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1.
Cell ; 163(6): 1484-99, 2015 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-26638075

RESUMO

The centrosome is the primary microtubule organizing center of the cells and templates the formation of cilia, thereby operating at a nexus of critical cellular functions. Here, we use proximity-dependent biotinylation (BioID) to map the centrosome-cilium interface; with 58 bait proteins we generate a protein topology network comprising >7,000 interactions. Analysis of interaction profiles coupled with high resolution phenotypic profiling implicates a number of protein modules in centriole duplication, ciliogenesis, and centriolar satellite biogenesis and highlights extensive interplay between these processes. By monitoring dynamic changes in the centrosome-cilium protein interaction landscape during ciliogenesis, we also identify satellite proteins that support cilia formation. Systematic profiling of proximity interactions combined with functional analysis thus provides a rich resource for better understanding human centrosome and cilia biology. Similar strategies may be applied to other complex biological structures or pathways.


Assuntos
Centrossomo/metabolismo , Cílios/metabolismo , Mapas de Interação de Proteínas , Biotinilação , Ciclo Celular , Humanos , Centro Organizador dos Microtúbulos/metabolismo
2.
Mol Cell ; 73(3): 621-638.e17, 2019 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-30554943

RESUMO

Targeting bromodomains (BRDs) of the bromo-and-extra-terminal (BET) family offers opportunities for therapeutic intervention in cancer and other diseases. Here, we profile the interactomes of BRD2, BRD3, BRD4, and BRDT following treatment with the pan-BET BRD inhibitor JQ1, revealing broad rewiring of the interaction landscape, with three distinct classes of behavior for the 603 unique interactors identified. A group of proteins associate in a JQ1-sensitive manner with BET BRDs through canonical and new binding modes, while two classes of extra-terminal (ET)-domain binding motifs mediate acetylation-independent interactions. Last, we identify an unexpected increase in several interactions following JQ1 treatment that define negative functions for BRD3 in the regulation of rRNA synthesis and potentially RNAPII-dependent gene expression that result in decreased cell proliferation. Together, our data highlight the contributions of BET protein modules to their interactomes allowing for a better understanding of pharmacological rewiring in response to JQ1.


Assuntos
Antineoplásicos/farmacologia , Azepinas/farmacologia , Terapia de Alvo Molecular/métodos , Neoplasias/tratamento farmacológico , Proteínas Nucleares/antagonistas & inibidores , Mapas de Interação de Proteínas/efeitos dos fármacos , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas de Ligação a RNA/antagonistas & inibidores , Fatores de Transcrição/antagonistas & inibidores , Triazóis/farmacologia , Antineoplásicos/química , Azepinas/química , Proteínas de Ciclo Celular , Proliferação de Células/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica , Células HEK293 , Células HeLa , Humanos , Células K562 , Modelos Moleculares , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/patologia , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Ligação Proteica , Conformação Proteica , Domínios e Motivos de Interação entre Proteínas , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Proteômica/métodos , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais/efeitos dos fármacos , Relação Estrutura-Atividade , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Triazóis/química
3.
EMBO J ; 38(14): e101109, 2019 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-31304627

RESUMO

Centriolar satellites are small electron-dense granules that cluster in the vicinity of centrosomes. Satellites have been implicated in multiple critical cellular functions including centriole duplication, centrosome maturation, and ciliogenesis, but their precise composition and assembly properties have remained poorly explored. Here, we perform in vivo proximity-dependent biotin identification (BioID) on 22 human satellite proteins, to identify 2,113 high-confidence interactions among 660 unique polypeptides. Mining this network, we validate six additional satellite components. Analysis of the satellite interactome, combined with subdiffraction imaging, reveals the existence of multiple unique microscopically resolvable satellite populations that display distinct protein interaction profiles. We further show that loss of satellites in PCM1-depleted cells results in a dramatic change in the satellite interaction landscape. Finally, we demonstrate that satellite composition is largely unaffected by centriole depletion or disruption of microtubules, indicating that satellite assembly is centrosome-independent. Together, our work offers the first systematic spatial and proteomic profiling of human centriolar satellites and paves the way for future studies aimed at better understanding the biogenesis and function(s) of these enigmatic structures.


Assuntos
Autoantígenos/genética , Proteínas de Ciclo Celular/genética , Centríolos/metabolismo , Proteômica/métodos , Autoantígenos/metabolismo , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular , Deleção de Genes , Humanos , Proteínas Associadas aos Microtúbulos/metabolismo , Mapas de Interação de Proteínas , Espectrometria de Massas em Tandem
4.
Int J Mol Sci ; 24(14)2023 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-37511222

RESUMO

The aim of this review article is to collate recent contributions of proteomic studies to cystic fibrosis transmembrane conductance regulator (CFTR) biology. We summarize advances from these studies and create an accessible resource for future CFTR proteomic efforts. We focus our attention on the CFTR interaction network at the cell surface, thus generating a CFTR 'surfaceome'. We review the main findings about CFTR interactions and highlight several functional categories amongst these that could lead to the discovery of potential biomarkers and drug targets for CF.


Assuntos
Membrana Celular , Regulador de Condutância Transmembrana em Fibrose Cística , Fibrose Cística , Proteômica , Humanos , Membrana Celular/fisiologia , Fibrose Cística/genética , Fibrose Cística/metabolismo , Regulador de Condutância Transmembrana em Fibrose Cística/genética , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Transporte de Íons , Mutação , Transdução de Sinais
5.
Int J Mol Sci ; 23(5)2022 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-35269585

RESUMO

Deletion of phenylalanine 508 (∆F508) of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) anion channel protein is the leading cause of Cystic Fibrosis (CF). Here, we report the analysis of CFTR and ∆F508-CFTR interactomes using BioID (proximity-dependent biotin identification), a technique that can also detect transient associations. We identified 474 high-confidence CFTR proximity-interactors, 57 of which have been previously validated, with the remainder representing novel interaction space. The ∆F508 interactome, comprising 626 proximity-interactors was markedly different from its wild type counterpart, with numerous alterations in protein associations categorized in membrane trafficking and cellular stress functions. Furthermore, analysis of the ∆F508 interactome in cells treated with Orkambi identified several interactions that were altered as a result of this drug therapy. We examined two candidate CFTR proximity interactors, VAPB and NOS1AP, in functional assays designed to assess surface delivery and overall chloride efflux. VAPB depletion impacted both CFTR surface delivery and chloride efflux, whereas NOS1AP depletion only affected the latter. The wild type and ∆F508-CFTR interactomes represent rich datasets that could be further mined to reveal additional candidates for the functional rescue of ∆F508-CFTR.


Assuntos
Aminofenóis/farmacologia , Aminopiridinas/farmacologia , Benzodioxóis/farmacologia , Regulador de Condutância Transmembrana em Fibrose Cística/genética , Regulador de Condutância Transmembrana em Fibrose Cística/metabolismo , Mapas de Interação de Proteínas/efeitos dos fármacos , Quinolonas/farmacologia , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Cloretos/metabolismo , Combinação de Medicamentos , Células HEK293 , Humanos , Espectrometria de Massas , Mutação , Proteínas de Transporte Vesicular/metabolismo
6.
Proteins ; 89(12): 1647-1672, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34561912

RESUMO

The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.


Assuntos
Modelos Moleculares , Conformação Proteica , Proteínas/química , Software , Sequência de Aminoácidos , Biologia Computacional , Microscopia Crioeletrônica , Cristalografia por Raios X , Análise de Sequência de Proteína
7.
Protein Expr Purif ; 175: 105697, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32681951

RESUMO

Trichoderma virens genome harbors two isoforms of GAPDH, one (gGPD) involved in glycolysis and the other one (vGPD) in secondary metabolism. vGPD is expressed as part of the "vir" cluster responsible for the biosynthesis of volatile sesquiterpenes. The secondary metabolism-associated GAPDH is tolerant to the anti-cancer metabolite heptelidic acid (HA), produced by T. virens. Characterizing the HA-tolerant form of GAPDH, thus has implications in cancer therapy. In order to get insight into the mechanism of HA-tolerance of vGPD, we have purified recombinant form of this protein. The protein displays biochemical and biophysical characteristics analogous to the gGPD isoform. It exists as a tetramer with Tm of about 56.5 °C, and displays phosphorylation enzyme activity with Km and Kcat of 0.38 mM and 2.55 sec-1, respectively. The protein weakly binds to the sequence upstream of the vir4 gene that codes for the core enzyme (a terpene cyclase) of the "vir" cluster. The EMSA analysis indicates that vGPD may not act as a transcription factor driving the "vir" cluster, at least not by directly binding to the promoter region. We also succeeded in obtaining small crystals of this protein. We have constructed structural models of vGPD and gGPD of T. virens. In silico constrained docking analysis reveals weaker binding of heptelidic acid in vGPD, compared to gGPD protein.


Assuntos
Proteínas Fúngicas , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora) , Hypocrea/genética , Simulação de Acoplamento Molecular , Estabilidade Enzimática , Proteínas Fúngicas/biossíntese , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Proteínas Fúngicas/isolamento & purificação , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/biossíntese , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/química , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/genética , Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/isolamento & purificação , Hypocrea/enzimologia , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Sesquiterpenos/química
8.
J Invertebr Pathol ; 156: 29-40, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-30003921

RESUMO

Lysinibacillus sphaericus parasporal BinAB toxin displays mosquito larvicidal activity against Culex and Anopheles, but several Aedes species are refractory. Recently reported crystal structure of BinAB revealed the presence of N-terminal lectin-like domain in BinA. Hemagglutination and hemolytic activities were not observed for BinA in the present studies. We attempted to characterize carbohydrate specificity of BinA by high-throughput approaches using extrinsic fluorescence and thermofluor shift assay. A total of 34 saccharides (mono-, di- and polysaccharides, and glycoproteins) were used for initial high-throughput screening. The promising glycans were identified based on significant change in the fluorescence intensity. Surface plasmon resonance revealed differential binding of BinA with glycoproteins (fetuin, asialofetuin and thyroglobulin) and affinity for simple sugars, l-fucose and l-arabinose. In the limited carbohydrate competition assay, arabinose, fucose and fetuin inhibited BinA toxicity towards Culex larvae. This study for the first time provides direct evidence that BinA is competent to bind diverse and structurally different glycosylated proteins. This activity may be linked to its intracellular cytotoxicity, as protein N-glycosylation is thought to be critical for development and survival of insect larvae. The glycoproteins do not form stable complexes with BinA, however, as observed in the pull-down assay using affinity immobilized BinA and in native-PAGE analysis. As BinA displays only mild affinity with receptor polypeptide, we hypothesize that toxin-receptor specificity of BinA in Culex may be mediated by dual interaction of BinA with glycan core of GPI anchor and receptor polypeptide. The study shall be useful for refining strategies for improving larvicidal activity and for broadening target specificity of BinAB toxin.


Assuntos
Aedes/parasitologia , Bacillaceae/química , Toxinas Bacterianas/química , Animais , Glicoconjugados , Larva/parasitologia , Controle Biológico de Vetores/métodos
9.
Bioconjug Chem ; 28(2): 410-418, 2017 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-28118708

RESUMO

Toxic strains of Lysinibacillus sphaericus have been used in the field for larval control of mosquito vector diseases. The high toxicity of L. sphaericus is attributed to the binary (BinAB) toxin produced as parasporal crystalline inclusions during the early stages of sporulation. BinA and BinB, the primary components of these spore-crystals, exert high toxicity when administered together. However, instability, short half-lives, and rapid proteolytic digestion can limit their use as an effective insecticide. BinA alone displays larvicidal toxicity, in the absence of BinB, albeit with much reduced activity. Here for the first time, we demonstrate the beneficial effect of PEGylation (covalent attachment of polyethylene glycol) on mosquito-larvicidal activity of BinA. Polymer conjugation was achieved using 750 Da polyethylene glycol (PEG) at two different pH values (pH 7.2 and 8.5). Two different isoforms of the biopolymers, purified to homogeneity, were highly water-soluble and resistant to trypsin and proteinase K. The mono-PEGylated BinA isoforms also displayed preservation of the toxin structure with improved thermal stability by about 3-5 °C, as evident from thermal denaturation studies by circular dichroism and differential scanning fluorimetry. Notably, PEGylation enhanced BinA toxicity by nearly 6-fold. The PEGylated BinA isoforms alone displayed high larvicidal activity (LC50 value of ∼3.4 ng/mL) against the third instar Culex larvae, which compares favorably against LC50 reported for the combination of BinA and BinB proteins. Since BinA can be synthesized easily through recombinant technology and easily PEGylated, the conjugated biopolymers offer a promising opportunity for mosquito control programs.


Assuntos
Bacillaceae/química , Toxinas Bacterianas/química , Toxinas Bacterianas/toxicidade , Culicidae , Inseticidas/química , Larva , Polietilenoglicóis/química , Animais , Toxinas Bacterianas/metabolismo , Estabilidade de Medicamentos , Concentração de Íons de Hidrogênio , Concentração Inibidora 50 , Modelos Moleculares , Estabilidade Proteica , Proteólise , Relação Estrutura-Atividade , Temperatura
10.
Mol Cell Proteomics ; 14(4): 946-60, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25659891

RESUMO

The myotubularins are a family of phosphatases that dephosphorylate the phosphatidylinositols phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-phosphate. Several family members are mutated in disease, yet the biological functions of the majority of myotubularins remain unknown. To gain insight into the roles of the individual enzymes, we have used affinity purification coupled to mass spectrometry to identify protein-protein interactions for the myotubularins. The myotubularin interactome comprises 66 high confidence (false discovery rate ≤1%) interactions, including 18 pairwise interactions between individual myotubularins. The results reveal a number of potential signaling contexts for this family of enzymes, including an intriguing, novel role for myotubularin-related protein 3 and myotubularin-related protein 4 in the regulation of abscission, the final step of mitosis in which the membrane bridge remaining between two daughter cells is cleaved. Both depletion and overexpression of either myotubularin-related protein 3 or myotubularin-related protein 4 result in abnormal midbody morphology and cytokinesis failure. Interestingly, myotubularin-related protein 3 and myotubularin-related protein 4 do not exert their effects through lipid regulation at the midbody, but regulate abscission during early mitosis, by interacting with the mitotic kinase polo-like kinase 1, and with centrosomal protein of 55 kDa (CEP55), an important regulator of abscission. Structure-function analysis reveals that, consistent with known intramyotubularin interactions, myotubularin-related protein 3 and myotubularin-related protein 4 interact through their respective coiled coil domains. The interaction between myotubularin-related protein 3 and polo-like kinase 1 relies on the divergent, nonlipid binding Fab1, YOTB, Vac1, and EEA1 domain of myotubularin-related protein 3, and myotubularin-related protein 4 interacts with CEP55 through a short GPPXXXY motif, analogous to endosomal sorting complex required for transport-I components. Disruption of any of these interactions results in abscission failure, by disrupting the proper recruitment of CEP55, and subsequently, of endosomal sorting complex required for transport-I, to the midbody. Our data suggest that myotubularin-related protein 3 and myotubularin-related protein 4 may act as a bridge between CEP55 and polo-like kinase 1, ensuring proper CEP55 phosphorylation and regulating CEP55 recruitment to the midbody. This work provides a novel role for myotubularin-related protein 3/4 heterodimers, and highlights the temporal and spatial complexity of the regulation of cytokinesis.


Assuntos
Proteínas de Ciclo Celular/metabolismo , Citocinese , Proteínas Nucleares/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas Tirosina Fosfatases não Receptoras/metabolismo , Proteínas Proto-Oncogênicas/metabolismo , Linhagem Celular Tumoral , Células HEK293 , Humanos , Metabolismo dos Lipídeos , Mitose , Fosforilação , Ligação Proteica , Quinase 1 Polo-Like
11.
Photosynth Res ; 129(1): 17-28, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27068646

RESUMO

The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the ß-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and ß- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of ß-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.


Assuntos
Cianobactérias/enzimologia , Modelos Moleculares , Ficoeritrina/química , Sequência de Aminoácidos , Proteínas de Bactérias/química , Cristalografia por Raios X , Transferência de Energia , Fluorescência , Concentração de Íons de Hidrogênio , Conformação Proteica , Alinhamento de Sequência , Análise de Sequência de Proteína
13.
Int J Biol Macromol ; 273(Pt 2): 133167, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38885868

RESUMO

The Nucleocapsid (N) protein of SARS-CoV-2 plays a crucial role in viral replication and pathogenesis, making it an attractive target for developing antiviral therapeutics. In this study, we used differential scanning fluorimetry to establish a high-throughput screening method for identifying high-affinity ligands of N-terminal domain of the N protein (N-NTD). We screened an FDA-approved drug library of 1813 compounds and identified 102 compounds interacting with N-NTD. The screened compounds were further investigated for their ability to inhibit the nucleic-acid binding activity of the N protein using electrophoretic mobility-shift assays. We have identified three inhibitors, Ceftazidime, Sennoside A, and Tannic acid, that disrupt the N protein's interaction with RNA probe. Ceftazidime and Sennoside A exhibited nano-molar range binding affinities with N protein, determined through surface plasmon resonance. The binding sites of Ceftazidime and Sennoside A were investigated using [1H, 15N]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. Ceftazidime and Sennoside A bind to the putative RNA binding site of the N protein, thus providing insights into the inhibitory mechanism of these compounds. These findings will contribute to the development of novel antiviral agents targeting the N protein of SARS-CoV-2.


Assuntos
Antivirais , Proteínas do Nucleocapsídeo de Coronavírus , SARS-CoV-2 , Antivirais/farmacologia , Antivirais/química , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/metabolismo , Proteínas do Nucleocapsídeo de Coronavírus/química , Proteínas do Nucleocapsídeo de Coronavírus/antagonistas & inibidores , Proteínas do Nucleocapsídeo de Coronavírus/metabolismo , Sítios de Ligação , Humanos , Ligação Proteica , Fosfoproteínas/metabolismo , Fosfoproteínas/química , Fosfoproteínas/antagonistas & inibidores , Taninos/química , Taninos/farmacologia , Tratamento Farmacológico da COVID-19 , Proteínas do Nucleocapsídeo/química , Proteínas do Nucleocapsídeo/antagonistas & inibidores , Proteínas do Nucleocapsídeo/metabolismo
14.
Development ; 137(21): 3675-85, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20940226

RESUMO

The high sterol concentration in eukaryotic cell membranes is thought to influence membrane properties such as permeability, fluidity and microdomain formation. Drosophila cannot synthesize sterols, but do require them for development. Does this simply reflect a requirement for sterols in steroid hormone biosynthesis, or is bulk membrane sterol also essential in Drosophila? If the latter is true, how do they survive fluctuations in sterol availability and maintain membrane homeostasis? Here, we show that Drosophila require both bulk membrane sterol and steroid hormones in order to complete adult development. When sterol availability is restricted, Drosophila larvae modulate their growth to maintain membrane sterol levels within tight limits. When dietary sterol drops below a minimal threshold, larvae arrest growth and development in a reversible manner. Strikingly, membrane sterol levels in arrested larvae are dramatically reduced (dropping sixfold on average) in most tissues except the nervous system. Thus, sterols are dispensable for maintaining the basic membrane biophysical properties required for cell viability; these functions can be performed by non-sterol lipids when sterols are unavailable. However, bulk membrane sterol is likely to have essential functions in specific tissues during development. In tissues in which sterol levels drop, the overall level of sphingolipids increases and the proportion of different sphingolipid variants is altered. These changes allow survival, but not growth, when membrane sterol levels are low. This relationship between sterols and sphingolipids could be an ancient and conserved principle of membrane homeostasis.


Assuntos
Drosophila/crescimento & desenvolvimento , Drosophila/metabolismo , Esteróis/metabolismo , Animais , Animais Geneticamente Modificados , Membrana Celular/metabolismo , Sobrevivência Celular , Células Cultivadas , Drosophila/embriologia , Drosophila/fisiologia , Embrião não Mamífero , Hormônios/metabolismo , Larva/crescimento & desenvolvimento , Larva/metabolismo , Modelos Biológicos , Esfingolipídeos/metabolismo , Esteroides/metabolismo , Sobrevida/fisiologia
15.
Int J Biol Macromol ; 247: 125792, 2023 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-37442507

RESUMO

UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.


Assuntos
Proteínas de Transporte , Fatores de Transcrição , Humanos , Reparo do DNA , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Domínios Proteicos , Mapeamento de Interação de Proteínas , Dicroísmo Circular , Espalhamento a Baixo Ângulo , Nêutrons , Mutação
16.
J Biomol Struct Dyn ; 41(9): 3752-3761, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-35354393

RESUMO

Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria Halomicronema sp. R31DM is purified and subjected for its structural characterisation by X-ray crystallography in order to understand its light-harvesting characteristics. The crystal structure is solved to a resolution-limit of 2.21 Å with reasonable R-factors values, 0.16/0.21 (Rwork/ Rfree). PE forms hexamer of hetero-dimers made up of two peptide chains, α- and ß-subunits containing 2 and 3 phycoerythrobilin (PEB) chromophores covalently attached to them, respectively. Geometry of five chromophores is analysed along with their relative position within the PE hexamer. Also, their interactions with the surrounding microenvironment are analysed. The plausible energy transfer pathways in hexamer structure have been predicted based on relative position and geometry of chromophores. This structure enriches the structural information of cyanobacterial PE in order to understand its light-harvesting capacity.Communicated by Ramaswamy H. Sarma.


Assuntos
Cianobactérias , Ficoeritrina , Ficoeritrina/química , Ficoeritrina/metabolismo , Cianobactérias/química , Cianobactérias/metabolismo , Cristalografia por Raios X , Peptídeos/metabolismo
17.
ACS Omega ; 8(48): 45606-45615, 2023 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-38075767

RESUMO

Mutations in the unique ATP-binding cassette anion channel, the cystic fibrosis conductance regulator (CFTR), lead to the inherited fatal disease known as cystic fibrosis (CF). Ivacaftor enhances channel gating of CFTR by stabilizing its open state and has been approved as monotherapy for CF patients with CFTR gating mutations (e.g., G551D) and as part of combination therapy with lumacaftor for CFTR folding mutations (e.g., ΔF508). However, in the latter context, ivacaftor may destabilize folding-rescued ΔF508-CFTR and membrane-associated proteins and attenuate lumacaftor pharmacotherapy. Here, we tested the hypothesis that the high lipophilicity of ivacaftor may contribute to this effect. We describe the synthesis of three glutamic acid ivacaftor derivatives with reduced lipophilicity that bear different charges at neutral pH (compounds 2, 3, 4). In a cellular ion flux assay, all three restored G551D-CFTR channel activity at comparable or better levels than ivacaftor. Furthermore, unlike ivacaftor, compound 3 did not attenuate levels of folding-rescued ΔF508 at the cell surface. Molecular modeling predicts that the increased polarity of compound 3 allows engagement with polar amino acids present in the binding pocket with hydrogen bonding and ionic interactions, which are collectively higher in strength as compared to hydrophobic interactions that stabilize ivacaftor. Overall, the data suggests that reduced lipophilicity may improve the efficacy of this class of CFTR potentiators when used for folding-rescued ΔF508-CFTR.

18.
3 Biotech ; 13(7): 247, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37366498

RESUMO

Phycobiliproteins is a family of chromophore-containing proteins having light-harvesting and antioxidant capacity. The phycocyanin (PC) is a brilliant blue coloured phycobiliprotein, found in rod structure of phycobilisome and has been widely studied for their therapeutic and fluorescent properties. In the present study, the hexameric assembly structure of phycocyanin (Syn-PC) from Synechococcus Sp. R42DM is characterized by X-ray crystallography to understand its light-harvesting and antioxidant properties. The crystal structure of Syn-PC is solved with 2.15 Å resolution and crystallographic R-factors, Rwork/Rfree, 0.16/0.21. The hexamer of Syn-PC is formed by heterodimer of two polypeptide chains, namely, α- and ß-subunits. The structure is analysed at atomic level to reveal the chromophore microenvironment and possible light energy transfer mechanism in Syn-PC. The chromophore arrangement in hexamer, deviation angle and distance between the chromophore contribute to the energy transfer efficiency of protein. The structural attributes responsible for the antioxidant potential of Syn-PC are recognized and annotated on its 3-dimensional structure. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03665-1.

19.
J Mol Evol ; 75(5-6): 155-67, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23188094

RESUMO

Translin and its interacting partner protein, TRAX, are members of the translin superfamily. These proteins are involved in mRNA regulation and in promoting RISC activity by removing siRNA passenger strand cleavage products, and have been proposed to play roles in DNA repair and recombination. Both homomeric translin and heteromeric translin-TRAX complex bind to ssDNA and RNA; however, the heteromeric complex is a key activator in siRNA-mediated silencing in human and drosophila. The residues critical for RNase activity of the complex reside in TRAX sequence. Both translin and TRAX are well conserved in eukaryotes. In present work, a single translin superfamily protein is detected in Chloroflexi eubacteria, in the known phyla of archaea and in some unicellular eukaryotes. The prokaryotic proteins essentially share unique sequence motifs with eukaryotic TRAX, while the proteins possessing both the unique sequences and conserved indels of TRAX or translin can be identified from protists. Intriguingly, TRAX protein in all the known genomes of extant Chloroflexi share high sequence similarity and conserved indels with the archaeal protein, suggesting occurrence of TRAX at least at the time of Chloroflexi divergence as well as evolutionary relationship between Chloroflexi and archaea. The mirror phylogeny in phylogenetic tree, constructed using diverse translin and TRAX sequences, indicates gene duplication event leading to evolution of translin in unicellular eukaryotes, prior to divergence of multicellular eukayrotes. Since Chloroflexi has been debated to be near the last universal common ancestor, the present analysis indicates that TRAX may be useful to understand the tree of life.


Assuntos
Proteínas de Ligação a DNA/genética , Evolução Molecular , Genoma , Família Multigênica , Proteínas de Ligação a RNA/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Archaea/genética , Proteínas de Transporte/química , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Eubacterium/genética , Eucariotos/genética , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Conformação Proteica , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , Alinhamento de Sequência
20.
Gene ; 788: 145663, 2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-33887372

RESUMO

The high radioresistance of Nostoc sp. strain PCC7120 is indicative of a robust DNA repair pathway. In the absence of NHEJ pathway and the canonical RecBCD proteins, the RecF pathway proteins are expected to play an important role in double strand break repair in this organism. The RecF, RecO and RecR proteins which are central to the RecF pathway have not been characterised in the ancient cyanobacteria, several of which are known to be radioresistant. The characterisation of these proteins was initiated through a mix of in silico, expression and complementation analysis. Differential expression of the recF, recO and recR genes was observed both at the transcript and the protein level under normal growth condition, which did not change significantly upon exposure to DNA damage stresses. Expression of RecR as a 23 kDa protein in vivo in Nostoc PCC7120 confirmed the re-annotation of the initiation codon of the gene (alr4977) to a rare initiation codon 'GTT' 267 bases upstream of the annotated initiation codon. Of the three proteins, Nostoc RecO and RecR proteins could complement the corresponding mutations in Escherichia coli, but not RecF. The Nostoc RecO protein exhibited low sequence and structural homology with other bacterial RecO protein, and was predicted to have a longer loop region. Phylogenetic as well as sequence analysis revealed high conservation among bacterial RecR proteins and least for RecO. In silico analysis revealed a comparatively smaller interactome for the Nostoc RecF, RecO and RecR proteins compared to other bacteria, with RecO predicted to interact with both RecF and RecR. The information gathered can form a stepping stone to further characterise these proteins in terms of deciphering their interactome, biochemical and physiological activities. This would help in establishing their importance in RecF pathway of DSB repair in Nostoc PCC7120.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Nostoc/crescimento & desenvolvimento , Clonagem Molecular , Códon de Iniciação , Simulação por Computador , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Evolução Molecular , Regulação Bacteriana da Expressão Gênica , Fixação de Nitrogênio , Nostoc/genética , Nostoc/metabolismo , Filogenia
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