the type of maps that are successful at such structure prediction. Long range contacts are found to encode more information than shorter range ones, especially for α and αβ‐proteins. However, this distinction reduces for β‐proteins. Choosing contacts that are a consensus from successful maps gives predictive sparse maps as does choosing contacts that are well spread out over the protein structure. Additionally, the folding of proteins can also be used to choose predictive sparse maps. Overall, we conclude that structure‐based models can be used to understand the efficacy of structure‐prediction restraints and could, in future, be tuned to include specific force‐field interactions, secondary structure errors and noise in the sparse maps.     

Reactivity of platina-β-diketones towards chelating nitrogen and sulfur donors: formation of acyl(hydrido)platinum(IV) and acyl(chloro)platinum(II) complexes

The platina-β-diketone [Pt₂{(COMe)₂H}₂(μ-Cl)₂] (1) was found to react with chelating N,N-ligands 2(R^′NCR)C₅H₄N (R/R^′=Ph/OH, H/Ph, Me/Ph) to form acyl(hydrido)platinum(IV) complexes [Pt(COMe)₂Cl(H){2-(R^′NCR)C₅H₄N}] (R/R^′=Ph/OH 2a; H/Ph 2b; Me/Ph (2c)). Reactions of complex 1 with chelating S,S- and N,S-donors (RS-CH₂-CH₂-SR, 2-(RSCH₂)C₅H₄N, R=Et, Ph, t-Bu) afforded acyl(chloro)platinum(II) complexes [Pt(COMe)Cl(RSCH₂CH₂SR)] (R=Et, 3a; Ph, 3b; t-Bu, 3c) and [Pt(COMe)Cl{2-(RSCH₂)C₅H₄N}] (R=Et, 4a; Ph, 4b; t-Bu, 4c), respectively. All complexes were fully characterized by microanalysis, IR and NMR (¹H, ¹³C) spectroscopy. Furthermore, molecular structures of complexes 3b and 4b were determined by single-crystal X-ray diffraction analyses revealing close to square-planar configuration. In complex 4b the acetyl ligand is trans to pyridine N atom (configuration index SP-4-2). The reactions are discussed in terms of consecutive oxidative addition and reductive elimination reactions.     

Golgi fragmentation occurs in the cells with prefibrillar alpha-synuclein aggregates and precedes the formation of fibrillar inclusion

Amyloid-like fibrillar aggregates of intracellular proteins are common pathological features of human neurodegenerative diseases. However, the nature of pathogenic aggregates and the biological consequences of their formation remain elusive. Here, we describe (i) a model cellular system in which prefibrillar alpha-synuclein aggregates and fibrillar inclusions are naturally formed in the cytoplasm with distinctive kinetics and (ii) a tight correlation between the presence of prefibrillar aggregates and the Golgi fragmentation. Consistent with the structural abnormality of Golgi apparatus, trafficking and maturation of dopamine transporter through the biosynthetic pathway were impaired in the presence of alpha-synuclein aggregates. Reduction in cell viability was also observed in the prefibrillar aggregate-forming condition and before the inclusion formation. The fibrillar inclusions, on the other hand, showed no correlation with Golgi fragmentation and were preceded by these events. Furthermore, at the early stage of inclusion formation, active lysosomes and mitochondria were enriched in the juxtanuclear area and co-aggregate into a compact inclusion body, suggesting that the fibrillar inclusions might be the consequence of an attempt of the cell to remove abnormal protein aggregates and damaged organelles. These results support the hypothesis that prefibrillar alpha-synuclein aggregates are the pathogenic species and suggest that Golgi fragmentation and subsequent trafficking impairment are the specific consequence of alpha-synuclein aggregation.     

Gelatin interpenetration in poly N-isopropylacrylamide network reduces the compressive modulus of the scaffold: A property employed to mimic hepatic matrix stiffness

The progression of liver disease from normal to cirrhotic state is characterized by modulation of the stiffness of the extracellular matrix (ECM). Mimicking this modulation in vitro scaffold could provide a better insight into hepatic cell behavior. In this study, interpenetrating poly(N-isopropylacrylamide-co-gelatin) cryogels were synthesized in 48 different compositions to yield scaffolds of different properties. It was observed that a high concentration of N-isopropylacrylamide (NIPAAm) leads to the formation of small pores while gelatin interpenetration on poly-NIPAAm framework renders porous structure. Swelling properties and porosity of the gels decreased with an increase in NIPAAm concentration owing to the increased compactness of the gels. Gelatin interpenetration relaxed the gels and enhanced these properties. An increase in gelatin concentration led to a reduction in compressive moduli indicating that gelatin interpenetration in the poly-NIPAAm network softens the cryogel. With the increase in NIPAAm concentration, the effect of gelatin interpenetration in reducing the compressive moduli expanded. The cytocompatibility studies indicated that the gels are cell-adherent and compatible with HepG2. Furthermore, biochemical and real-time polymerase chain reaction studies revealed that HepG2 and Huh-7 cells cultured on scaffolds mimicking the ECM stiffness of normal liver (1.5–2.5 kPa) exhibited optimum liver-specific functionalities. Increasing the stiffness to fibrotic (4–9 kPa) and cirrhotic (10–20 kPa) ECM decreases the functionality.     

Protein unfolding rates correlate as strongly as folding rates with native structure

Although the folding rates of proteins have been studied extensively, both experimentally and theoretically, and many native state topological parameters have been proposed to correlate with or predict these rates, unfolding rates have received much less attention. Moreover, unfolding rates have generally been thought either to not relate to native topology in the same manner as folding rates, perhaps depending on different topological parameters, or to be more difficult to predict. Using a dataset of 108 proteins including two-state and multistate folders, we find that both unfolding and folding rates correlate strongly, and comparably well, with well-established measures of native topology, the absolute contact order and the long range order, with correlation coefficient values of 0.75 or higher. In addition, compared to folding rates, the absolute values of unfolding rates vary more strongly with native topology, have a larger range of values, and correlate better with thermodynamic stability. Similar trends are observed for subsets of different protein structural classes. Taken together, these results suggest that choosing a scaffold for protein engineering may require a compromise between a simple topology that will fold sufficiently quickly but also unfold quickly, and a complex topology that will unfold slowly and hence have kinetic stability, but fold slowly. These observations, together with the established role of kinetic stability in determining resistance to thermal and chemical denaturation as well as proteases, have important implications for understanding fundamental aspects of protein unfolding and folding and for protein engineering and design.     

Pinda shrirangii,a new elegant species of Apiaceae from the northern Western Ghats,India

A new species, Pinda shrirangii Gosavi & Chandore, is described and illustrated from a high-elevation region of northern Western Ghats, India. The new species is closely allied to the only other species in the genus, Pinda concanensis (Dalzell) P.K.Mukh. & Constance which was also described from the northern Western Ghats of Maharashtra state of India. Coloured photographs and illustrations are provided to facilitate the identification.