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1.
J Clin Monit Comput ; 36(1): 121-130, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-33315176

RESUMO

Brain monitors which track quantitative electroencephalogram (EEG) signatures to monitor sedation levels are drug and patient specific. There is a need for robust sedation level monitoring systems to accurately track sedation levels across all drug classes, sex and age groups. Forty-four quantitative features estimated from a pooled dataset of 204 EEG recordings from 66 healthy adult volunteers who received either propofol, dexmedetomidine, or sevoflurane (all with and without remifentanil) were used in a machine learning based automated system to estimate the depth of sedation. Model training and evaluation were performed using leave-one-out cross validation methodology. We trained four machine learning models to predict sedation levels and evaluated the influence of remifentanil, age, and sex on the prediction performance. The area under the receiver-operator characteristic curve (AUC) was used to assess the performance of the prediction model. The ensemble tree with bagging outperformed other machine learning models and predicted sedation levels with an AUC = 0.88 (0.81-0.90). There were significant differences in the prediction probability of the automated systems when trained and tested across different age groups and sex. The performance of the EEG based sedation level prediction system is drug, sex, and age specific. Nonlinear machine-learning models using quantitative EEG features can accurately predict sedation levels. The results obtained in this study may provide a useful reference for developing next generation EEG based sedation level prediction systems using advanced machine learning algorithms. Clinical trial registration: NCT02043938 and NCT03143972.


Assuntos
Eletroencefalografia , Propofol , Adulto , Algoritmos , Eletroencefalografia/métodos , Humanos , Aprendizado de Máquina , Dor , Remifentanil
2.
Luminescence ; 36(4): 849-859, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33569861

RESUMO

Eu3+ -activated Ba2 V2 O7 (Ba2-x V2 O7 :xEu3+ ) phosphor materials were synthesized using a hydrothermal method and different concentrations of europium (x = 0.01, 0.02, 0.03, 0.04, and 0.05%). Phase purity, structural, morphological, optical, and luminescence characteristics of the as-synthesized phosphors were studied using powder X-ray diffraction (XRD), high resolution scanning electron microscopy, UV-visible spectroscopy, and fluorescence spectrometry. The recorded XRD patterns of the as-synthesized phosphors were indexed and predicted to be a triclinic structure. A cube-like morphology was obtained for the as-prepared samples. Broad absorption in the UV region from 200 nm to 380 nm was observed and the good transparency in the visible region at 400-800 nm originated from the [VO4 ]3- group charge transfer (CT) transition. The broad emission peak centred at 499 nm was due to the CT band of the [VO4 ]3- group. Also, a sharp peak observed at 613 nm was due to the electric dipole transition of 5 D0 →7 F2 of Eu3+ ions that occupied the lattice sites without inversion symmetry for all concentrations. The colour qualities of the as-prepared samples were calculated using Commission International de l'Eclairage coordinates. The colour-rending index (CRI) value was 86 for the Ba1.97 V2 O7 :0.03Eu3+ phosphor. Furthermore, a WLED with a high CRI value of 95 was achieved by coupling the 3 W 356 nm near-UV light-emitting diode (LED) chip with the Ba2-x V2 O7 :xEu3+ phosphor. These results suggested that the as-prepared phosphor materials are potential candidates for fabrication of near-UV chip excited WLEDs.


Assuntos
Substâncias Luminescentes , Európio , Luminescência , Microscopia Eletrônica de Varredura , Difração de Raios X
3.
Proteins ; 2020 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-32865821

RESUMO

N-acetylglucosamine 6-phosphate deacetylase (NagA) catalyzes the conversion of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate in amino sugar catabolism. This conversion is an essential step in the catabolism of sialic acid in several pathogenic bacteria, including Pasteurella multocida, and thus NagA is identified as a potential drug target. Here, we report the unique structural features of NagA from P. multocida (PmNagA) resolved to 1.95 Å. PmNagA displays an altered quaternary architecture with unique interface interactions compared to its close homolog, the Escherichia coli NagA (EcNagA). We confirmed that the altered quaternary structure is not a crystallographic artifact using single particle electron cryo-microscopy. Analysis of the determined crystal structure reveals a set of hot-spot residues involved in novel interactions at the dimer-dimer interface. PmNagA binds to one Zn2+ ion in the active site and demonstrates kinetic parameters comparable to other bacterial homologs. Kinetic studies reveal that at high substrate concentrations (~10-fold the KM ), the tetrameric PmNagA displays hysteresis similar to its distant neighbor, the dimeric Staphylococcus aureus NagA (SaNagA). Our findings provide key information on structural and functional properties of NagA in P. multocida that could be utilized to design novel antibacterials.

4.
Proc Natl Acad Sci U S A ; 113(41): 11513-11518, 2016 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-27688756

RESUMO

The walleye (Sander vitreus) is a golden yellow fish that inhabits the Northern American lakes. The recent sightings of the blue walleye and the correlation of its sighting to possible increased UV radiation have been proposed earlier. The underlying molecular basis of its adaptation to increased UV radiation is the presence of a protein (Sandercyanin)-ligand complex in the mucus of walleyes. Degradation of heme by UV radiation results in the formation of Biliverdin IXα (BLA), the chromophore bound to Sandercyanin. We show that Sandercyanin is a monomeric protein that forms stable homotetramers on addition of BLA to the protein. A structure of the Sandercyanin-BLA complex, purified from the fish mucus, reveals a glycosylated protein with a lipocalin fold. This protein-ligand complex absorbs light in the UV region (λmax of 375 nm) and upon excitation at this wavelength emits in the red region (λmax of 675 nm). Unlike all other known biliverdin-bound fluorescent proteins, the chromophore is noncovalently bound to the protein. We provide here a molecular rationale for the observed spectral properties of Sandercyanin.


Assuntos
Proteínas/química , Biliverdina/química , Cristalografia por Raios X , Fluorescência , Modelos Moleculares , Proteínas Recombinantes/química
5.
Tumour Biol ; 40(5): 1010428318780859, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29888653

RESUMO

The goal of this study was to isolate cancer stem-like cells marked by high expression of CD44, a putative cancer stem cell marker, from primary oral squamous cell carcinomas and identify distinctive gene expression patterns in these cells. From 1 October 2013 to 4 September 2015, 76 stage III-IV primary oral squamous cell carcinoma of the gingivobuccal sulcus were resected. In all, 13 tumours were analysed by immunohistochemistry to visualise CD44-expressing cells. Expression of CD44 within The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma RNA-sequencing data was also assessed. Seventy resected tumours were dissociated into single cells and stained with antibodies to CD44 as well as CD45 and CD31 (together referred as Lineage/Lin). From 45 of these, CD44+Lin- and CD44-Lin- subpopulations were successfully isolated using fluorescence-activated cell sorting, and good-quality RNA was obtained from 14 such sorted pairs. Libraries from five pairs were sequenced and the results analysed using bioinformatics tools. Reverse transcription quantitative polymerase chain reaction was performed to experimentally validate the differential expression of selected candidate genes identified from the transcriptome sequencing in the same 5 and an additional 9 tumours. CD44 was expressed on the surface of poorly differentiated tumour cells, and within the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma samples, its messenger RNA levels were higher in tumours compared to normal. Transcriptomics revealed that 102 genes were upregulated and 85 genes were downregulated in CD44+Lin- compared to CD44-Lin- cells in at least 3 of the 5 tumours sequenced. The upregulated genes included those involved in immune regulation, while the downregulated genes were enriched for genes involved in cell adhesion. Decreased expression of PCDH18, MGP, SPARCL1 and KRTDAP was confirmed by reverse transcription quantitative polymerase chain reaction. Lower expression of the cell-cell adhesion molecule PCDH18 correlated with poorer overall survival in the The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma data highlighting it as a potential negative prognostic factor in this cancer.


Assuntos
Caderinas/biossíntese , Carcinoma de Células Escamosas/genética , Adesão Celular/genética , Receptores de Hialuronatos/genética , Neoplasias Bucais/genética , Células-Tronco Neoplásicas/patologia , Ácido Aspártico Endopeptidases/biossíntese , Biomarcadores Tumorais/imunologia , Proteínas de Ligação ao Cálcio/biossíntese , Carcinoma de Células Escamosas/patologia , Linhagem Celular Tumoral , Proteínas da Matriz Extracelular/biossíntese , Citometria de Fluxo , Regulação Neoplásica da Expressão Gênica/genética , Papillomavirus Humano 16/genética , Papillomavirus Humano 16/isolamento & purificação , Papillomavirus Humano 18/genética , Papillomavirus Humano 18/isolamento & purificação , Humanos , Receptores de Hialuronatos/imunologia , Receptores de Hialuronatos/metabolismo , Antígenos Comuns de Leucócito/imunologia , Neoplasias Bucais/patologia , Molécula-1 de Adesão Celular Endotelial a Plaquetas/imunologia , Protocaderinas , RNA Mensageiro/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Proteína de Matriz Gla
6.
Microb Cell Fact ; 17(1): 192, 2018 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-30509260

RESUMO

INTRODUCTION: Chemical industries are constantly in search of an expeditious and environmentally benign method for producing chiral synthons. Ketoreductases have been used as catalysts for enantioselective conversion of desired prochiral ketones to their corresponding alcohol. We chose reported promiscuous ketoreductases belonging to different protein families and expressed them in E. coli to evaluate their ability as whole-cell catalysts for obtaining chiral alcohol intermediates of pharmaceutical importance. Apart from establishing a method to produce high value (S)-specific alcohols that have not been evaluated before, we propose an in silico analysis procedure to predict product chirality. RESULTS: Six enzymes originating from Sulfolobus sulfotaricus, Zygosaccharomyces rouxii, Hansenula polymorpha, Corynebacterium sp. ST-10, Synechococcus sp. PCC 7942 and Bacillus sp. ECU0013 with reported efficient activity for dissimilar substrates are compared here to arrive at an optimal enzyme for the method. Whole-cell catalysis of ketone intermediates for drugs like Aprepitant, Sitagliptin and Dolastatin using E. coli over-expressing these enzymes yielded (S)-specific chiral alcohols. We explain this chiral specificity for the best-performing enzyme, i.e., Z. rouxii ketoreductase using in silico modelling and MD simulations. This rationale was applied to five additional ketones that are used in the synthesis of Crizotinib, MA-20565 (an antifungal agent), Sulopenem, Rivastigmine, Talampanel and Barnidipine and predicted the yield of (S) enantiomers. Experimental evaluation matched the in silico analysis wherein ~ 95% (S)-specific alcohol with a chemical yield of 23-79% was obtained through biotransformation. Further, the cofactor re-cycling was optimized by switching the carbon source from glucose to sorbitol that improved the chemical yield to 85-99%. CONCLUSIONS: Here, we present a strategy to synthesize pharmaceutically relevant chiral alcohols by ketoreductases using a cofactor balanced whole-cell catalysis scheme that is useful for the industry. Based on the results obtained in these trials, Zygosaccharomyces rouxii ketoreductase was identified as a proficient enzyme to obtain (S)-specific alcohols from their respective ketones. The whole-cell catalyst when combined with nutrient modulation of using sorbitol as a carbon source helped obtain high enantiomeric and chemical yield.


Assuntos
Biotransformação , Etanol/metabolismo , Cetonas/metabolismo , Catálise
7.
Mol Cell ; 40(3): 433-43, 2010 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-21070969

RESUMO

WD40-repeat ß-propellers are found in a wide range of proteins involved in distinct biological activities. We define a large subset of WD40 ß-propellers as a class of ubiquitin-binding domains. Using the ß-propeller from Doa1/Ufd3 as a paradigm, we find the conserved top surface of the Doa1 ß-propeller binds the hydrophobic patch of ubiquitin centered on residues I44, L8, and V70. Mutations that disrupt ubiquitin binding abrogate Doa1 function, demonstrating the importance of this interaction. We further demonstrate that WD40 ß-propellers from a functionally diverse set of proteins bind ubiquitin in a similar fashion. This set includes members of the F box family of SCF ubiquitin E3 ligase adaptors. Using mutants defective in binding, we find that ubiquitin interaction by the F box protein Cdc4 promotes its autoubiquitination and turnover. Collectively, our results reveal a molecular mechanism that may account for how ubiquitin controls a broad spectrum of cellular activities.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/química , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas F-Box/metabolismo , Sequências Repetitivas de Aminoácidos , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Ubiquitina/metabolismo , Sítios de Ligação , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Cristalografia por Raios X , Proteínas F-Box/química , Proteína 7 com Repetições F-Box-WD , Humanos , Modelos Moleculares , Processamento de Proteína Pós-Traducional , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Reprodutibilidade dos Testes , Relação Estrutura-Atividade , Propriedades de Superfície , Ubiquitina-Proteína Ligases/química , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitinação
8.
Biochemistry ; 56(28): 3632-3646, 2017 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-28640600

RESUMO

During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. The apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators 2,2'-bipyridine and 1,10-phenanthroline displace the water and form a pentacoordinated zinc. The enzyme-NADH complex has a closed conformation similar to that of ternary complexes with coenzyme and substrate analogues; the coordination of the catalytic zinc is similar to that found in the apoenzyme, except that a minor, alternative position for the catalytic zinc is ∼1.3 Šfrom the major position and closer to Glu-68, which could form the alternative coordination to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide or N-benzylformamide (or with NAD+ and fluoro alcohols) have the classical tetracoordinated zinc, and no water is bound to the zinc or the nicotinamide rings. The major forms of the enzyme in the mechanism have a tetracoordinated zinc, where the carboxylate group of Glu-68 could participate in the exchange of water and substrates on the zinc. Hydride transfer in the Michaelis complexes does not involve a nearby water.


Assuntos
Álcool Desidrogenase/metabolismo , Fígado/enzimologia , Zinco/metabolismo , 2,2'-Dipiridil/metabolismo , Adenosina Difosfato Ribose/metabolismo , Álcool Desidrogenase/química , Animais , Domínio Catalítico , Cristalografia por Raios X , Formamidas/metabolismo , Cavalos , Cinética , Fígado/metabolismo , Modelos Moleculares , NAD/metabolismo , Fenantrolinas/metabolismo , Ligação Proteica , Conformação Proteica , Água/química , Água/metabolismo , Zinco/química
9.
Arch Biochem Biophys ; 591: 35-42, 2016 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-26743849

RESUMO

Yeast alcohol dehydrogenase I is a homotetramer of subunits with 347 amino acid residues, catalyzing the oxidation of alcohols using NAD(+) as coenzyme. A new X-ray structure was determined at 3.0 Å where both subunits of an asymmetric dimer bind coenzyme and trifluoroethanol. The tetramer is a pair of back-to-back dimers. Subunit A has a closed conformation and can represent a Michaelis complex with an appropriate geometry for hydride transfer between coenzyme and alcohol, with the oxygen of 2,2,2-trifluoroethanol ligated at 2.1 Å to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. Subunit B has an open conformation, and the coenzyme interacts with amino acid residues from the coenzyme binding domain, but not with residues from the catalytic domain. Coenzyme appears to bind to and dissociate from the open conformation. The catalytic zinc in subunit B has an alternative, inverted coordination with Cys-43, Cys-153, His-66 and the carboxylate of Glu-67, while the oxygen of trifluoroethanol is 3.5 Å from the zinc. Subunit B may represent an intermediate in the mechanism after coenzyme and alcohol bind and before the conformation changes to the closed form and the alcohol oxygen binds to the zinc and displaces Glu-67.


Assuntos
Álcool Desidrogenase/química , Álcool Desidrogenase/ultraestrutura , NAD/química , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/ultraestrutura , Trifluoretanol/química , Sítios de Ligação , Catálise , Coenzimas/química , Coenzimas/ultraestrutura , Simulação por Computador , Ativação Enzimática , Modelos Químicos , Modelos Moleculares , NAD/ultraestrutura , Ligação Proteica , Conformação Proteica , Especificidade por Substrato
10.
BMC Plant Biol ; 15: 212, 2015 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-26315624

RESUMO

BACKGROUND: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. RESULTS: The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. CONCLUSIONS: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.


Assuntos
Regulação da Expressão Gênica de Plantas , Genoma de Planta , Ocimum/genética , Índia , Ocimum/metabolismo , Folhas de Planta/metabolismo , Plantas Medicinais/genética , Plantas Medicinais/metabolismo
11.
Phys Rev Lett ; 114(9): 098302, 2015 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-25793858

RESUMO

A paradigm for internally driven matter is the active nematic liquid crystal, whereby the equations of a conventional nematic are supplemented by a minimal active stress that violates time-reversal symmetry. In practice, active fluids may have not only liquid-crystalline but also viscoelastic polymer degrees of freedom. Here we explore the resulting interplay by coupling an active nematic to a minimal model of polymer rheology. We find that adding a polymer can greatly increase the complexity of spontaneous flow, but can also have calming effects, thereby increasing the net throughput of spontaneous flow along a pipe (a "drag-reduction" effect). Remarkably, active turbulence can also arise after switching on activity in a sufficiently soft elastomeric solid.


Assuntos
Modelos Biológicos , Modelos Químicos , Substâncias Viscoelásticas/química , Bactérias/química , Fenômenos Fisiológicos Bacterianos , Cristais Líquidos/química , Reologia/métodos , Natação
12.
Biochemistry ; 53(36): 5791-803, 2014 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-25157460

RESUMO

Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.


Assuntos
Álcool Desidrogenase/metabolismo , Saccharomyces cerevisiae/enzimologia , Álcool Desidrogenase/química , Biocatálise , Domínio Catalítico , Cristalografia por Raios X , Modelos Moleculares , Conformação Proteica
13.
J Biol Chem ; 288(10): 6890-902, 2013 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-23300079

RESUMO

NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins) are intracellular pattern recognition receptors that activate inflammation and autophagy. These pathways rely on the caspase recruitment domains (CARDs) within the receptors, which serve as protein interaction platforms that coordinately regulate immune signaling. We show that NOD1 CARD binds ubiquitin (Ub), in addition to directly binding its downstream targets receptor-interacting protein kinase 2 (RIP2) and autophagy-related protein 16-1 (ATG16L1). NMR spectroscopy and structure-guided mutagenesis identified a small hydrophobic surface of NOD1 CARD that binds Ub. In vitro, Ub competes with RIP2 for association with NOD1 CARD. In vivo, we found that the ligand-stimulated activity of NOD1 with a mutant CARD lacking Ub binding but retaining ATG16L1 and RIP2 binding is increased relative to wild-type NOD1. Likewise, point mutations in the tandem NOD2 CARDs at positions analogous to the surface residues defining the Ub interface on NOD1 resulted in loss of Ub binding and increased ligand-stimulated NOD2 signaling. These data suggest that Ub binding provides a negative feedback loop upon NOD-dependent activation of RIP2.


Assuntos
Proteína Adaptadora de Sinalização NOD1/metabolismo , Proteína Adaptadora de Sinalização NOD2/metabolismo , Transdução de Sinais , Ubiquitina/metabolismo , Sequência de Aminoácidos , Proteínas Relacionadas à Autofagia , Sítios de Ligação/genética , Proteínas de Transporte/química , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Células HEK293 , Humanos , Immunoblotting , Cinética , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Dados de Sequência Molecular , Mutação , Proteína Adaptadora de Sinalização NOD1/química , Proteína Adaptadora de Sinalização NOD1/genética , Proteína Adaptadora de Sinalização NOD2/química , Proteína Adaptadora de Sinalização NOD2/genética , Ligação Proteica , Estrutura Terciária de Proteína , Proteína Serina-Treonina Quinase 2 de Interação com Receptor/química , Proteína Serina-Treonina Quinase 2 de Interação com Receptor/genética , Proteína Serina-Treonina Quinase 2 de Interação com Receptor/metabolismo , Homologia de Sequência de Aminoácidos , Ubiquitina/química , Ubiquitina/genética
14.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 7): 1801-11, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25004958

RESUMO

Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.


Assuntos
Proteínas de Bactérias/metabolismo , Ácido N-Acetilneuramínico/metabolismo , Periplasma/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Sequência de Bases , Sítios de Ligação , Calorimetria , Primers do DNA , Ensaio de Imunoadsorção Enzimática , Fusobacterium nucleatum/metabolismo , Dados de Sequência Molecular , Pasteurella multocida/metabolismo , Reação em Cadeia da Polimerase , Conformação Proteica , Homologia de Sequência de Aminoácidos , Termodinâmica , Vibrio cholerae/metabolismo
15.
Biochem Biophys Res Commun ; 445(1): 36-42, 2014 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-24491551

RESUMO

3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp., cloned, sequenced and expressed. The 3-NTDO gene revealed a multi component structure having a reductase, a ferredoxin and two oxygenase subunits. Clones expressing the different subunits were constructed in pET21a expression vector system and overexpressed in E. coli BL21(DE3) host. Each subunit was individually purified separately to homogeneity. The active recombinant enzyme was reconstituted in vitro by mixing all three purified subunits. The reconstituted recombinant enzyme could catalyse biotransformations on a variety of organic aromatics.


Assuntos
Proteínas de Bactérias/metabolismo , Comamonadaceae/enzimologia , Dioxigenases/metabolismo , Tolueno/análogos & derivados , Proteínas de Bactérias/genética , Comamonadaceae/genética , Comamonadaceae/metabolismo , Dinitrobenzenos/química , Dinitrobenzenos/metabolismo , Dioxigenases/genética , Eletroforese em Gel de Poliacrilamida , Escherichia coli/genética , Ferredoxinas/genética , Ferredoxinas/metabolismo , Regulação Bacteriana da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Hidrocarbonetos Aromáticos/química , Hidrocarbonetos Aromáticos/metabolismo , Estrutura Molecular , Oxirredutases/genética , Oxirredutases/metabolismo , Oxigenases/genética , Oxigenases/metabolismo , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Especificidade por Substrato , Tolueno/química , Tolueno/metabolismo
16.
EMBO J ; 28(22): 3613-22, 2009 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-19798052

RESUMO

The inhibitory interaction of phosphodiesterase-6 (PDE6) with its gamma-subunit (Pgamma) is pivotal in vertebrate phototransduction. Here, crystal structures of a chimaeric PDE5/PDE6 catalytic domain (PDE5/6cd) complexed with sildenafil or 3-isobutyl-1-methylxanthine and the Pgamma-inhibitory peptide Pgamma(70-87) have been determined at 2.9 and 3.0 A, respectively. These structures show the determinants and the mechanism of the PDE6 inhibition by Pgamma and suggest the conformational change of Pgamma on transducin activation. Two variable H- and M-loops of PDE5/6cd form a distinct interface that contributes to the Pgamma-binding site. This allows the Pgamma C-terminus to fit into the opening of the catalytic pocket, blocking cGMP access to the active site. Our analysis suggests that disruption of the H-M loop interface and Pgamma-binding site is a molecular cause of retinal degeneration in atrd3 mice. Comparison of the two PDE5/6cd structures shows an overlap between the sildenafil and Pgamma(70-87)-binding sites, thereby providing critical insights into the side effects of PDE5 inhibitors on vision.


Assuntos
Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/antagonistas & inibidores , Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/química , 1-Metil-3-Isobutilxantina/química , 1-Metil-3-Isobutilxantina/metabolismo , 1-Metil-3-Isobutilxantina/farmacologia , Sequência de Aminoácidos , Animais , Domínio Catalítico , Bovinos , Nucleotídeo Cíclico Fosfodiesterase do Tipo 5/química , Nucleotídeo Cíclico Fosfodiesterase do Tipo 5/metabolismo , Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/metabolismo , Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/fisiologia , Inibidores Enzimáticos/química , Inibidores Enzimáticos/metabolismo , Inibidores Enzimáticos/farmacologia , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Fragmentos de Peptídeos/farmacologia , Piperazinas/química , Piperazinas/metabolismo , Piperazinas/farmacologia , Ligação Proteica , Subunidades Proteicas/química , Subunidades Proteicas/fisiologia , Purinas/química , Purinas/metabolismo , Purinas/farmacologia , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/metabolismo , Homologia de Sequência de Aminoácidos , Citrato de Sildenafila , Relação Estrutura-Atividade , Sulfonas/química , Sulfonas/metabolismo , Sulfonas/farmacologia
17.
Eur Phys J E Soft Matter ; 36(5): 52, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23703695

RESUMO

Using active gel theory we study theoretically the properties of the cortical actin layer of animal cells. The cortical layer is described as a non-equilibrium wetting film on the cell membrane. The actin density is approximately constant in the layer and jumps to zero at its edge. The layer thickness is determined by the ratio of the polymerization velocity and the depolymerization rate of actin.


Assuntos
Actinas/química , Animais , Membrana Celular/química , Células HeLa , Humanos , Interações Hidrofóbicas e Hidrofílicas , Modelos Químicos , Movimento (Física) , Polimerização
18.
Biochemistry ; 51(19): 4035-48, 2012 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-22531044

RESUMO

Structures of horse liver alcohol dehydrogenase complexed with NAD(+) and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 Å resolution, providing estimates of atomic positions with overall errors of ~0.02 Å, the geometry of ligand binding, descriptions of alternative conformations of amino acid residues and waters, and evidence of a strained nicotinamide ring. The four independent subunits from the two homodimeric structures differ only slightly in the peptide backbone conformation. Alternative conformations for amino acid side chains were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 adopt different conformations to accommodate the different alcohols at the active site. Each fluoroalcohol occupies one position, and the fluorines of the alcohols are well-resolved. These structures closely resemble the expected Michaelis complexes with the pro-R hydrogens of the methylene carbons of the alcohols directed toward the re face of C4N of the nicotinamide rings with a C-C distance of 3.40 Å. The oxygens of the alcohols are ligated to the catalytic zinc at a distance expected for a zinc alkoxide (1.96 Å) and participate in a low-barrier hydrogen bond (2.52 Å) with the hydroxyl group of Ser-48 in a proton relay system. As determined by X-ray refinement with no restraints on bond distances and planarity, the nicotinamide rings in the two complexes are slightly puckered (quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to the plane of the other atoms) and have bond distances that are somewhat different compared to those found for NAD(P)(+). It appears that the nicotinamide ring is strained toward the transition state on the path to alcohol oxidation.


Assuntos
Álcool Desidrogenase/química , Álcool Desidrogenase/metabolismo , Fígado/enzimologia , Álcool Desidrogenase/antagonistas & inibidores , Animais , Álcoois Benzílicos/química , Álcoois Benzílicos/metabolismo , Domínio Catalítico , Cristalografia por Raios X , Inibidores Enzimáticos/química , Cavalos , Leucina/química , Ligantes , Modelos Moleculares , Niacinamida/química , Niacinamida/metabolismo , Oxirredução , Conformação Proteica , Trifluoretanol/química , Trifluoretanol/metabolismo
19.
Reproduction ; 143(4): 513-22, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22232743

RESUMO

In primates, the time course of Sertoli cell proliferation and differentiation during puberty and its relationship with the expansion of undifferentiated type A spermatogonia that occurs at this critical stage of development are poorly defined. Mid and late juvenile and early and late pubertal male rhesus monkeys were studied. Testes were immersion fixed, embedded in paraffin, and sectioned at 5 µm. Sertoli cell number per testis, S-phase labeling (BrdU), and growth fraction (Ki67 labeling) were determined and correlated with corresponding parameters for undifferentiated type A spermatogonia (A dark and A pale). Dual fluorescence labeling was used in addition to histochemistry to monitor spermatogonial differentiation during the peripubertal period using GFRα-1 and cKIT as markers. While the adult complement of Sertoli cells/testis was attained in early pubertal monkeys after only a few weeks of exposure to the elevated gonadotropin secretion characteristic of this developmental stage, the number of undifferentiated type A spermatogonia several months later in mid pubertal monkeys was only 50% of that in adult testes. Both A dark and A pale spermatogonia exhibited high S-phase BrdU labeling at all stages of juvenile and pubertal development. Spermatogonial differentiation, as reflected histochemically and by relative changes in GFRα-1 and cKIT expression, was not observed until after the initiation of puberty. In the rhesus monkey and maybe in other higher primates including human, the pubertal proliferation of undifferentiated spermatogonia is insidious and proceeds in the wake of a surge in Sertoli cell proliferation following termination of the juvenile stage of development.


Assuntos
Diferenciação Celular , Macaca mulatta/fisiologia , Células de Sertoli/citologia , Maturidade Sexual , Espermatogônias/fisiologia , Animais , Proliferação de Células , Masculino , Tamanho do Órgão , Proteínas Proto-Oncogênicas c-kit/metabolismo , Testículo/anatomia & histologia
20.
Acta Crystallogr Sect E Struct Rep Online ; 68(Pt 10): o2839-40, 2012 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-23125644

RESUMO

The asymmetric unit of the title compound, C(30)H(27)F(2)N(3)O(2), contains two independent mol-ecules. The pyrrolidine five-membered ring assumes an envelope conformation (with the CH(2) atom at the flap) in one mol-ecule and a twisted conformation in the other one. In both independent mol-ecules, the 4-piperidinone rings adopt a similar twisted chair conformation. In the crystal, the two independent mol-ecules form an R(2) (2)(8) dimer through a pair of N-H⋯O hydrogen bonds; the R(2) (2)(8) dimers are connected via weak C-H⋯O hydrogen bonds, leading to a chain extending along the c axis.

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