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1.
Int J Mol Sci ; 25(15)2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39125895

ABSTRACT

The branched architecture of neuronal dendrites is a key factor in how neurons form ordered networks and discoveries continue to be made identifying proteins and protein-protein interactions that direct or execute the branching and extension of dendrites. Our prior work showed that the molecular scaffold Pdlim5 and delta-catenin, in conjunction, are two proteins that help regulate the branching and elongation of dendrites in cultured hippocampal neurons and do so through a phosphorylation-dependent mechanism triggered by upstream glutamate signaling. In this report we have focused on Pdlim5's multiple scaffolding domains and how each contributes to dendrite branching. The three identified regions within Pdlim5 are the PDZ, DUF, and a trio of LIM domains; however, unresolved is the intra-molecular conformation of Pdlim5 as well as which domains are essential to regulate dendritic branching. We address Pdlim5's structure and function by examining the role of each of the domains individually and using deletion mutants in the context of the full-length protein. Results using primary hippocampal neurons reveal that the Pdlim5 DUF domain plays a dominant role in increasing dendritic branching. Neither the PDZ domain nor the LIM domains alone support increased branching. The central role of the DUF domain was confirmed using deletion mutants in the context of full-length Pdlim5. Guided by molecular modeling, additional domain mapping studies showed that the C-terminal LIM domain forms a stable interaction with the N-terminal PDZ domain, and we identified key amino acid residues at the interface of each domain that are needed for this interaction. We posit that the central DUF domain of Pdlim5 may be subject to modulation in the context of the full-length protein by the intra-molecular interaction between the N-terminal PDZ and C-terminal LIM domains. Overall, our studies reveal a novel mechanism for the regulation of Pdlim5's function in the regulation of neuronal branching and highlight the critical role of the DUF domain in mediating these effects.


Subject(s)
Dendrites , Hippocampus , LIM Domain Proteins , PDZ Domains , Dendrites/metabolism , Animals , Hippocampus/metabolism , Hippocampus/cytology , LIM Domain Proteins/metabolism , LIM Domain Proteins/chemistry , LIM Domain Proteins/genetics , Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/chemistry , Adaptor Proteins, Signal Transducing/genetics , Protein Domains , Neurons/metabolism , Rats , Cells, Cultured , Humans
2.
J Am Chem Soc ; 146(26): 17974-17985, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38957136

ABSTRACT

The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of peptides binding to a PDZ domain and fragment ligands binding to the protein PIN1. The method can also be extended to measure the affinity of nonphoto-CIDNP-polarizable ligands in competition binding experiments. Finally, we demonstrate a strong correlation between the ligand-reduced signals in photo-CIDNP-based NMR fragment screening and the well-established saturation transfer difference (STD) NMR. Thus, our methodology measures protein-ligand affinities in the micro- to millimolar range in only a few minutes and informs on the binding epitope in a single-scan experiment, opening new avenues for early stage drug discovery approaches.


Subject(s)
Nuclear Magnetic Resonance, Biomolecular , Ligands , Protein Binding , Photochemical Processes , NIMA-Interacting Peptidylprolyl Isomerase/metabolism , NIMA-Interacting Peptidylprolyl Isomerase/chemistry , Proteins/chemistry , Proteins/metabolism , Peptides/chemistry , Peptides/metabolism , Magnetic Resonance Spectroscopy/methods , Models, Molecular , PDZ Domains
3.
Nat Commun ; 15(1): 6068, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39025931

ABSTRACT

Neurexins are key adhesion proteins that coordinate extracellular and intracellular synaptic components. Nonetheless, the low abundance of these multidomain proteins has complicated any localization and structure-function studies. Here we combine an ALFA tag (AT)/nanobody (NbALFA) tool with classic genetics, cell biology and electrophysiology to examine the distribution and function of the Drosophila Nrx-1 in vivo. We generate full-length and ΔPDZ ALFA-tagged Nrx-1 variants and find that the PDZ binding motif is key to Nrx-1 surface expression. A PDZ binding motif provided in trans, via genetically encoded cytosolic NbALFA-PDZ chimera, fully restores the synaptic localization and function of NrxΔPDZ-AT. Using cytosolic NbALFA-mScarlet intrabody, we achieve compartment-specific detection of endogenous Nrx-1, track live Nrx-1 transport along the motor neuron axons, and demonstrate that Nrx-1 co-migrates with Rab2-positive vesicles. Our findings illustrate the versatility of the ALFA system and pave the way towards dissecting functional domains of complex proteins in vivo.


Subject(s)
Drosophila Proteins , Single-Domain Antibodies , Animals , Drosophila Proteins/metabolism , Drosophila Proteins/genetics , Single-Domain Antibodies/metabolism , Drosophila melanogaster/metabolism , Motor Neurons/metabolism , PDZ Domains , Axons/metabolism , Neural Cell Adhesion Molecules/metabolism , Neural Cell Adhesion Molecules/genetics , Protein Transport , Cell Adhesion Molecules, Neuronal
4.
Phys Chem Chem Phys ; 26(31): 21249-21259, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39076021

ABSTRACT

While allosteric signal transduction is crucial for protein signaling and regulation, the dynamic process of allosteric communication remains poorly understood. The third PDZ domain (PDZ stands for the common structural domain shared by the postsynaptic density protein (PSD95), Drosophila disc large tumor suppressor (DlgA), and zonula occludens-1 protein (ZO-1)) serves as a classic example of a single-domain allosteric protein, demonstrating a long-range coupling between the C-terminal α helix (known as the α3 helix) and ligand binding. A molecular level understanding of how the α3 helix modulates the ligand binding affinity of the PDZ3 domain is still lacking. In this study, extensive molecular dynamics simulations corroborated with principal component analysis (PCA), ligand binding free energy calculations, energetic frustration analysis and Markov state model analysis are employed to uncover such molecular details. We demonstrate the definite presence of a binding competent closed-like state in the conformational landscape of wild-type PDZ3. The population modulations of this closed state and other binding incompetent states in the landscape due to α3-truncation/mutation of PDZ3 are explored. A correlation between the closed state population and calculated binding free energy is established, which supports the conformation selection mechanism. Covariance analysis identified the presence of correlated motion between two distant loops (ß1-ß2 and ß2-ß3) in the wild-type PDZ3 system, which weakened due to truncation/mutation in the distant α3 helix. It has also been observed that whenever the α3 helix was perturbed, the ß2-ß3 loop got further away from the binding groove and it is found to be correlated with the binding free energy values. Energetic frustration analysis of the PDZ3 domain also showed that the ß2-ß3 loop is highly frustrated. Finally, MSM analysis revealed a relevant timescale (closed to open state transition), which is similar to the observed experimental signal transduction timescale for the system. These observations led to the conclusion that the distantly located α3 helix plays a pivotal role in regulating the conformational landscape of the PDZ3 domain, determining the ligand binding affinity and resulting in allosteric behavior of the domain.


Subject(s)
Molecular Dynamics Simulation , PDZ Domains , Allosteric Regulation , Protein Binding , Thermodynamics , Principal Component Analysis , Ligands , Protein Conformation
5.
Biochem J ; 481(14): 945-955, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-38899489

ABSTRACT

The PDZ (Postsynaptic density protein-95[PSD-95]/Discs-large) domain, prevalent as a recognition module, has attracted significant attention given its ability to specifically recognize ligands with consensus motifs (also termed PDZ binding motifs [PBMs]). PBMs typically bear a C-terminal carboxylate as a recognition handle and have been extensively characterized, whilst internal ligands are less well known. Here we characterize a short linear motif (SLiM) - EESTSFQGP - as an internal PBM based on its strong binding affinity towards the SHANK1 PDZ domain (SHANK1656-762 hereafter referred to as SHANK1). Using the acetylated analogue Ac-EESTSFQGP-CONH2 as a competitor for the interaction of SHANK1 with FAM-Ahx-EESTSFQGP-CONH2 or a typical fluorophore-labelled C-terminal PBM - GKAP - FITC-Ahx-EAQTRL-COOH - the internal SLiM was demonstrated to show comparable low-micromolar IC50 by competition fluorescent anisotropy. To gain further insight into the internal ligand interaction at the molecular level, we obtained the X-ray co-crystal structure of the Ac-EESTSFQGP-CONH2/SHANK1 complex and compared this to the Ac-EAQTRL-COOH/SHANK1 complex. The crystallographic studies reveal that the SHANK1 backbones for the two interactions overlap significantly. The main structural differences were shown to result from the flexible loops which reorganize to accommodate the two PBMs with distinct lengths and terminal groups. In addition, the two C-terminal residues Gly and Pro in Ac-EESTSFQGP-CONH2 were shown not to participate in interaction with the target protein, implying further truncation and structural modification using peptidomimetic approaches on this sequence may be feasible. Taken together, the SLiM Ac-EESTSFQGP-CONH2 holds potential as an internal ligand for targeting SHANK1.


Subject(s)
Nerve Tissue Proteins , PDZ Domains , Protein Binding , Nerve Tissue Proteins/chemistry , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Crystallography, X-Ray , Humans , Ligands , Animals , Amino Acid Sequence , Amino Acid Motifs , Binding Sites
6.
J Virol ; 98(7): e0073524, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38874360

ABSTRACT

Oncogenic HPV E6 proteins have a PDZ-binding motif (PBM) which plays important roles in both the viral life cycle and tumor development. The PBM confers interaction with a large number of different PDZ domain-containing substrates, one of which is Sorting Nexin 27. This protein is part of the retromer complex and plays an important role in endocytic sorting pathways. It has been shown that at least two SNX27 interacting partners, GLUT1 and TANC2, are aberrantly trafficked due to the E6 PBM-dependent interaction with SNX27. To investigate further which other components of the endocytic trafficking pathway might be affected by the SNX27-HPV E6 interaction, we analyzed the SNX27 proteome interaction profile in a previously described HeLa cell line expressing GFP-SNX27, both in the presence and absence of the HPV-18 E6 oncoprotein. In this study, we identify a novel interacting partner of SNX27, secreted glycoprotein EMILIN2, whose release is blocked by HPV18 E6 in a PBM-dependent manner. Mechanistically, E6 can block EMILIN2 interaction with the WNT1 ligand, thereby enhancing WNT1 signaling and promoting cell proliferation. IMPORTANCE: This study demonstrates that HPV E6 blocks EMILIN2 inhibition of WNT1 signaling, thereby enhancing cell proliferation in HPV-positive tumor cells. This involves a novel mechanism whereby the E6 PBM actually contributes toward enhancing the interaction between SNX27 and EMILIN2, suggesting that the mode of recognition of SNX27 by E6 and EMILIN2 is different. This is the first example of the E6 PBM altering a PDZ domain-containing protein to enhance potential substrate recognition.


Subject(s)
Human papillomavirus 18 , Oncogene Proteins, Viral , Sorting Nexins , Wnt Signaling Pathway , Humans , Sorting Nexins/metabolism , Sorting Nexins/genetics , Oncogene Proteins, Viral/metabolism , Oncogene Proteins, Viral/genetics , HeLa Cells , Human papillomavirus 18/metabolism , Human papillomavirus 18/genetics , Protein Binding , Repressor Proteins/metabolism , Repressor Proteins/genetics , PDZ Domains , HEK293 Cells , Papillomavirus Infections/virology , Papillomavirus Infections/metabolism , DNA-Binding Proteins
7.
Sci Rep ; 14(1): 13059, 2024 06 06.
Article in English | MEDLINE | ID: mdl-38844490

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 has highlighted the urgent need for innovative antiviral strategies to fight viral infections. Although a substantial part of the overall effort has been directed at the Spike protein to create an effective global vaccination strategy, other proteins have also been examined and identified as possible therapeutic targets. Among them, although initially underestimated, there is the SARS-CoV-2 E-protein, which turned out to be a key factor in viral pathogenesis due to its role in virus budding, assembly and spreading. The C-terminus of E-protein contains a PDZ-binding motif (PBM) that plays a key role in SARS-CoV-2 virulence as it is recognized and bound by the PDZ2 domain of the human tight junction protein ZO-1. The binding between the PDZ2 domain of ZO-1 and the C-terminal portion of SARS-CoV-2 E-protein has been extensively characterized. Our results prompted us to develop a possible adjuvant therapeutic strategy aimed at slowing down or inhibiting virus-mediated pathogenesis. Such innovation consists in the design and synthesis of externally PDZ2-ZO1 functionalized PLGA-based nanoparticles to be used as intracellular decoy. Contrary to conventional strategies, this innovative approach aims to capitalize on the E protein-PDZ2 interaction to prevent virus assembly and replication. In fact, the conjugation of the PDZ2 domain to polymeric nanoparticles increases the affinity toward the E protein effectively creating a "molecular sponge" able to sequester E proteins within the intracellular environment of infected cells. Our in vitro studies on selected cellular models, show that these nanodevices significantly reduce SARS-CoV-2-mediated virulence, emphasizing the importance of exploiting viral-host interactions for therapeutic benefit.


Subject(s)
Nanoparticles , PDZ Domains , SARS-CoV-2 , Humans , SARS-CoV-2/drug effects , SARS-CoV-2/metabolism , Nanoparticles/chemistry , COVID-19/virology , COVID-19/metabolism , Zonula Occludens-1 Protein/metabolism , Coronavirus Envelope Proteins/metabolism , Coronavirus Envelope Proteins/chemistry , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , COVID-19 Drug Treatment , Animals , Protein Binding
8.
Protein Eng Des Sel ; 372024 Jan 29.
Article in English | MEDLINE | ID: mdl-38757573

ABSTRACT

With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.


Subject(s)
Algorithms , Peptides , Peptides/chemistry , Peptides/pharmacology , Humans , Drug Design , PDZ Domains
9.
Nat Commun ; 15(1): 4592, 2024 May 30.
Article in English | MEDLINE | ID: mdl-38816423

ABSTRACT

The mitochondrial serine protease HtrA2 is a human homolog of the Escherichia coli Deg-proteins exhibiting chaperone and proteolytic roles. HtrA2 is involved in both apoptotic regulation via its ability to degrade inhibitor-of-apoptosis proteins (IAPs), as well as in cellular maintenance as part of the cellular protein quality control machinery, by preventing the possible toxic accumulation of aggregated proteins. In this study, we use advanced solution NMR spectroscopy methods combined with biophysical characterization and biochemical assays to elucidate the crucial role of the substrate recognizing PDZ domain. This domain regulates the protease activity of HtrA2 by triggering an intricate allosteric network involving the regulatory loops of the protease domain. We further show that divalent metal ions can both positively and negatively modulate the activity of HtrA2, leading to a refined model of HtrA2 regulation within the apoptotic pathway.


Subject(s)
Apoptosis , High-Temperature Requirement A Serine Peptidase 2 , PDZ Domains , High-Temperature Requirement A Serine Peptidase 2/metabolism , High-Temperature Requirement A Serine Peptidase 2/genetics , Humans , Allosteric Regulation , Substrate Specificity , Mitochondria/metabolism , Models, Molecular , Magnetic Resonance Spectroscopy
10.
Commun Biol ; 7(1): 543, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38714795

ABSTRACT

The Wnt-planar cell polarity (Wnt-PCP) pathway is crucial in establishing cell polarity during development and tissue homoeostasis. This pathway is found to be dysregulated in many pathological conditions, including cancer and autoimmune disorders. The central event in Wnt-PCP pathway is the activation of Weak-similarity guanine nucleotide exchange factor (WGEF) by the adapter protein Dishevelled (Dvl). The PDZ domain of Dishevelled2 (Dvl2PDZ) binds and activates WGEF by releasing it from its autoinhibitory state. However, the actual Dvl2PDZ binding site of WGEF and the consequent activation mechanism of the GEF have remained elusive. Using biochemical and molecular dynamics studies, we show that a unique "internal-PDZ binding motif" (IPM) of WGEF mediates the WGEF-Dvl2PDZ interaction to activate the GEF. The residues at P2, P0, P-2 and P-3 positions of IPM play an important role in stabilizing the WGEFpep-Dvl2PDZ interaction. Furthermore, MD simulations of modelled Dvl2PDZ-WGEFIPM peptide complexes suggest that WGEF-Dvl2PDZ interaction may differ from the reported Dvl2PDZ-IPM interactions. Additionally, the apo structure of human Dvl2PDZ shows conformational dynamics different from its IPM peptide bound state, suggesting an induced fit mechanism for the Dvl2PDZ-peptide interaction. The current study provides a model for Dvl2 induced activation of WGEF.


Subject(s)
Dishevelled Proteins , Guanine Nucleotide Exchange Factors , Molecular Dynamics Simulation , Protein Binding , Dishevelled Proteins/metabolism , Dishevelled Proteins/chemistry , Dishevelled Proteins/genetics , Humans , Guanine Nucleotide Exchange Factors/metabolism , Guanine Nucleotide Exchange Factors/chemistry , Guanine Nucleotide Exchange Factors/genetics , PDZ Domains , Amino Acid Motifs , Wnt Signaling Pathway , Peptides/metabolism , Peptides/chemistry , Binding Sites , Microfilament Proteins , Intracellular Signaling Peptides and Proteins
11.
ACS Chem Neurosci ; 15(10): 2070-2079, 2024 05 15.
Article in English | MEDLINE | ID: mdl-38691676

ABSTRACT

PDZ domains are modular domains that conventionally bind to C terminal or internal motifs of target proteins to control cellular functions through the regulation of protein complex assemblies. Almost all reported structures of PDZ-target protein complexes rely on fragments or peptides as target proteins. No intact target protein complexed with PDZ was structurally characterized. In this study, we used NMR spectroscopy and other biochemistry and biophysics tools to uncover insights into structural coupling between the PDZ domain of protein interacting with C-kinase 1 (PICK1) and α7 nicotinic acetylcholine receptors (α7 nAChR). Notably, the intracellular domains of both α7 nAChR and PICK1 PDZ exhibit a high degree of plasticity in their coupling. Specifically, the MA helix of α7 nAChR interacts with residues lining the canonical binding site of the PICK1 PDZ, while flexible loops also engage in protein-protein interactions. Both hydrophobic and electrostatic interactions mediate the coupling. Overall, the resulting structure of the α7 nAChR-PICK1 complex reveals an unconventional PDZ binding mode, significantly expanding the repertoire of functionally important PDZ interactions.


Subject(s)
Carrier Proteins , PDZ Domains , Protein Binding , alpha7 Nicotinic Acetylcholine Receptor , alpha7 Nicotinic Acetylcholine Receptor/metabolism , Carrier Proteins/metabolism , Protein Binding/physiology , Humans , Nuclear Proteins/metabolism , Nuclear Proteins/chemistry , Binding Sites/physiology
12.
Mol Biol Cell ; 35(6): ar87, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38656797

ABSTRACT

Recent findings indicate that Solo, a RhoGEF, is involved in cellular mechanical stress responses. However, the mechanism of actin cytoskeletal remodeling via Solo remains unclear. Therefore, this study aimed to identify Solo-interacting proteins using the BioID, a proximal-dependent labeling method, and elucidate the molecular mechanisms of function of Solo. We identified PDZ-RhoGEF (PRG) as a Solo-interacting protein. PRG colocalized with Solo in the basal area of cells, depending on Solo localization, and enhanced actin polymerization at the Solo accumulation sites. Additionally, Solo and PRG interaction was necessary for actin cytoskeletal remodeling. Furthermore, the purified Solo itself had little or negligible GEF activity, even its GEF-inactive mutant directly activated the GEF activity of PRG through interaction. Moreover, overexpression of the Solo and PRG binding domains, respectively, had a dominant-negative effect on actin polymerization and actin stress fiber formation in response to substrate stiffness. Therefore, Solo restricts the localization of PRG and regulates actin cytoskeletal remodeling in synergy with PRG in response to the surrounding mechanical environment.


Subject(s)
Actin Cytoskeleton , Actins , Rho Guanine Nucleotide Exchange Factors , Humans , Actin Cytoskeleton/metabolism , Rho Guanine Nucleotide Exchange Factors/metabolism , Actins/metabolism , PDZ Domains , Protein Binding , Cytoskeleton/metabolism , Animals , HEK293 Cells
13.
Antonie Van Leeuwenhoek ; 117(1): 41, 2024 Feb 24.
Article in English | MEDLINE | ID: mdl-38400879

ABSTRACT

In the search of new enzymatic activities with a possible industrial application, we focused on those microorganisms and their molecular mechanisms that allow them to succeed in the environment, particularly in the proteolytic activity and its central role in the microorganisms' successful permanence. The use of highly active serine proteases for industrial applications is a modern need, especially for the formulation of detergents, protein processing, and hair removal from animal skins. This report provides the isolation and identification of a highly proteolytic fragment derived from DegQ produced by a Pseudomonas fluorescens environmental strain isolated from a frog carcass. Zymograms demonstrate that a 10 kDa protein mainly generates the total proteolytic activity of this strain, which is enhanced by the detergent SDS. Mass spectroscopy analysis revealed that the protein derived a couple of peptides, the ones showing the highest coverage belonging to DegQ. Interestingly, this small protein fragment contains a PDZ domain but no obvious residues indicating that it is a protease. Protein model analysis shows that this fragment corresponds to the main PDZ domain from DegQ, and its unique sequence and structure render a proteolytic peptide. The results presented here indicate that a novel DegQ fragment is sufficient for obtaining high protease activity highlighting that the analysis of environmental microorganisms can render new strains or enzymes with helpful biotechnological characteristics.


Subject(s)
PDZ Domains , Pseudomonas , Animals , Pseudomonas/genetics , Pseudomonas/metabolism , Serine Endopeptidases/chemistry , Serine Endopeptidases/metabolism , Peptides , Serine Proteases
14.
FEBS Lett ; 598(2): 233-241, 2024 01.
Article in English | MEDLINE | ID: mdl-37904289

ABSTRACT

Aberrant brain-derived neurotrophic factor (BDNF) signaling has been proposed to contribute to the pathophysiology of depression and other neurological disorders such as Angelman syndrome. We have previously shown that targeting the tropomyosin receptor kinase B/postsynaptic density protein-95 (PSD-95) nexus in the BDNF signaling pathway by peptidomimetic inhibitors is a promising approach for therapeutic intervention. Here, we used structure-based knowledge to develop a new Syn3 peptidomimetic compound series that fuses peptides derived from the PSD-95-binding protein SynGAP to our prototype compound CN2097. The new compounds target the PSD-95 PDZ3 domain and adjoining αC helix to achieve bivalent binding that results in up to 7-fold stronger affinity compared to CN2097. These compounds were designed to improve CN2097 specificity for the PSD-95 PDZ3 domain, and structure-activity relationship studies were performed to improve their resistance to proteolysis.


Subject(s)
Brain-Derived Neurotrophic Factor , Peptidomimetics , Peptidomimetics/pharmacology , Disks Large Homolog 4 Protein/metabolism , Signal Transduction , PDZ Domains
15.
J Biol Chem ; 300(1): 105575, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38110034

ABSTRACT

The carboxy-terminal tail of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope protein (E) contains a PDZ-binding motif (PBM) which is crucial for coronavirus pathogenicity. During SARS-CoV-2 infection, the viral E protein is expressed within the Golgi apparatus membrane of host cells with its PBM facing the cytoplasm. In this work, we study the molecular mechanisms controlling the presentation of the PBM to host PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins. We show that at the level of the Golgi apparatus, the PDZ-binding motif of the E protein is not detected by E C-terminal specific antibodies nor by the PDZ domain-containing protein-binding partner. Four alanine substitutions upstream of the PBM in the central region of the E protein tail is sufficient to generate immunodetection by anti-E antibodies and trigger robust recruitment of the PDZ domain-containing protein into the Golgi organelle. Overall, this work suggests that the presentation of the PBM to the cytoplasm is under conformational regulation mediated by the central region of the E protein tail and that PBM presentation probably does not occur at the surface of Golgi cisternae but likely at post-Golgi stages of the viral cycle.


Subject(s)
Coronavirus Envelope Proteins , Cytoplasm , SARS-CoV-2 , Humans , Amino Acid Motifs , Coronavirus Envelope Proteins/chemistry , Coronavirus Envelope Proteins/metabolism , COVID-19/pathology , COVID-19/virology , Cytoplasm/metabolism , Cytoplasm/virology , Golgi Apparatus/chemistry , Golgi Apparatus/metabolism , Guanylate Kinases/metabolism , PDZ Domains , Protein Binding , Protein Conformation , Protein Transport , SARS-CoV-2/chemistry , SARS-CoV-2/metabolism
16.
Biochem Soc Trans ; 51(6): 2005-2016, 2023 12 20.
Article in English | MEDLINE | ID: mdl-38095060

ABSTRACT

The PDZ and LIM domain (PDLIM) proteins are associated with the actin cytoskeleton and have conserved in roles in metazoan actin organisation and function. They primarily function as scaffolds linking various proteins to actin and its binding partner α-actinin via two conserved domains; an N-terminal postsynaptic density 95, discs large and zonula occludens-1 (PDZ) domain, and either single or multiple C-terminal LIN-11, Isl-1 and MEC-3 (LIM) domains in the actinin-associated LIM protein (ALP)- and Enigma-related proteins, respectively. While their role in actin organisation, such as in stress fibres or in the Z-disc of muscle fibres is well known, emerging evidence also suggests a role in actin-dependent membrane trafficking in the endosomal system. This is mediated by a recently identified interaction with the sorting nexin 17 (SNX17) protein, an adaptor for the trafficking complex Commander which is itself intimately linked to actin-directed formation of endosomal recycling domains. In this review we focus on the currently understood structural basis for PDLIM function. The PDZ domains mediate direct binding to distinct classes of PDZ-binding motifs (PDZbms), including α-actinin and other actin-associated proteins, and a highly specific interaction with the type III PDZbm such as the one found in the C-terminus of SNX17. The structures of the LIM domains are less well characterised and how they engage with their ligands is completely unknown. Despite the lack of experimental structural data, we find that recently developed machine learning-based structure prediction methods provide insights into their potential interactions and provide a template for further studies of their molecular functions.


Subject(s)
Actinin , Actins , Animals , Actins/metabolism , Actinin/chemistry , Actinin/metabolism , PDZ Domains , Actin Cytoskeleton/metabolism , LIM Domain Proteins/metabolism , Protein Binding
17.
Nat Commun ; 14(1): 8441, 2023 Dec 19.
Article in English | MEDLINE | ID: mdl-38114480

ABSTRACT

LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the 'x-Φ-G-Φ' motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.


Subject(s)
Lim Kinases , PDZ Domains , Animals , Lim Kinases/genetics , Lim Kinases/metabolism , Actins/metabolism , Saccharomyces cerevisiae/metabolism , Phosphorylation , Actin Depolymerizing Factors/metabolism , Homeostasis , Mammals/metabolism
18.
J Virol ; 97(10): e0124123, 2023 10 31.
Article in English | MEDLINE | ID: mdl-37772824

ABSTRACT

IMPORTANCE: CD34+ hematopoietic progenitor cells (HPCs) are an important cellular reservoir for latent human cytomegalovirus (HCMV). Several HCMV genes are expressed during latency that are involved with the maintenance of the viral genome in CD34+ HPC. However, little is known about the process of viral reactivation in these cells. Here, we describe a viral protein, pUL8, and its interaction and stabilization with members of the Wnt/ß-catenin pathway as an important component of viral reactivation. We further define that pUL8 and ß-catenin interact with DVL2 via a PDZ-binding domain, and loss of UL8 interaction with ß-catenin-DVL2 restricts viral reactivation. Our findings will be instrumental in understanding the molecular processes involved in HCMV reactivation in order to design new antiviral therapeutics.


Subject(s)
Antigens, CD34 , Cytomegalovirus , Dishevelled Proteins , Hematopoietic Stem Cells , Viral Proteins , Virus Activation , beta Catenin , Humans , Antigens, CD34/metabolism , beta Catenin/chemistry , beta Catenin/metabolism , Cytomegalovirus/genetics , Cytomegalovirus/physiology , Dishevelled Proteins/chemistry , Dishevelled Proteins/metabolism , Hematopoietic Stem Cells/metabolism , Hematopoietic Stem Cells/virology , PDZ Domains , Viral Proteins/chemistry , Viral Proteins/metabolism , Virus Latency/genetics
19.
Antiviral Res ; 217: 105675, 2023 09.
Article in English | MEDLINE | ID: mdl-37481039

ABSTRACT

Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.


Subject(s)
Human T-lymphotropic virus 1 , Humans , Antiviral Agents/pharmacology , Antiviral Agents/metabolism , Human T-lymphotropic virus 1/metabolism , PDZ Domains , Proteins , T-Lymphocytes/metabolism
20.
J Med Entomol ; 60(4): 690-697, 2023 07 12.
Article in English | MEDLINE | ID: mdl-37235642

ABSTRACT

In diapausing mosquitoes, cold tolerance and prolonged lifespan are important features that are crucial for overwintering success. In the mosquito Culex pipiens, we suggest that PDZ domain-containing protein (PDZ) (post synaptic density protein [PSD95], drosophila disc large tumor suppressor [Dlg1], and zonula occludens-1 protein [zo-1]) domain-containing protein is involved with these diapause features for overwintering survival in Culex mosquitoes. The expression level of pdz was significantly higher in diapausing adult females in the early stage in comparison to their nondiapausing counterparts. Suppression of the gene that encodes PDZ by RNA interference significantly decreased actin accumulation in the midgut of early-stage adult diapausing females. Inhibition of pdz also significantly reduced the survivability of diapausing females which indicates that this protein could play a key role in preserving the midgut tissues during early diapause.


Subject(s)
Culex , Culicidae , Female , Animals , Culex/physiology , PDZ Domains
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