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1.
Nat Commun ; 11(1): 4171, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32820176

RESUMO

Spiralia is a large, ancient and diverse clade of animals, with a conserved early developmental program but diverse larval and adult morphologies. One trait shared by many spiralians is the presence of ciliary bands used for locomotion and feeding. To learn more about spiralian-specific traits we have examined the expression of 20 genes with protein motifs that are strongly conserved within the Spiralia, but not detectable outside of it. Here, we show that two of these are specifically expressed in the main ciliary band of the mollusc Tritia (also known as Ilyanassa). Their expression patterns in representative species from five more spiralian phyla-the annelids, nemerteans, phoronids, brachiopods and rotifers-show that at least one of these, lophotrochin, has a conserved and specific role in particular ciliated structures, most consistently in ciliary bands. These results highlight the potential importance of lineage-specific genes or protein motifs for understanding traits shared across ancient lineages.


Assuntos
Motivos de Aminoácidos/genética , Cílios/genética , Invertebrados/genética , Proteínas/genética , Animais , Anelídeos/classificação , Anelídeos/genética , Anelídeos/fisiologia , Evolução Biológica , Cílios/fisiologia , Comportamento Alimentar/fisiologia , Perfilação da Expressão Gênica/métodos , Invertebrados/classificação , Invertebrados/fisiologia , Larva/genética , Larva/fisiologia , Locomoção/fisiologia , Moluscos/classificação , Moluscos/genética , Moluscos/fisiologia , Filogenia , Especificidade da Espécie
2.
Water Sci Technol ; 81(12): 2585-2598, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32857745

RESUMO

Bioleaching, a technologically and economically feasible technology, is considered as the high efficiency method to improve dewaterability in sewage sludge. The objective of this study was to investigate the effect of different sludge concentrations on bioleaching dewaterability and understand the mechanism of the effect of bioleaching on sludge dewaterability. Variation in pH, oxidation-reduction potential (ORP), capillary suction time (CST), specific resistance to filtration (SRF) and different fractions of extracellular polymeric substances (EPS) including slime EPS (S-EPS), loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS) were determined. Different sludge concentrations (5, 10, 15, 20 and 30 g·L-1) were selected to investigate during bioleaching. Results indicated that sludge buffering capacity significantly inhibited bioleaching efficiency as sludge concentrations increased. Optimum enhancements in sludge dewaterability were observed during the 10 g·L-1 sludge concentration treatment, and reached a maximum when the pH was 2.11. The variation of different fractions of EPS revealed that the ratio of S-EPS/TB-EPS significantly affected sludge dewaterability. Principal component analysis and Pearson's correlation analysis both provided evidence that the higher TB-EPS followed by a very large reduction was positively correlated with sludge dewaterability. However, the increase of protein and DNA in S-EPS content was negatively correlated with sludge dewaterability.


Assuntos
Esgotos , Água , Matriz Extracelular de Substâncias Poliméricas , Filtração , Proteínas
3.
Nat Commun ; 11(1): 4045, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792484

RESUMO

Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.


Assuntos
Luz , Optogenética/métodos , Cromatografia de Afinidade , Escherichia coli/genética , Escherichia coli/metabolismo , Células HEK293 , Humanos , Ligação Proteica/efeitos da radiação , Proteínas/química , Proteínas/metabolismo
4.
J Med Life ; 13(2): 241-248, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32742521

RESUMO

Cell culture is one of the most commonly used techniques in the production of biological products. Many physical and chemical parameters may affect cell growth and proliferation. This study was conducted to investigate the effect of chemical components as supplements using the experimental design method, which aimed at reducing the number of experiments. For this purpose, supplements including chemical components using four levels, with three replications in suspension and batch culture conditions, were examined for 72 hours using the Taguchi experimental design method. From the experiments, it was concluded that the culture media composition had a significant impact on final cell count and pH. High concentrations of different media composition alone were insufficient to ensure higher cell count. According to the results, this insufficiency was associated with an increase of 20% in the number of final cells. In the majority of cultures, the number of final cells at 48 hours increased relative to the number of final cells at 24 hours after culturing the cells.


Assuntos
Técnicas de Cultura de Células/métodos , Vírus da Febre Aftosa/imunologia , Rim/citologia , Vacinas Virais/imunologia , Aminoácidos/farmacologia , Animais , Contagem de Células , Células Cultivadas , Cricetinae , Vírus da Febre Aftosa/efeitos dos fármacos , Glucose/farmacologia , Concentração de Íons de Hidrogênio , Polietilenoglicóis/química , Proteínas/farmacologia , Vitaminas/farmacologia
5.
PLoS Comput Biol ; 16(8): e1007966, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32760072

RESUMO

Protein activity is often regulated by ligand binding or by post-translational modifications such as phosphorylation. Moreover, proteins that are regulated in this way often contain multiple ligand binding sites or modification sites, which can operate to create an ultrasensitive dose response. Here, we consider the contribution of the individual modification/binding sites to the activation process, and how their individual values affect the ultrasensitive behavior of the overall system. We use a generalized Monod-Wyman-Changeux (MWC) model that allows for variable conformational free energy contributions from distinct sites, and associate a so-called activation parameter to each site. Our analysis shows that the ultrasensitivity generally increases as the conformational free energy contribution from one or more sites is strengthened. Furthermore, ultrasensitivity depends on the mean of the activation parameters and not on their variability. In some cases, we find that the best way to maximize ultrasensitivity is to make the contribution from all sites as strong as possible. These results provide insights into the performance objectives of multiple modification/binding sites and thus help gain a greater understanding of signaling and its role in diseases.


Assuntos
Sítios de Ligação/fisiologia , Metabolismo Energético/fisiologia , Processamento de Proteína Pós-Traducional/fisiologia , Proteínas , Transdução de Sinais/fisiologia , Ligantes , Modelos Biológicos , Fosforilação/fisiologia , Conformação Proteica , Subunidades Proteicas , Proteínas/química , Proteínas/metabolismo , Termodinâmica
6.
J Chem Inf Model ; 60(8): 3910-3934, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32786511

RESUMO

Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.


Assuntos
Desenho de Fármacos , Descoberta de Drogas , Mapas de Interação de Proteínas/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/farmacologia , Algoritmos , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/metabolismo , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/metabolismo , Bases de Dados de Proteínas , Humanos , Ligantes , Aprendizado de Máquina , Simulação de Acoplamento Molecular , Terapia de Alvo Molecular , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/metabolismo , Proteínas/química , Proteínas/metabolismo , Bibliotecas de Moléculas Pequenas/química
7.
Biochem Biophys Res Commun ; 530(1): 4-9, 2020 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-32828312

RESUMO

COVID-19 has become one of the worst epidemic in the world, currently already more than four million people have been infected, which probably co-exist with human beings, and has a significant impact on the global economy and political order. In the process of fighting against the epidemic in China, the clinical value of a variety of herbal medicines has been recognized and written into the clinical application guide. However, their effective molecular mechanism and potential targets are still not clear. Pathology and pharmacology research will gradually attract attention in the post-epidemic outbreak term. Here, we constructed a COVID-19 protein microarray of potential therapy targets, which contains the main drug targets to the SARS-CoV-2 virus and the anti-virus, anti-inflammatory cellar targets of the host. Series of quality controls test has been carried out, which showed that it could be applied for drug target screening of bio-active natural products. The establishment of this microarray will provide a useful tool for the study of the molecular pharmacology of natural products.


Assuntos
Antivirais/farmacologia , Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Medicamentos de Ervas Chinesas/farmacologia , Pneumonia Viral/tratamento farmacológico , Proteínas/metabolismo , Proteínas Virais/metabolismo , Betacoronavirus/metabolismo , Produtos Biológicos/farmacologia , Ácido Clorogênico/farmacologia , Infecções por Coronavirus/metabolismo , Diterpenos/farmacologia , Descoberta de Drogas , Glucosídeos/farmacologia , Células HEK293 , Humanos , Simulação de Acoplamento Molecular , Terapia de Alvo Molecular , Pandemias , Pneumonia Viral/metabolismo , Análise Serial de Proteínas , Estilbenos/farmacologia
8.
Phys Rev Lett ; 125(7): 078102, 2020 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-32857533

RESUMO

Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation, and filtration processes. Their current description via diffusion equations with mixed boundary conditions is limited to simple surface reactions with infinite or constant reactivity. In this Letter, we propose a probabilistic approach based on the concept of boundary local time to investigate the intricate dynamics of diffusing particles near a reactive surface. Reformulating surface-particle interactions in terms of stopping conditions, we obtain in a unified way major diffusion-reaction characteristics such as the propagator, the survival probability, the first-passage time distribution, and the reaction rate. This general formalism allows us to describe new surface reaction mechanisms such as for instance surface reactivity depending on the number of encounters with the diffusing particle that can model the effects of catalyst fooling or membrane degradation. The disentanglement of the geometric structure of the medium from surface reactivity opens far-reaching perspectives for modeling, optimization, and control of diffusion-mediated surface phenomena.


Assuntos
Modelos Biológicos , Modelos Químicos , Membrana Celular/química , DNA/química , Difusão , Proteínas/química , Propriedades de Superfície , Termodinâmica
9.
Medicine (Baltimore) ; 99(29): e20574, 2020 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-32702813

RESUMO

RATIONALE: Schaaf-Yang syndrome, a rare imprinted hereditary disease caused by MAGEL2 variants, manifests as developmental delay/intellectual disability, neonatal hypotonia, feeding difficulties, contractures, and autism spectrum disorder. PATIENT CONCERNS: Patient 1 and 2 were infant girls presenting facial dysmorphisms, contractures of interphalangeal joints, neonatal hypotonia, feeding difficulties, congenital heart diseases, and respiratory complications. Besides, Patient 2 presented with delayed psychomotor development. DIAGNOSIS: Whole-exome sequencing was performed and heterozygous mutations of the MAGEL2 gene were detected in the patients. They were diagnosed as Schaaf-Yang syndrome. INTERVENTIONS: The patients received supportive treatment including mechanical ventilation, parenteral nutrition and gastric tube feeding. OUTCOMES: Whole-exome sequencing revealed de novo heterozygous c.1996dupC pathogenic mutations in the MAGEL2 gene in the 2 patients. They died due to respiratory failure at the age of 20 days and 98 days, respectively. LESSONS: Our results indicate that MAGEL2 variants can cause congenital heart disease and fatal respiratory complications, broadening the phenotypic spectrum and adding to the fatal cases of Schaaf-Yang syndrome. We highly suggest that the MAGEL2 gene should be added to gene-panels or gene-filters in next-generation sequencing-based diagnostics, which is of great significance for early diagnosis and early intervention of Schaaf-Yang syndrome patients.


Assuntos
Anormalidades Múltiplas/genética , Testes Genéticos/métodos , Proteínas/genética , Sequenciamento Completo do Exoma/métodos , Criança , Contratura/genética , Anormalidades Craniofaciais/genética , Deficiências do Desenvolvimento/genética , Evolução Fatal , Transtornos da Alimentação e da Ingestão de Alimentos/genética , Feminino , Articulações dos Dedos/fisiopatologia , Cardiopatias Congênitas/genética , Humanos , Lactente , Recém-Nascido , Masculino , Hipotonia Muscular/genética , Atrofia Muscular/genética , Cuidados Paliativos , Insuficiência Respiratória/genética , Síndrome
10.
Nat Protoc ; 15(8): 2341-2386, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32690956

RESUMO

Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler (https://github.com/CCprofiler/CCprofiler). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis.


Assuntos
Cromatografia em Gel , Espectrometria de Massas , Proteínas/isolamento & purificação , Proteínas/metabolismo , Proteômica/métodos , Células HEK293 , Humanos
11.
PLoS One ; 15(7): e0235263, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32639981

RESUMO

Dependent peptide searching is a method for discovering covalently-modified peptides-and therefore proteins-in mass-spectrometry-based proteomics experiments. Being more permissive than standard search methods, it has the potential to discover novel modifications (e.g., post-translational modifications occurring in vivo, or modifications introduced in vitro). However, few studies have explored dependent peptide search results in an untargeted way. In the present study, we sought to evaluate dependent peptide searching as a means of characterising proteins that have been modified in vitro. We generated a model data set by analysing N-ethylmaleimide-treated bovine serum albumin, and performed dependent peptide searches using the popular MaxQuant software. To facilitate interpretation of the search results (hundreds of dependent peptides), we developed a series of visualisation tools (R scripts). We used the tools to assess the diversity of putative modifications in the albumin, and to pinpoint hypothesised modifications. We went on to explore the tools' generality via analyses of public data from studies of rat and human proteomes. Of 19 expected sites of modification (one in rat cofilin-1 and 18 across six different human plasma proteins), eight were found and correctly localised. Apparently, some sites went undetected because chemical enrichment had depleted necessary analytes (potential 'base' peptides). Our results demonstrate (i) the ability of the tools to provide accurate and informative visualisations, and (ii) the usefulness of dependent peptide searching for characterising in vitro protein modifications. Our model data are available via PRIDE/ProteomeXchange (accession number PXD013040).


Assuntos
Peptídeos/análise , Proteínas/química , Proteômica/métodos , Animais , Proteínas Sanguíneas/química , Bovinos , Bases de Dados de Proteínas , Etilmaleimida/análogos & derivados , Humanos , Processamento de Proteína Pós-Traducional , Ratos , Soroalbumina Bovina/química
12.
BMC Bioinformatics ; 21(1): 275, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32611389

RESUMO

BACKGROUND: Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutations in functionally essential residues to optimize their function. However, the discovery of beneficial mutations for proteins is a complex task, with a time-consuming and high cost for experimental validation. Hence, computational approaches have been used to propose new insights for experiments narrowing the search space and reducing the costs. RESULTS: In this study, we developed Proteus (an acronym for Protein Engineering Supporter), a new algorithm for proposing mutation pairs in a target 3D structure. These suggestions are based on contacts observed in other known structures from Protein Data Bank (PDB). Proteus' basic assumption is that if a non-interacting pair of amino acid residues in the target structure is exchanged to an interacting pair, this could enhance protein stability. This trade is only allowed if the main-chain conformation of the residues involved in the contact is conserved. Furthermore, no steric impediment is expected between the proposed mutations and the surrounding protein atoms. To evaluate Proteus, we performed two case studies with proteins of industrial interests. In the first case study, we evaluated if the mutations suggested by Proteus for four protein structures enhance the number of inter-residue contacts. Our results suggest that most mutations proposed by Proteus increase the number of interactions into the protein. In the second case study, we used Proteus to suggest mutations for a lysozyme protein. Then, we compared Proteus' outcomes to mutations with available experimental evidence reported in the ProTherm database. Four mutations, in which our results agree with the experimental data, were found. This could be initial evidence that changes in the side-chain of some residues do not cause disturbances that harm protein structure stability. CONCLUSION: We believe that Proteus could be used combined with other methods to give new insights into the rational development of engineered proteins. Proteus user-friendly web-based tool is available at < http://proteus.dcc.ufmg.br >.


Assuntos
Proteínas/química , Interface Usuário-Computador , Algoritmos , Bases de Dados de Proteínas , Muramidase/química , Muramidase/genética , Muramidase/metabolismo , Mutagênese , Engenharia de Proteínas/métodos , Estrutura Terciária de Proteína , Proteínas/genética , Proteínas/metabolismo
13.
Adv Exp Med Biol ; 1250: 35-48, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32601936

RESUMO

Injectable in situ-forming hydrogels have been used clinically in diverse biomedical applications. These hydrogels have distinct advantages such as easy management and minimal invasiveness. The hydrogels are aqueous formulations, and a simple injection at the target site replaces a traditional surgical procedure. Here, we review injectable in situ-forming hydrogels that are formulated by physical and chemical methods to deliver proteins and peptides. Prospects for using in situ-forming hydrogels for several specific applications are also discussed.


Assuntos
Hidrogéis , Peptídeos , Proteínas , Sistemas de Liberação de Medicamentos , Humanos , Hidrogéis/administração & dosagem , Hidrogéis/química , Injeções , Peptídeos/administração & dosagem , Proteínas/administração & dosagem
14.
Nat Commun ; 11(1): 3336, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620782

RESUMO

We describe theory, experiments, and analyses of three-color Förster resonance energy transfer (FRET) spectroscopy for probing sub-millisecond conformational dynamics of protein folding and binding of disordered proteins. We devise a scheme that uses single continuous-wave laser excitation of the donor instead of alternating excitation of the donor and one of the acceptors. This scheme alleviates photophysical problems of acceptors such as rapid photobleaching, which is crucial for high time resolution experiments with elevated illumination intensity. Our method exploits the molecular species with one of the acceptors absent or photobleached, from which two-color FRET data is collected in the same experiment. We show that three FRET efficiencies and kinetic parameters can be determined without alternating excitation from a global maximum likelihood analysis of two-color and three-color photon trajectories. We implement co-parallelization of CPU-GPU processing, which leads to a significant reduction of the likelihood calculation time for efficient parameter determination.


Assuntos
Algoritmos , Transferência Ressonante de Energia de Fluorescência/métodos , Modelos Teóricos , Conformação Proteica , Dobramento de Proteína , Proteínas/química , Cor , Transferência Ressonante de Energia de Fluorescência/instrumentação , Transferência Ressonante de Energia de Fluorescência/estatística & dados numéricos , Proteínas Intrinsicamente Desordenadas/química , Proteínas Intrinsicamente Desordenadas/metabolismo , Cinética , Microscopia Confocal , Fotodegradação , Fótons , Ligação Proteica , Proteínas/metabolismo , Fatores de Tempo
15.
Nat Commun ; 11(1): 3368, 2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32632093

RESUMO

Blood pressure (BP) was inconsistently associated with migraine and the mechanisms of BP-lowering medications in migraine prophylaxis are unknown. Leveraging large-scale summary statistics for migraine (Ncases/Ncontrols = 59,674/316,078) and BP (N = 757,601), we find positive genetic correlations of migraine with diastolic BP (DBP, rg = 0.11, P = 3.56 × 10-06) and systolic BP (SBP, rg = 0.06, P = 0.01), but not pulse pressure (PP, rg = -0.01, P = 0.75). Cross-trait meta-analysis reveals 14 shared loci (P ≤ 5 × 10-08), nine of which replicate (P < 0.05) in the UK Biobank. Five shared loci (ITGB5, SMG6, ADRA2B, ANKDD1B, and KIAA0040) are reinforced in gene-level analysis and highlight potential mechanisms involving vascular development, endothelial function and calcium homeostasis. Mendelian randomization reveals stronger instrumental estimates of DBP (OR [95% CI] = 1.20 [1.15-1.25]/10 mmHg; P = 5.57 × 10-25) on migraine than SBP (1.05 [1.03-1.07]/10 mmHg; P = 2.60 × 10-07) and a corresponding opposite effect for PP (0.92 [0.88-0.95]/10 mmHg; P = 3.65 × 10-07). These findings support a critical role of DBP in migraine susceptibility and shared biology underlying BP and migraine.


Assuntos
Pressão Sanguínea/genética , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/métodos , Metanálise como Assunto , Transtornos de Enxaqueca/genética , Polimorfismo de Nucleotídeo Único , Humanos , Hipertensão/genética , Cadeias beta de Integrinas/genética , Análise da Randomização Mendeliana/métodos , Proteínas/genética , Receptores Adrenérgicos alfa 2/genética , Fatores de Risco , Telomerase/genética
16.
Nat Commun ; 11(1): 3409, 2020 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-32641778

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is associated with high mortality and therapy resistance. Here, we show that low expression of κB-Ras GTPases is frequently detected in PDAC and correlates with higher histologic grade. In a model of KRasG12D-driven PDAC, loss of κB-Ras accelerates tumour development and shortens median survival. κB-Ras deficiency promotes acinar-to-ductal metaplasia (ADM) during tumour initiation as well as tumour progression through intrinsic effects on proliferation and invasion. κB-Ras proteins are also required for acinar regeneration after pancreatitis, demonstrating a general role in control of plasticity. Molecularly, upregulation of Ral GTPase activity and Sox9 expression underlies the observed phenotypes, identifying a previously unrecognized function of Ral signalling in ADM. Our results provide evidence for a tumour suppressive role of κB-Ras proteins and highlight low κB-Ras levels and consequent loss of Ral control as risk factors, thus emphasizing the necessity for therapeutic options that allow interference with Ral-driven signalling.


Assuntos
Células Acinares/metabolismo , Carcinoma Ductal Pancreático/genética , GTP Fosfo-Hidrolases/genética , Neoplasias Pancreáticas/genética , Pancreatite/genética , Proteínas/genética , Células Acinares/patologia , Idoso , Animais , Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/patologia , Linhagem Celular Tumoral , Feminino , GTP Fosfo-Hidrolases/metabolismo , Regulação da Expressão Gênica , Humanos , Proteínas I-kappa B/genética , Proteínas I-kappa B/metabolismo , Estimativa de Kaplan-Meier , Masculino , Metaplasia/genética , Metaplasia/metabolismo , Camundongos Endogâmicos C57BL , Camundongos Knockout , Pessoa de Meia-Idade , Neoplasias Pancreáticas/metabolismo , Neoplasias Pancreáticas/patologia , Pancreatite/metabolismo , Proteínas/metabolismo , Fatores de Transcrição SOX9/genética , Fatores de Transcrição SOX9/metabolismo , Proteínas ral de Ligação ao GTP/genética , Proteínas ral de Ligação ao GTP/metabolismo , Proteínas ras/genética , Proteínas ras/metabolismo
17.
Opt Express ; 28(12): 18479-18492, 2020 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-32680046

RESUMO

Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.


Assuntos
Grafite , Nanopartículas Metálicas , Espectrofotometria Infravermelho/instrumentação , Ressonância de Plasmônio de Superfície/instrumentação , Técnicas Biossensoriais/instrumentação , Técnicas Biossensoriais/métodos , Desenho de Equipamento/métodos , Proteínas/análise , Ressonância de Plasmônio de Superfície/métodos
18.
Wei Sheng Yan Jiu ; 49(3): 453-457, 2020 May.
Artigo em Chinês | MEDLINE | ID: mdl-32693896

RESUMO

OBJECTIVE: To study the digestive stability of 5-enolpyruvylshikimate-3-phosphate synthase(EPSPS) protein and phosphinothricina cetyltransferase(PAT) protein in simulated gastric fluid. METHODS: The component of simulated gastric fluid was based on the method of target protein digestive stability in simulative gastric and intestinal in national standard of the People's Republic of China(Published by the Ministry of Agriculture No. 869-2-2007). The test model of stability of different protein to digestion in Simulated Gastric Fluid was established by dodecyl sulfate, sodium salt-polyacrylamide gel electrophoresis(SDS-PAGE)and western blot. The degradation of EPSPS protein and PAT protein in simulated gastric fluid at different digestion time points were analyzed. RESULTS: The experiment showed that EPSPS protein and PAT protein were completely digested within 15 s in simulated gastric fluid, no any remain of protein was detected by SDS-PAGE and Western blot, indicating that EPSPS protein and PAT protein were easily digested in the simulated gastric. CONCLUSION: EPSPS protein and PAT protein do not have immunogenicity after digestion with simulated gastric fluid.


Assuntos
Digestão , Proteínas , Western Blotting , China , Eletroforese em Gel de Poliacrilamida
19.
PLoS One ; 15(6): e0235153, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603341

RESUMO

The secondary structure prediction of proteins is a classic topic of computational structural biology with a variety of applications. During the past decade, the accuracy of prediction achieved by state-of-the-art algorithms has been >80%; meanwhile, the time cost of prediction increased rapidly because of the exponential growth of fundamental protein sequence data. Based on literature studies and preliminary observations on the relationships between the size/homology of the fundamental protein dataset and the speed/accuracy of predictions, we raised two hypotheses that might be helpful to determine the main influence factors of the efficiency of secondary structure prediction. Experimental results of size and homology reductions of the fundamental protein dataset supported those hypotheses. They revealed that shrinking the size of the dataset could substantially cut down the time cost of prediction with a slight decrease of accuracy, which could be increased on the contrary by homology reduction of the dataset. Moreover, the Shannon information entropy could be applied to explain how accuracy was influenced by the size and homology of the dataset. Based on these findings, we proposed that a proper combination of size and homology reductions of the protein dataset could speed up the secondary structure prediction while preserving the high accuracy of state-of-the-art algorithms. Testing the proposed strategy with the fundamental protein dataset of the year 2018 provided by the Universal Protein Resource, the speed of prediction was enhanced over 20 folds while all accuracy measures remained equivalently high. These findings are supposed helpful for improving the efficiency of researches and applications depending on the secondary structure prediction of proteins. To make future implementations of the proposed strategy easy, we have established a database of size and homology reduced protein datasets at http://10.life.nctu.edu.tw/UniRefNR.


Assuntos
Estrutura Secundária de Proteína , Proteínas/química , Algoritmos , Biologia Computacional , Confiabilidade dos Dados , Bases de Dados de Proteínas , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
20.
Sci Total Environ ; 742: 140597, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-32629271

RESUMO

Polychlorinated biphenyls (PCBs) and halogen flame retardants (HFRs) are major pollutants in e-waste recycling area. High internal exposure levels of PCBs and HFRs are harmful to human thyroid hormone (TH) equilibrium. To examine their disrupting effects on TH, we conducted a study on children (n = 114) of an e-waste recycling and a control area in South China. Concentrations of PCBs, HFRs, and TH levels were determined in serum samples. TH related proteins and their corresponding gene were also monitored as markers of such disruption. Levels of these chemicals in the exposed group were much greater than those in the control group. Results of the linear regression and generalized additive model indicated the presence of close relationships between the internal exposure levels and the responses of TH related proteins, gene expression. More extensive exposure concentrations of these chemicals led to higher expression of iodothyronine deiodinase I and decreased the concentrations of thyroid-stimulating hormone, expression of TH receptor α, indicating the exertion of discrepant and even contrary influences on equilibrium of TH, and a compensation of these mechanisms may kept the homeostasis of TH. These results for children warrant further investigation on the health risks of PCBs and HFRs exposure in e-waste area.


Assuntos
Resíduo Eletrônico/análise , Retardadores de Chama , Bifenilos Policlorados/análise , Criança , China , Halogênios , Humanos , Proteínas , Reciclagem , Hormônios Tireóideos
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