Podcasts about pdz

Op den Velde groep won tijdens de Zaanse Ondernemersdag 2023 de PDZ jeugdjuryprijs. Een interview met Wout op den Velde en Virgil Deen van dit gelauwerde Zaanse bedrijf. Door: Silva Honig en Edwin Kleiss.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.24.550336v1?rss=1 Authors: Kumar, R., Tatiya, P., Dey, D., Ratra, Y., Mian, S. Y., Chaudhary, S., Suhag, K., Basak, S., Banerjee, M. Abstract: Downregulation of the host cell pro-apoptotic pathways confers a selective advantage to viral pathogens, and many viruses interfere with such regulatory mechanisms in order to enhance their propagation in infected cells. The Scribble cell polarity complex, which is composed of multiple adapter proteins including human Scribble, Dlg and MAGI, controls a variety of host cell functionalities including apoptosis, morphology, polarity, signaling and migration. In the recent years, components from several viral pathogens, including oncogenic viruses, have been found to associate with and modulate the activities of this complex, particularly that of the pro-apoptotic protein Scribble. Here, we establish a critical role for the downregulation of Scribble expression for the potentiation of Chikungunya Virus (CHIKV) infection. CHIKV is a well-known mosquito-borne alphavirus, which has caused outbreaks in more than 100 countries and constitutes a global health hazard. While the majority of the CHIKV proteome is well characterized, the role of a small structural protein 6K, and its transframe variant, TF, which is generated from the 6K sequence by ribosomal slippage and frameshifting, is not established as yet. We show that TF triggers the punctation, ubiquitination and degradation of Scribble during CHIKV infection, and that the downregulation of Scribble during CHIKV infection. We show that the association of TF with the PDZ domains of Scribble is mediated through a PDZ-domain binding motif at the C-terminus of TF. Thus, our work establishes a role for the downregulation of Scribble in alphavirus infections for the first time, while allocating a novel role in host modulation to the mysterious 6K/TF component of alphaviruses. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.03.06.531332v1?rss=1 Authors: Sneddon, W. B., Friedman, P. A., Mamonova, T. Abstract: The Na+-dependent phosphate cotransporter-2A (NPT2A, SLC34A1) is a primary regulator of extracellular phosphate homeostasis. Its most prominent structural element is a carboxy-terminal PDZ ligand that binds Na+/H+ Exchanger Regulatory Factor-1 (NHERF1, SLC9A3R1). NHERF1, a multidomain PDZ protein,establishes NPT2A membrane localization and is required for hormone-sensitive phosphate transport. NPT2A also possesses an uncharacterized internal PDZ ligand. Two recent clinical reports describe congenital hypophosphatemia in children harboring Arg495His or Arg495Cys variants within the internal PDZ motif. The wild-type internal 494TRL496 PDZ ligand binds NHERF1 PDZ2, which we consider a regulatory domain. Ablating the internal PDZ ligand with a 494AAA496 substitution blocked hormone-sensitive phosphate transport. Complementary approaches, including CRISPR/Cas9 technology, site-directed mutagenesis, confocal microscopy, and modeling, showed that NPT2A Arg495His or Arg495Cys variants do not support PTH or FGF23 action on phosphate transport. Coimmunoprecipitation experiments indicate that both variants bind NHERF1 similarly to WT NPT2A. However, in contrast to WT NPT2A, NPT2A Arg495His or Arg495Cys variants remain at the apical membrane and are not internalized in response to PTH. We predict that Cys or His substitution of the charged Arg495 changes the electrostatics, preventing phosphorylation of the upstream Thr494, interfering with phosphate uptake in response to hormone action, and inhibiting NPT2A trafficking. We advance a model wherein the carboxyterminal PDZ ligand defines apical localization NPT2A, while the internal PDZ ligand is essential for hormone-triggered phosphate transport. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.28.530466v1?rss=1 Authors: Chatterjee, P., Morgan, C. P., Krey, J. F., Benson, C., Goldsmith, J., Bateschell, M., Ricci, A., Barr-Gillespie, P. G. Abstract: GIPC3 has been implicated in auditory function. Initially localized to the cytoplasm of inner and outer hair cells of the cochlea, GIPC3 increasingly concentrated in cuticular plates and at cell junctions over the first two weeks of postnatal development. Early postnatal Gipc3KO/KO mice had mostly normal mechanotransduction currents, but by one month of age they had a complete loss of their auditory brainstem response. During postnatal development, cuticular plates rounded up in Gipc3KO/KO hair cells, then degenerated after postnatal day 15. GIPC3 bound directly to MYO6, and the loss of MYO6 led to altered distribution of GIPC3. In addition, junctions between inner hair cells and intervening inner phalangeal cells were severely disrupted in Gipc3KO/KO. Immunoaffinity isolation of GIPC3 from chicken inner ear extracts identified co-precipitating proteins associated with adherens junctions, intermediate filament networks, and the cuticular plate. Several of these immunoprecipitated proteins contained GIPC-family consensus PDZ binding motifs (PBMs), including MYO18A, which binds directly to the PDZ domain of GIPC3. We propose that GIPC3 and MYO6 couple to PBMs of cytoskeletal and cell-junction proteins to shape the cuticular plate. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.02.06.527276v1?rss=1 Authors: Hees, J. T., Harbauer, A. B. Abstract: Mitochondrial quality control failure is frequently observed in neurodegenerative diseases. The detection of damaged mitochondria by stabilization of PTEN-induced kinase 1 (PINK1) requires transport of Pink1 mRNA by tethering it to the mitochondrial surface. Here, we report that inhibition of AMPK by activation of the insulin signaling cascade prevents Pink1 mRNA binding to mitochondria. Mechanistically, AMPK phosphorylates the RNA anchor complex subunit SYNJ2BP within its PDZ domain, a phosphorylation site that is necessary for its interaction with the RNA-binding protein SYNJ2. Interestingly, loss of mitochondrial Pink1 mRNA association upon insulin addition is required for PINK1 protein activation and its function as a ubiquitin kinase in the mitophagy pathway, thus placing PINK1 function under metabolic control. Induction of insulin-resistance in vitro by the key genetic Alzheimer-risk factor apolipoprotein E4 retains Pink1 mRNA at the mitochondria and prevents proper PINK1 activity especially in neurites. Our results thus identify a metabolic switch controlling Pink1 mRNA localization and PINK1 activity via insulin and AMPK signaling in neurons and propose a mechanistic connection between insulin resistance and mitochondrial dysfunction. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.01.514384v1?rss=1 Authors: Das, M., Cheng, D., Matzat, T., Auld, V. Abstract: Glial cells in the peripheral nerve wrap axons to insulate them and ensure efficient conduction of neuronal signals. In the myelin sheath, it is proposed that the autotypic tight junctions and adherens junctions form glia-glia complexes that stabilize the glia sheath in myelinating glia. Yet the role of adhesion junctions in non-myelinating glia of vertebrates or invertebrates has not been clearly established. Many components of adhering junctions contain PDZ (PSD-95, Dlg, ZO1) domains or are recruited to these junctions by PDZ binding motifs. To test for the role of PDZ domain proteins in glial sheath formation, we carried out an RNAi screen using Drosophila melanogaster to knockdown each of the 66 predicted PDZ domain proteins in the peripheral glia. We identified six PDZ genes with potential roles in glial morphology, and further investigated Discs-large 5 (Dlg5), a scaffolding protein with no previously known function in glia. Knockdown of Dlg5 disrupts subperineurial glia (SPG) morphology, including gaps in the membrane that coincide with disruption of septate junction proteins. To further our investigation of Dlg5, we focused on cadherins and found both N-Cadherin and E-Cadherin are expressed throughout peripheral glia. Knockdown of Ecad phenocopied the loss of Dlg5 leading to gaps in the SPG and septate junctions while only simultaneous loss of both N-Cadherins (Ncad, and CadN2) had the same effect. The loss of all three Cadherins enhanced these phenotypes as did loss of Dlg5 when paired with Cadherin knockdown. This leads to a model where Dlg5 plays a role in conjunction with Cadherins in glial membrane stabilization and SJ formation in the subperineurial glia. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.21.513252v1?rss=1 Authors: Yang, Q., Perfitt, T. L., Quay, J., Hu, L., Colbran, R. J. Abstract: Clustering of neuronal L-type voltage-gated Ca2+ channels (LTCC) in the plasma membrane is increasingly implicated in creating highly localized Ca2+ signaling nanodomains. For example, LTCC activation can increase phosphorylation of the nuclear CREB transcription factor by increasing Ca2+ concentrations within a nanodomain close to the channel, without requiring bulk Ca2+ increases in the cytosol or nucleus. However, the molecular basis for LTCC clustering is poorly understood. The postsynaptic scaffolding protein Shank3 specifically associates with one of the major neuronal LTCCs, the CaV1.3 calcium channel, and is required for optimal LTCC-dependent excitation-transcription coupling. Here, we co-expressed CaV1.3 1 subunits with two distinct epitope-tags with or without Shank3 in HEK cells. Co-immunoprecipitation studies using the cell lysates revealed that Shank3 can assemble multiple CaV1.3 1 subunits in a complex under basal conditions. Moreover, CaV1.3 LTCC complex formation was facilitated by CaV{beta} subunits ({beta}3 and {beta}2a), which also interact with Shank3. Shank3 interactions with CaV1.3 LTCCs and multimeric CaV1.3 LTCC complex assembly were disrupted following addition of Ca2+ and calmodulin (Ca2+/CaM) to cell lysates, perhaps simulating conditions within an activated CaV1.3 LTCC nanodomain. In intact HEK293T cells, co-expression of Shank3 enhanced the intensity of membrane-localized CaV1.3 LTCC clusters under basal conditions, but not after Ca2+ channel activation. Live cell imaging studies also revealed that Ca2+ influx through LTCCs disassociated Shank3 from CaV1.3 LTCCs clusters and reduced the CaV1.3 cluster intensity. Deletion of the PDZ domain from Shank3 prevented both binding to CaV1.3 and the changes in multimeric CaV1.3 LTCC complex assembly in vitro and in HEK293 cells. Finally, we found that shRNA knock-down of Shank3 expression in cultured rat primary hippocampal neurons reduced the intensity of surface-localized CaV1.3 LTCC clusters in dendrites. Taken together, our findings reveal a novel molecular mechanism contributing to neuronal LTCC clustering under basal conditions. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.10.20.513002v1?rss=1 Authors: Oliveira Mendes, B., Alameh, M., Ollivier, B., Montnach, J., Bidere, N., Souaze, F., Escriou, N., Charpentier, F., Baro, I., De Waard, M., Loussouarn, G. Abstract: Controversial reports have suggested that SARS-CoV E and 3a proteins may be viroporins that conduct currents through the plasma membrane of the infected cells. If true, these proteins would represent accessible targets for the development of new antiviral drugs by using high-throughput patch-clamp techniques. Here we aimed at better characterizing the cell responses induced by E or 3a protein with a particular focus on the ion conductances measured at the cell surface. First, we show that expression of SARS-CoV-2 E or 3a protein in CHO cells gives rise to cells with newly-acquired round shape, tending to detach from the Petri dish. This suggests that cell death is induced upon expression of E or 3a protein. We confirmed this hypothesis by using flow cytometry, in agreement with earlier reports on other cell types. In adhering cells expressing E or 3a protein, whole-cell currents were in fact not different from the control condition indicating that E and 3a proteins are not plasma membrane viroporins. In contrast, recording currents on detached cells uncovered outwardly-rectifying currents, much larger than those observed in control. The current characteristics are reminiscent of what was previously observed in cells expressing SARS-CoV-1 E or 3a proteins. Herein, we illustrate for the first time that carbenoxolone blocks these outward currents suggesting that they are conducted by pannexin channels, mostly likely activated by cell morphology change and/or cell death. Alongside we also demonstrate that truncation of the C-terminal PDZ binding motifs reduces the proportion of dying cells but does not prevent pannexin currents suggesting distinct pathways for cell death and pannexin currents induced by E and 3a proteins. We conclude that SARS-CoV-2 E and 3a proteins are not acting as viroporins expressed at the plasma membrane. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.09.27.509791v1?rss=1 Authors: Schaan Profes, M., Tiroumalechetty, A., Patel, N., Lauar, S. S., Sidoli, S., Kurshan, P. Abstract: Neurexins are highly-spliced transmembrane cell adhesion molecules that bind an array of partners via their extracellular domains. However, much less is known about the signaling pathways downstream of neurexin's largely-invariant intracellular domain. C. elegans contains a single neurexin gene that we have previously shown is required for presynaptic assembly and stabilization. To gain insight into the signaling pathways mediating neurexin's presynaptic functions, we endogenously tagged neurexin's intracellular domain with TurboID, a proximity ligation method, allowing us to isolate adjacent biotinylated proteins by streptavidin pull-down and mass spectrometry. We compared our experimental strain to a control strain containing neurexin still tagged with TurboID but in which neurexin's PDZ-binding motif was endogenously deleted, leading to its dissociation from presynaptic active zones. Using this approach we identified both known and novel intracellular interactors of neurexin, including active zone scaffolds, actin-binding proteins, signaling molecules, and mediators of RNA trafficking, protein synthesis and degradation, among others. Characterization of mutants for candidate neurexin interactors revealed that they recapitulate aspects of the nrx-1 mutant phenotype, suggesting they may be involved in neurexin signaling. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.09.27.509791v1?rss=1 Authors: Schaan Profes, M., Tiroumalechetty, A., Patel, N., Lauar, S. S., Sidoli, S., Kurshan, P. Abstract: Neurexins are highly-spliced transmembrane cell adhesion molecules that bind an array of partners via their extracellular domains. However, much less is known about the signaling pathways downstream of neurexin's largely-invariant intracellular domain. C. elegans contains a single neurexin gene that we have previously shown is required for presynaptic assembly and stabilization. To gain insight into the signaling pathways mediating neurexin's presynaptic functions, we endogenously tagged neurexin's intracellular domain with TurboID, a proximity ligation method, allowing us to isolate adjacent biotinylated proteins by streptavidin pull-down and mass spectrometry. We compared our experimental strain to a control strain containing neurexin still tagged with TurboID but in which neurexin's PDZ-binding motif was endogenously deleted, leading to its dissociation from presynaptic active zones. Using this approach we identified both known and novel intracellular interactors of neurexin, including active zone scaffolds, actin-binding proteins, signaling molecules, and mediators of RNA trafficking, protein synthesis and degradation, among others. Characterization of mutants for candidate neurexin interactors revealed that they recapitulate aspects of the nrx-1 mutant phenotype, suggesting they may be involved in neurexin signaling. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

The Electrix de retour en live au PDZ de Besançon ce vendredi 25 mars, Fontaines D.C., Working Man's… L'article Emission Sensation rock du mercredi 23 mars 2022 est apparu en premier sur Sensation Rock - webzine français.

Listen to the latest oncology-focused research published in this week's issue of Oncotarget, Volume 12, Issue 22. https://www.oncotarget.com/archive/v12/i22/ Research Paper (Cover) - “P10s-PADRE vaccine combined with neoadjuvant chemotherapy in ER-positive breast cancer patients induces humoral and cellular immune responses” https://doi.org/10.18632/oncotarget.28083 Research Paper - “Dishevelled-1 DIX and PDZ domain lysine residues regulate oncogenic Wnt signaling” https://doi.org/10.18632/oncotarget.28089 Research Paper - “THSB2 as a prognostic biomarker for patients diagnosed with metastatic pancreatic ductal adenocarcinoma” https://doi.org/10.18632/oncotarget.28099 Research Paper - “Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization” https://doi.org/10.18632/oncotarget.28092 Review - “Emerging approaches of wound healing in experimental models of high-grade oral mucositis induced by anticancer therapy” https://doi.org/10.18632/oncotarget.28091 Editorial - “Future directions for immunotherapy in meningioma treatment” https://doi.org/10.18632/oncotarget.27994 (PDF Download) Editorial - “Clinicopathological utility of human epidermal growth factor receptor 2 (HER2)-heterogeneity for next-generation treatments of triple-negative breast cancer” https://doi.org/10.18632/oncotarget.28007 (PDF Download) Keywords - cancer vaccine, dishevelled (DVL), next-generation sequencing (NGS), oral mucositis, meningioma, immunotherapy, HER2 low, pancreatic cancer, breast cancer, non-small cell lung cancer (NSCLC), colorectal cancer, cancer, science, research, oncology About Oncotarget Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com/ or connect with: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget LinkedIn - https://www.linkedin.com/company/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/oncotargetyoutube Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget Oncotarget is published by Impact Journals, LLC. Please visit https://www.impactjournals.com/ or connect with @ImpactJrnls Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

Perde-se o amigo mas não perde-se a piada. Será? No retorno do Papo de Zé a podosfera, debatemos os limites do humor, se eles de fato existem, o que é bom senso e o que está datado. Lembrando, ninguém no PdZ é humorista. Então, não nos processe. Participam desse episódio: Adriano Valério, Caio Cesar e Michele Magalhães Roteiro: Equipe PdZ Edição: Adriano Valério Arte: Andressa Cristine Vinheta: Brunno Vianna Isologo: Luan Alves Sigam as nossas redes sociais: twitter.com/papodeze instagram.com/papodezeoficial

O documentário "AmarElo: É tudo para ontem" lançado pela plataforma Netflix procurou contar um pouco da história do Brasil sob a perspectiva de artistas negros, falando de rap, samba, semana de arte moderna, escravidão e formação da cidade de São Paulo. Nesse episódio, o PdZ fala sobre o impacto da produção do Emicida e sua companhia, a Laboratório Fantasma. Participam desse episódio: Adriano Valério e Andressa Cristine Logo: Visiting Card Vinhetas: Brunno Vianna Roteiro e arte: Andressa Edição: Adriano Siga a gente nas rede: https://www.instagram.com/papodezeoficial https://www.facebook.com/papodezeoficial Se você é das antigas e prefere mandar um e-mail: podcastpapodeze@gmail.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.11.378240v1?rss=1 Authors: Sanders, S. S., Hernandez, L. M., Soh, H., Karnam, S., Walikonis, R. S., Tzingounis, A., Thomas, G. M. Abstract: The palmitoyl acyltransferase (PAT) ZDHHC14 is highly expressed in the hippocampus and is the only PAT predicted to bind Type I PDZ domain-containing proteins. However, ZDHHC14's neuronal roles are unknown. Here, we identify the PDZ domain-containing Membrane-associated Guanylate Kinase (MaGUK) PSD93 as a direct ZDHHC14 interactor and substrate. PSD93, but not other MaGUKs, localizes to the Axon Initial Segment (AIS). Using lentiviral-mediated shRNA knockdown in rat hippocampal neurons, we find that ZDHHC14 controls palmitoylation and AIS clustering of PSD93 and also of Kv1 potassium channels, which directly bind PSD93. Neurodevelopmental expression of ZDHHC14 mirrors that of PSD93 and Kv1 channels and, consistent with ZDHHC14's importance for Kv1 channel clustering, loss of ZDHHC14 decreases outward currents and increases action potential firing in hippocampal neurons. To our knowledge, these findings identify the first neuronal roles and substrates for ZDHHC14 and reveal a previously unappreciated role for palmitoylation in control of neuronal excitability. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.12.336461v1?rss=1 Authors: Herborg, F., Jensen, K. L., Tolstoy, S., Arends, N. V., Posselt, L. P., Shekar, A., Aguilar, J., Lund, V. K., Erreger, K., Rickhag, M., Lycas, M. D., Lonsdale, M. N., Rahbek-Clemmensen, T., Sorensen, A. T., Newman, A. H., Loekkegaard, A., Kjaerulff, O., Werge, T., Moeller, L. B., Matthies, H. J., Galli, A., Hjermind, L. E., Gether, U. Abstract: Dopaminergic dysfunction is central to movement disorders and mental diseases. The dopamine transporter (DAT) is essential for the regulation of extracellular dopamine but the genetic and mechanistic link between DAT function and dopamine-related pathologies remains elusive. Particularly, the pathophysiological significance of monoallelic missense mutations in DAT is unknown. Here we identify a novel coding DAT variant, DAT-K619N, in a patient with early-onset parkinsonism and comorbid neuropsychiatric disease and in 22 individuals from exome-sequenced samples of neuropsychiatric patients. The variant localizes to the critical C-terminal PDZ-binding motif of DAT and causes reduced uptake capacity, decreased surface expression, and accelerated turnover of DAT in vitro. In vivo, we demonstrate that expression of DAT-K619N in mice and dropsophila imposes impairments in dopamine transmission with accompanying changes in dopamine-directed behaviors. Importantly, both cellular studies and viral overexpression of DAT-K619N in mice show that DAT-K619N has a dominant-negative effect which collectively implies that a single dominant-negative genetic DAT variant can confer risk for neuropsychiatric disease and neurodegenerative early-onset parkinsonism. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.06.327742v1?rss=1 Authors: Kliche, J., Ali, M., Ivarsson, Y. Abstract: The spike protein of the SARS-CoV-2 interacts with angiotensin converting enzyme 2 (ACE2) and enters the host cell by receptor-mediated endocytosis. Concomitantly, evidence is pointing to the involvement of additional host cell receptors, such as integrins. The cytoplasmic tails of ACE2 and integrin beta3 contain a plethora of predicted binding motifs. Here, we confirm the functionality of some of these motifs through affinity measurements. The class I PDZ binding motif in the ACE2 cytoplasmic tail binds the first PDZ domain of the scaffold protein NHERF3. The clathrin-adaptor subunit AP2 Mu2 interacts with an endocytic motif in the ACE2 with low affinity and the interaction is abolished by phosphorylation of Tyr781. Furthermore, the C-terminal region of integrin beta3 contains a LC3-interacting region, and its interaction with ATG8 domains is enhanced by phosphorylation. Together, our data provides possible molecular links between host cell receptors and endocytosis and autophagy Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.06.328617v1?rss=1 Authors: Stevens, A. O., He, Y. Abstract: The PDZ domain is a highly abundant protein-protein interaction domain that exists in many signaling proteins, such as PICK1. Despite the highly conserved structure of the PDZ family, the PDZ family has an extremely low sequence identity, making each PDZ domain unique. PICK1 is the only protein in the human genome that is comprised of a PDZ domain and a BAR domain. PICK1 regulates surface membrane proteins and has been identified as an integral player in drug addiction. Like many PDZ-containing proteins, PICK1 is positively regulated by its PDZ domain and has thus drawn attention to be a potential drug target to curb the effects of substance abuse. The goal of this study is to use all-atom molecular dynamics simulations and the electrostatic analysis program, DelPhi, to better understand the unique interactions and dynamic changes in the PICK1 PDZ domain upon complex formation. Our results demonstrated that the PICK1 PDZ domain shares similar canonical PDZ-ligand hydrogen bonding networks and fluctuations of the carboxylate-binding loop to other PDZ domains. Furthermore, our results are unique to the PICK1 PDZ domain as we reveal that the binding of ligand opens up the binding pocket and, at the same time, reduces the fluctuations of both the central part of the binding pocket and the short loop region between the A-helix and {beta}C-strand. More importantly, the binding of ligand resulted in charge redistribution at the binding pocket region as well as the N- and C-termini of the PDZ domain that are not a part of the binding pocket. These results suggest that the electrostatic allostery resulted from ligand binding could be the key factor leading to the changes in dynamics which may be associated with the activation of PICK1. Based on these results, an effective drug to target PDZ domain must not only stably bind to the PICK1 PDZ domain but also prevent the electrostatic allostery of the PDZ domain. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.28.317172v1?rss=1 Authors: Ear, J., Ali Abd El-Hafeez, A., Roy, S., Ngo, T., Rajapakse, N., Choi, J., Khandelwal, S., Ghassemian, M., McCaffrey, L., Kufareva, I., Sahoo, D., Ghosh, P. Abstract: PDZ domains are one of the most abundant protein domains in eukaryotes and frequently found on junction-localized scaffold proteins. Various signaling molecules bind to PDZ proteins via PDZ-binding motifs (PBM) and finetune cellular signaling. Here we describe the presence of a PBM on GIV/Girdin (CCDC88A) that is conserved throughout evolution, from invertebrates to vertebrates, and is generated as a long isoform-variant in humans, which we named GIV-L. Unlike GIV, which lacks PBM and is cytosolic, GIV-L localizes to the cell junctions, and has a unique PDZ-interactome, which impacts GIV-L's ability to bind and activate trimeric G-protein, Gi through its guanine-nucleotide exchange modulator (GEM) module; the GEM module is found exclusively in vertebrates. Thus, the two functional modules in GIV evolved sequentially: the ability to bind PDZ proteins via the PBM evolved earlier in invertebrates, whereas G-protein binding and activation may have evolved later only among vertebrates. Phenotypic studies in Caco-2 cells revealed that GIV and GIV-L may have antagonistic effects on cell growth, proliferation (cell cycle), and survival. Immunohistochemical analyses in human colon tissues showed that GIV expression increases with a concomitant decrease in GIV-L during cancer initiation. Taken together, these findings reveal how GIV/CCDC88A in humans displays evolutionary flexibility in modularity, which allows the resultant isoforms to play opposing roles either as a tumor suppressor (GIV-L) or as an oncogene (GIV). Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.24.264226v1?rss=1 Authors: Guclu, T. F., Kocatug, N., Atilgan, A. R., ATILGAN, C. Abstract: PDZ domains constitute common models to study single domain allostery without significant structural changes. The third PDZ domain of PSD-95 (PDZ3) is known to have selective structural features that confer unique modulatory roles to this unit. In this model system two residues, H372 directly connected to the binding site and G330 holding an off-binding-site position, were designated to assess the effect of mutations on binding selectivity. It has been observed that the H372A and G330T/H372A mutations change ligand preferences from class I (T/S amino acid at position -2 of the ligand) to class II (hydrophobic amino acid at the same position). Alternatively, the G330T single mutation leads to the recognition of both ligand classes. We have performed a series of molecular dynamics (MD) simulations for wild-type, H372A, G330T single mutants and a double mutant of PDZ3 in the absence and presence of both types of ligands. With the combination of free energy difference calculations and a detailed analysis of MD trajectories, "class switching" and "class bridging" behavior of PDZ3 mutants, as well as their effects on ligand selection and binding affinities are explained. We show that the dynamics of the charged N-terminus plays a fundamental role in determining the binding preferences in PDZ3 by altering the electrostatic energy. These findings are corroborated by simulations on N-termini truncated versions of these systems. The dynamical allostery orchestrated by the N-terminus offers a fresh perspective to the study of communication pathways in proteins. Copy rights belong to original authors. Visit the link for more info

O podcast Caminhos do Brasil desta semana trata de um dos setores mais resilientes durante a pandemia: o portuário. O secretário nacional de portos e transportes aquaviários, Diogo Piloni, fala das medidas adotadas durante a crise, da alta na movimentação do último semestre, da aprovação do PDZ de Santos, do BR do Mar, além do extenso cronograma de concessões previsto para 2020. Não perca! Edição: Guilherme Baldi Arte: Vinicius Rosa

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.24.220376v1?rss=1 Authors: Gogl, G., Tugaeva, K. V., Eberling, P., Kostmann, C., Trave, G., Sluchanko, N. N. Abstract: In tumors induced by high-risk mucosal human papillomaviruses (hrm-HPVs), HPV E6 oncoproteins inhibit apoptotic processes and sustain cell proliferation. E6 from all hrm-HPVs harbor a C-terminal short PDZ domain-binding motif (PBM), whose phosphorylation down-regulates PDZ binding but triggers E6 binding to 14-3-3 proteins. Here we classify PBMs of E6 proteins depending on their principle ability to be phosphorylated and subsequently acquire a 14-3-3-binding motif III consensus, (pS/pT)XX-COOH. Systematic competitive fluorescence polarization measurements show that the PBMs from four selected E6 oncoproteins bind all seven human 14-3-3 isoforms with distinct, wide-ranging affinities, obeying remarkable trends assigned to 14-3-3 isoform specificity and small E6 sequence variations. We crystallized the hrm-HPV18 E6 PBM bound to 14-3-3{zeta}, revealing a 14-3-3-motif III complex at 1.9 [A] resolution. Using fluorescence polarization and crystallography, we also demonstrate that fusicoccin, a molecule that reinforces many known 14-3-3 complexes, destabilizes the 14-3-3-E6 interaction, indicating the druggability of that complex. Copy rights belong to original authors. Visit the link for more info

Fundação Settaport e RBA Litoral, promovem um debate virtual para discutir o novo PDZ do Porto de Santos. "A Cidade que temos e o Porto que Queremos".

O vereador Chico Nogueira explica as consequências do PDZ , Plano de Desenvolvimento e Zoneamento do Porto de Santos.

Muita gente tem se pergutando como fica o Enem com a pandemia... mas e a educação como um todo? Até que ponto a pandemia afetou a forma e a qualidade da educação brasileira? Acompanhe a discussão nessa grande mesa de bar virtual que é o PDZ! Edição: Equipe PdZ | Logomarca: Visiting Card | instagram.com/papodezeoficial | facebook.com/papodezeoficial | twitter.com/papodeze | podcastpapodeze@gmail.com

A pauta agora é o porto de Santos e a qualidade de vida dos santistas. Em questão, o novo Plano de Desenvolvimento e Zoneamento do Porto, o PDZ. Moradores da Ponta da Praia reclamam de problemas desencadeados pelo cais. Para falar mais sobre esse assunto, recebemos o Luiz Antônio da Silva, presidente da Sociedade de Melhoramentos da Ponta da Praia.

Hoje, às 15h, na Câmara Municipal de Santos, acontecerá uma audiência pública para debater sobre o novo Plano de Desenvolvimento do Zoneamento do porto, o PDZ. Para falar mais sobre esse evento, conversamos com o vereador santista Chico Nogueira.

The success of acrosomal exocytosis, a complex process with a variety of inter-related steps, relies on the coordinated interaction of participating signaling molecules. Since the acrosome reaction resembles Ca(2+)-regulated exocytosis in neurons, we investigated whether cognate neuronal binding partners of the multi-PDZ domain protein MUPP1, which recruits molecules that control the initial tethering and/or docking between the acrosomal vesicle and the plasma membrane, are also expressed in spermatozoa, and whether they contribute to the regulation of acrosomal secretion. We observed that CaMKIIalpha colocalizes with MUPP1 in the acrosomal region of epididymal spermatozoa where the kinase selectively binds to a region encompassing PDZ domains 10-11 of MUPP1. Furthermore, we found that pre-treating mouse spermatozoa with a CaMKII inhibitor that directly blocks the catalytic region of the kinase, as well as a competitive displacement of CaMKIIalpha from PDZ domains 10-11, led to a significant increase in spontaneous acrosomal exocytosis. Since Ca(2+)-calmodulin releases CaMKIIalpha from the PDZ scaffolding protein, MUPP1 represents a central signaling platform to dynamically regulate the assembly and disassembly of binding partners pertinent to acrosomal secretion, thereby precisely adjusting an increase in Ca(2+) to synchronized fusion pore formation.

In episode 28 of This Week in Virology, hosts Vincent Racaniello, Alan Dove, Dick Despommier, and Eric F. Donaldson discuss a new test for influenza H5N1, poliovirus in Minnesota, Koala retrovirus, batteries made from viruses, and SARS. Links for this episode: New rapid test for influenza H5N1 based on PDZ binding. Definition of ELISA. Poliovirus isolated from Minnesotan (article 1 and 2) Koala retrovirus: Japan story and review article Batteries made from viruses (cathode and anode). Image of phage M13. iMoleBuilder (iTunes link and review at Sunset Lake Software) Discovery of Norwalk virus Regulatin’ Genes (YouTube link) Science blog of the week: The Great Beyond by Nature Science podcast pick of the week: Sorting Out Science Science book of the week: A Slot Machine, A Broken Test Tube by S.E. Luria (out of print - check your library)

Idiopathic Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimers disease. The specific molecular events that provoke neurodegeneration in PD are still unknown, which is an impediment to the development of neuroprotective drugs. Only recently, genes linked to hereditary forms of PD have been identified. Idiopathic and hereditary variants of PD share important pathological features, most notably the demise of dopaminergic neurons in the substantia nigra. Functional characterization of PD-associated gene products might help to understand the molecular mechanisms underlying the pathogenesis and maybe, in the future, to find preventive and curative treatments for PD. Among the mutated genes is the parkin gene (PARK2), encoding a E3 ubiquitin ligase. Mutations in the parkin gene are responsible for the majority of autosomal recessive parkinsonism. Previous work of our group revealed that misfolding and aggregation of parkin is a major mechanism of parkin inactivation, accounting for the loss-of-function phenotype of various pathogenic parkin mutants, including C-terminal deletion mutants and some missense mutants [1,2]. Remarkably, also wildtype parkin is prone to misfolding under certain cellular conditions, suggesting a more general role of parkin in the pathogenesis of PD. One aim of this thesis was to study the folding characteristics of parkin. To this end, I cloned several parkin mutants and analyzed them in cell-culture based assays to determine their folding properties. Folding analysis of these mutants revealed that pathogenic mutations can lead to aberrant parkin conformers with two distinct phenotypes. One class of mutations destabilized the native conformation of parkin, leading to its proteasomal degradation immediately after synthesis. Another class of mutants first adopted a detergent-soluble conformation, similarly to wildtype parkin. However, within hours these mutants formed relatively stable detergent-insoluble aggregates. A comparative analysis of HHARI, an E3 ubiquitin ligase with a similar modular signature, revealed that folding of parkin is specifically dependent on the integrity of the C-terminal domain, but not on the presence of a putative PDZ binding motif at the extreme C-terminus. This study provided new insight into the propensity of parkin to misfold and suggested that pathogenic mutations can induce the formation of non-native conformers at distinct steps in the folding pathway of parkin. Another focus of this thesis was the functional characterization of parkin. We and others observed that parkin protects neurons against diverse cellular insults in different model systems, indicating that it may play a role in maintaining neuronal integrity. To address the underlying mechanism, we analyzed the effect of parkin on different signaling pathways. Our results revealed that parkin has a permissive effect on NFkappaB signaling by ubiquitylating two components of the signaling cascade in a non-degradative manner. Notably, parkin lost its neuroprotective capacity in the presence of a dominant negative inhibitor of NFkappaB. In addition, we could show that parkin expression is significantly up-regulated in neurons under stress conditions, indicating that parkin is a stress-responsive protein.

I am getting Perfect Dark Zero as an Xmas present and I am going online to play with some with you all. We will also cover a few gamers playing PDZ with me as well by turning on the headset and talking to each other, and you will hear what is said on the headset! The release is somewhere next week, but take a look at this VIDEO preview of our next episode!

Various stimuli like thrombin induce endothelial cell shape change and stress fiber formation via Rho/Rho-kinase-mediated reorganization of the actin cytoskeleton. LIM-kinases regulate actin cytoskeletal reorganization through phosphorylation of cofilin at Ser3. The LIMK family kinases possess characteristic structural features, consisting of two LIM domains, a PDZ domain and a C-terminal kinase domain. In cell transfection studies it has been shown that LIMK2 is phosphorylated at Thr505 by Rho-kinase thereby activating the enzyme. Recently it has been reported that nuclear LIMKs suppress cyclin D1 expression in a manner independent of cofilin phosphorylation and actin polymerization. In this study, we found that endothelial cells express both LIMK1 and LIMK2. By using live cell imaging, we confirm previous findings that thrombin induces stress fiber formation, ruffle formation and cell contraction. Furthermore, the cell-cell contacts were disrupted and F-actin fibers connecting two cells were broken. Thrombin induced a rapid and sustained Rho-kinase activation and subsequent phosphorylation of LIM-kinase and cofilin. Pretreatment of endothelial cells with the specific Rho-kinase inhibitor Y27632 inhibited MYPT1 phosphorylation, LIM-kinase and cofilin phosphorylation and blocked stress fiber formation in thrombin-stimulated cells. Notably, thrombin induced actin stress fiber formation was abolished in cells transfected with dominant negative LIMK2. LIMK2 was mainly localized in the cytoplasm. By using Leptomycin B (a specific inhibitor of CRM-1 dependent nuclear export) and FRAP and FLIP analysis, we demonstrate that LIMK2 in resting endothelial cells shuttles between the nucleus and cytoplasm. The LIM domains of LIMK2, but not of LIMK1 inhibited its nuclear import thereby keeping LIMK2 mainly in the cytoplasm. Mutational analysis of the unique basic amino acid-rich motif (amino acids 480-503) indicated that this motif regulates the nuclear and nucleolar localization of LIMK2. Activation of PKC in PMA-stimulated endothelial cells stimulated the phosphorylation of LIMK2 at Ser283 and the translocation of LIMK2 and the PDZ-kinase construct of LIMK2 from the nucleus to the cytoplasm. Of the various PKC isoforms, PKC- and PKC- were found to be mainly responsible for Ser283 phosphorylation and the regulation of translocation of LIMK2. Mutational analysis indicated that LIMK2 phosphorylation at Ser283 and Thr494 play a role in the regulation of nucleocytoplasmic shuttling of LIMK2 by PKC. These results show that LIM-kinase activation is mediated by Rho-kinase in stimulated endothelial cells, and that LIM-kinase-mediated cofilin phosphorylation plays an essential role in thrombin-induced stress fiber formation. LIMK2 shuttles between nucleus and cytoplasm in resting endothelial cells. Phosphorylation of LIMK2 at Ser283 and Thr494 by PKC regulates nucleocytoplasmic shuttling and suggests that LIMK2 might also have a function in the nucleus such as the suppression of cyclin D1 expression.

Eph receptors and their membrane associated ephrin ligands mediate cell-cell repulsion to guide migrating cells and axons. A peculiarity of this signaling system is that both receptors and ligands can transduce signals into the cell resulting in a bidirectional signaling mode. An important step of ephrinB ligand ‘reverse signaling’ is the regulated tyrosine phosphorylation of the cytoplasmic domain, initiating docking sites for downstream signaling adaptors. Moreover, ephrinB ligands can signal by interactions with various PDZ-domain containing proteins. Using a broad range of in vitro assays the presented work demonstrates that upon binding to their cognate receptor, ephrinB ligands rapidly activate Src family kinases (SFKs) which subsequently phosphorylate ephrinB. Tyrosine phosphorylation appears to be a transient event that is downregulated by the tyrosine phosphatase PTP-BL, which interacts with ephrinB via one of its PDZ-domains. Studies on PTP-BL and another multiple PDZ domain containing protein GRIP (Glutamate Receptor Interacting Protein) revealed that PDZ interactions with ephrinB are also regulated by EphB receptor binding but, unlike tyrosine phosphorylation, these interactions are long lasting. These findings led to postulate a ‘switch model’ for ephrinB reverse signaling: Tyrosine dependent signaling appears to be a rapid and transient event which is later replaced by stable PDZ-dependent signaling. EphB ‘forward’ signaling as well as ephrinB ‘reverse’ signaling are important for axonal pathfinding and cell migration during development. Prior to their repellent effect on migrating cells and growth cones, Eph receptors form a high affinity complex with their ligands at sites of cell-cell contact. Therefore, mechanisms have to be in place that allow cells to detach from each other permitting retraction and withdrawal. To overcome this adhesive barrier, the ectodomain of ephrinA ligands is cleaved by metalloproteinases and shed upon receptor binding. Intrigued by the previous findings that activated ephrins cluster in cells, we hypothesized that these Eph/ephrin clusters undergo endocytosis. We developed immunofluorescence internalization and co-culture assays to study clustering and endocytosis at cell-cell contact sites. We established an experimental setup to perform fast time lapse imaging studies of cells expressing different fluorescently tagged proteins. Cell contact-induced ephrinB-EphB complexes are rapidly endocytosed during the retraction of cells and neuronal growth cones. Endocytosis occurs in a bidirectional manner, leading to internalized complexes of full length receptor and ligand, a yet rarely observed phenomenon. Signaling inactive mutants of EphB receptors and ephrinB ligands lead to a strong adhesion between cells. Endocytosis is sufficient to convert this adhesion into the detachment of cells. Bidirectional endocytosis is necessary to efficiently promote axon detachment during growth cone collapse mediated by ephrinB ligands. On the cell biological level, bidirectional endocytosis of two full length transmembrane (TM) proteins is a new phenomenon. Moreover, these studies reveal a novel mechanism of signal termination, de-adhesion and promotion of cell repulsion after intercellular (trans) interaction between two TM proteins.