Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.

The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.

N-acetylglucosamine transporter, Ngt1, undergoes sugar-responsive endosomal trafficking in Candida albicans.

N-acetylglucosamine (GlcNAc), an important amino sugar at the infection sites of the fungal pathogen Candida albicans, triggers multiple cellular processes. GlcNAc import at the cell surface is mediated by GlcNAc transporter, Ngt1 which seems to play a critical role during GlcNAc signaling. We have investigated the Ngt1 dynamics that provide a platform for further studies aimed at understanding the mechanistic insights of regulating process(es) in C. albicans. The expression of this transporter is prolific and highly sensitive to even very low levels (˂2 µM) of GlcNAc. Under these conditions, Ngt1 undergoes phosphorylation-associated ubiquitylation as a code for internalization. This ubiquitylation process involves the triggering proteins like protein kinase Snf1, arrestin-related trafficking adaptors (ART) protein Rod1, and yeast ubiquitin ligase Rsp5. Interestingly, analysis of ∆snf1 and ∆rsp5 mutants revealed that while Rsp5 is promoting the endosomal trafficking of Ngt1-GFPɤ, Snf1 hinders the process. Furthermore, colocalization experiments of Ngt1 with Vps17 (an endosomal marker), Sec7 (a trans-Golgi marker), and a vacuolar marker revealed the fate of Ngt1 during sugar-responsive endosomal trafficking. ∆ras1 and ∆ubi4 mutants showed decreased ubiquitylation and delayed endocytosis of Ngt1. According to our knowledge, this is the first report which illustrates the mechanistic insights that are responsible for endosomal trafficking of a GlcNAc transporter in an eukaryotic organism.

Receptor tyrosine kinases (RTKs) consociate in regulatory clusters in Alzheimer's disease and type 2 diabetes.

Alzheimer's disease (AD) and type 2 diabetes (T2D) share the common hallmark of insulin resistance. It is conjectured that receptor tyrosine kinases (RTKs) play definitive roles in the process. To decipher the signaling overlap behind this phenotypic resemblance, the activity status of RTKs is probed in post-mortem AD and T2D tissues and cell models. Activities of only about one-third changed in a similar fashion, whereas about half of them showed opposite outcomes when exposed to contrasting signals akin to AD and T2D. Interestingly, irrespective of disease type, RTKs with enhanced and compromised activities clustered distinctly, indicating separate levels of regulations. Similar regulatory mechanisms within an activity cluster could be inferred, which have potential to impact future therapeutic developments.

Palmitoylation of the ciliary GTPase ARL13b is necessary for its stability and its role in cilia formation.

Primary cilia are hairlike extensions of the plasma membrane of most mammalian cells that serve specialized signaling functions. To traffic properly to cilia, multiple cilia proteins rely on palmitoylation, the post-translational attachment of a saturated 16-carbon lipid. However, details regarding the mechanism of how palmitoylation affects cilia protein localization and function are unknown. Herein, we investigated the protein ADP-ribosylation factor-like GTPase 13b (ARL13b) as a model palmitoylated ciliary protein. Using biochemical, cellular, and in vivo studies, we found that ARL13b palmitoylation occurs in vivo in mouse kidneys and that it is required for trafficking to and function within cilia. Myristoylation, a 14-carbon lipid, is shown to largely substitute for palmitoylation with regard to cilia localization of ARL13b, but not with regard to its function within cilia. The functional importance of palmitoylation results in part from a dramatic increase in ARL13b stability, which is not observed with myristoylation. Additional results show that blockade of depalmitoylation slows the degradation of ARL13b that occurs during cilia resorption, raising the possibility that the sensitivity of ARL13b stability to palmitoylation may be exploited by the cell to accelerate degradation of ARL13b by depalmitoylating it. Together, the results show that palmitoylation plays a unique and critical role in controlling the localization, stability, abundance, and thus function of ARL13b. Pharmacological manipulation of protein palmitoylation may be a strategy to alter cilia function.

Polycystin-1, the product of the polycystic kidney disease gene PKD1, is post-translationally modified by palmitoylation.

Multiple distinct mutations in the protein polycystin 1 (PC1) cause autosomal dominant polycystic kidney disease (ADPKD), a common cause of end stage renal disease. Growing evidence supports the theory that the severity and rate of progression of kidney cysts is correlated with the level of functional PC1 expressed in the primary cilia. Factors that regulate trafficking of PC1 to cilia are thus of great interest both as potential causes of ADPKD, but also as possible modifiable factors to treat ADPKD. Cysteine palmitoylation is a common post-translational modification that frequently alters protein trafficking, localization, and expression levels. Here, using multiple complementary approaches, we show that PC1 is palmitoylated, likely at a single cysteine in the carboxyl terminal fragment that is generated by autoproteolysis of PC1. Additional data suggest that protein palmitoylation is important for PC1 localization and expression levels. These data together identify palmitoylation as a novel post-translational modification of PC1 and a possible pharmacologic target to augment PC1 expression in cilia.

Interaction of Grb2 SH3 domain with UVRAG in an Alzheimer's disease-like scenario.

Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein which participates in trafficking pathways alongside its role in signaling. Proteins important for actin remodeling and cellular compartmentalization contain SRC Homology 3 (SH3) binding motifs that interact with Grb2. While studying the Grb2-amyloid precursor protein (APP) intracellular domain (AICD) interaction in Alzheimer's disease cell line models, it was seen that Grb2 colocalized to compartments that mature into autophagosomes. The entrapping of AICD in the Grb2 vesicles and its clearance via autophagosomes was a survival contrivance on the part of the cell. Here, we report that Grb2, when in excess, interacts with ultraviolet radiation resistance-associated gene protein (UVRAG) under excess conditions of AICD-Grb2 or Grb2. The N-terminal SH3 domain of Grb2 specifically interacts with UVRAG, unlike the C-terminal SH3 domain. This interaction helps to understand the role of Grb2 in the autophagic maturation of vesicles.

Assessment of the Push-Out Bond Strength for Glass Fiber Posts After Different Surface Treatments: An In Vitro Study.

AIM: The goal of the study was to assess the push-out bond strength of the glass fibre post after different surface treatments. MATERIALS AND METHODS: For the purpose of the investigation, 40 mandibular premolars were chosen. After gaining access, the biomechanical preparation was completed using the step-back approach up to a size 40K file, and the canals were sealed using gutta-percha cones and the lateral condensation procedure with AH Plus sealer (epoxide-amine resin pulp canal sealer). Peeso reamers were used to remove the canal fillings, leaving 5mm of gutta-percha apically. Drills included in the package were used to prepare the post spaces so that the posts would fit in their respective post slots. These were attached to self-curing acrylic resin blocks. Fibre posts were split into four groupings of n = 10 each for surface treatment, i.e., control, hydrogen fluoride, sandblasting, and hydrogen peroxide. The cementation of posts was done by utilising dual-cure resin cement. Two millimetres of the anatomical crown were removed from each sample. Each sample's 1-mm cervical segment was taken utilising the isotope from the remaining coronal area. To perform a push-out test, at the rate of 0.5mm/min of the crosshead, every sample was inserted into a universal testing device. Each post's dislodge force from the pre-set post spacing was measured. Statistics were utilised to analyse the data. RESULTS: Strongest bonds were made by silanization, followed by sandblasting (p value=0.002). The weakest bonds were made by the control group. CONCLUSION: The ultimate deduction was that when glass fibre posts underwent various types of surface treatments followed by silanization, it had a significant impact on increasing their strength.

Srg1, a putative protein phosphatase from the HAD-family, is involved in stress adaptation in Candida albicans.

BACKGROUND: The cell stress response plays an important role in the survival of organisms. Studies have revealed that the pathogenic yeast Candida albicans that constantly encounters various environmental insults inside the host has emerged as an ideal system to understand the molecular mechanism (s) of stress response. In this study, we characterize a stress-inducible gene SRG1 which is a Halo Acid Dehalogenase (HAD) family member from C. albicans. METHODS: We used confocal microscopy, site-directed mutagenesis, gene deletion techniques, and tandem-affinity purification and co-immunoprecipitation studies to functionally characterize SRG1. RESULTS: The sub-cellular localization of Srg1 is predominantly cytoplasmic and includes punctate mitochondrial staining in the presence of salt. Protein purification studies coupled with LC-MS analysis showed that Srg1 is a phosphoprotein. The Srg1 mutant carrying S47A and S49A mutations failed to migrate to mitochondria in the presence of salt but retained its phosphatase activity. Srg1 migrates to the nucleus in ∆hog1 mutant cells indicating an unorthodox role for HAD family proteins in stress-mediated transcriptional response. Srg1 also interacts with Erg13, a component involved in the mitochondrial membrane lipid biosynthesis pathway. CONCLUSIONS: A multistep relay mechanism that includes a positive modulation by the MAP kinase Hog1 and a negative modulation by the global repressor Tup1 controls SRG1 expression. GENERAL SIGNIFICANCE: Taken together, our work contributes towards gaining a functional insight into a class of phosphatases that probably have evolved with novel specificities in the pathogenic yeast C. albicans to counteract stressful conditions.

Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide.

Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na+, 1 K+, and 2 Cl- across cell membranes. NKCC1 mediates trans-epithelial Cl- secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association.

The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2.

NKCC and KCC transporters mediate coupled transport of Na++K++Cl- and K++Cl- across the plasma membrane, thus regulating cell Cl- concentration and cell volume and playing critical roles in transepithelial salt and water transport and in neuronal excitability. The function of these transporters has been intensively studied, but a mechanistic understanding has awaited structural studies of the transporters. Here, we present the cryo-electron microscopy (cryo-EM) structures of the two neuronal cation-chloride cotransporters human NKCC1 (SLC12A2) and mouse KCC2 (SLC12A5), along with computational analysis and functional characterization. These structures highlight essential residues in ion transport and allow us to propose mechanisms by which phosphorylation regulates transport activity.

Lipid Modifications in Cilia Biology.

Cilia are specialized cellular structures with distinctive roles in various signaling cascades. Ciliary proteins need to be trafficked to the cilium to function properly; however, it is not completely understood how these proteins are delivered to their final localization. In this review, we will focus on how different lipid modifications are important in ciliary protein trafficking and, consequently, regulation of signaling pathways. Lipid modifications can play a variety of roles, including tethering proteins to the membrane, aiding trafficking through facilitating interactions with transporter proteins, and regulating protein stability and abundance. Future studies focusing on the role of lipid modifications of ciliary proteins will help our understanding of how cilia maintain specific protein pools strictly connected to their functions.

Cellular levels of Grb2 and cytoskeleton stability are correlated in a neurodegenerative scenario.

Alzheimer's disease (AD) manifests as neuronal loss. On the premise of Grb2 overexpression in AD mouse brain and brain tissues of AD patients, our study primarily focuses on the stability of cytoskeletal proteins in the context of degenerative AD-like conditions. Two predominant molecular features of AD, extracellular accumulation of ß-amyloid oligomers and intracellular elevation of amyloid precursor protein intracellular domain levels, have been used to closely inspect the series of signalling events. In their presence, multiple signalling pathways involving ROCK and PAK1 proteins lead to disassembly of the cytoskeleton, and Grb2 partially counterbalances the cytoskeletal loss. Increased Grb2-NOX4 interactions play a preventive role against cytoskeletal disassembly, in turn blocking the activity of nitrogen oxides and decreasing the expression of slingshot homolog 1 (SSH-1) protein, a potent inducer of cytoskeleton disassembly. This study unravels a unique role of Grb2 in protecting the cytoskeletal architecture in AD-like conditions and presents a potential new strategy for controlling neurodegeneration.

Differential expression of neuroblastoma cellular proteome due to AICD overexpression.

Amyloid-ß protein precursor intracellular domain (AICD), which exerts intracellular effects by interacting with proteins involved in a plethora of biological processes, is a key player behind the pathophysiology of Alzheimer's disease (AD). Keeping in mind that overwhelming presence of AICD would mimic AD-like conditions in neuroblastoma cell lines, we hypothesized alteration in the proteomic expression pattern in these cells in the presence of AICD compared to their normal proteome. The rationale behind the study was to distinguish between symptomatic pathophysiological effects as opposed to any artifactual consequence due to protein overload in the cell lines. Using 2D-DIGE analysis and MALDI-MS identifications in neuro2A (mouse) and SHSY5Y (human) cell lines, we have identified several proteins belonging to different functional classes and involved in several biological pathways including protein folding, cytoskeletal dynamics, metabolism, and stress. Many of these were being upregulated or downregulated due to AICD effects and could be correlated directly with AD phenotypes.

Growth factor receptor-bound protein 2 promotes autophagic removal of amyloid-ß protein precursor intracellular domain overload in neuronal cells.

The ascertainment of elevated levels of amyloid-ß protein precursor intracellular domain (AICD) in Alzheimer's disease (AD) brains and the fact that it contributes to AD-like pathology has geared the search toward a new paradigm. While studying endogenous as well as overexpressed Grb2-AICD interaction in AD cell models, it was found that Grb2 co-localized to compartments along with AICD. We report now that these vesicles form in a clathrin and dynamin independent manner. Both types of vesicles mature into autophagosomes, merge with lysosomes, and relieve the cells of AICD overload. Inhibiting autophagosome formation results in vesicle accumulation. AICD-level is reduced in Grb2 excess condition in Cycloheximide Chase setup. Reduced caspase activity and apoptosis point toward the fact that the cytotoxic effect of AICD is alleviated by its sequestration in autolysosomes. Hence we state that the entrapping of AICD in Grb2 vesicles and its clearance via autophagosomes is a survival contrivance on the part of the cell. This study unravels, for the first time, the roles of Grb2 in autophagy and in handling toxic protein overload in an AD-like scenario.

The N-terminal SH3 domain of Grb2 is required for endosomal localization of AßPP.

Based on the observations that Grb2 overexpression altered the trafficking route of amyloid-ß protein precursor (AßPP) by inhibiting its release via exosomal vesicles, and subsequently increased its endogenous level, in the present study we aimed to elucidate the mechanism of traffic impairment and the role of different Grb2 domains in this process. We found that the N-SH3 domain of Grb2 was involved in the protein vesicular localization. The C-SH3 domain could also form very small puncta, but were not characteristic Grb2 containing vesicles. Vesicles containing the N-SH3-SH2 domain had a mixed population of early and late endosomes but C-SH3-SH2 domain containing vesicles were of early endosomal type. The N-SH3 domain therefore seems to be involved in the maturation of early endosomes to late endosomes. Almost all the features shown by overexpression of full-length type Grb2, for example, entrapment of endogenous AßPP in vesicles, affecting the turnover of AßPP in terms of decrease in exosomal release and increase in endogenous concentration of the protein, could be reproduced by the N-SH3-SH2 domain and, to a very limited extent, by the C-SH3-SH2 domain. The middle SH2 domain alone did not show any involvement in AßPP trafficking. By mutational analysis of both N and C terminal SH3 domains, attempts were made to elucidate the molecular basis of this functional anomaly.