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1.
Chinese Journal of Biotechnology ; (12): 3142-3150, 2021.
Article in Chinese | WPRIM | ID: wpr-921412

ABSTRACT

The hinge structure, also known as hinge region or bend, is a special structure found in some antimicrobial peptides. Most studies on antimicrobial peptides focused on the standard secondary structure of α-helix and β-sheet, while the hinge structure and its functions were rarely studied. The hinge structure confers the antimicrobial peptides an improved structural flexibility, which may promote their disruptive effect on bacterial membrane or their binding efficiency to the intracellular targets, thus resulting in a higher antibacterial activity. Meanwhile, the hinge structure may reduce the structural rigidity, which may eliminate the cytotoxicity of antimicrobial peptides to eukaryotic cells. This article reviews the structural characteristics of the hinge structure, its effects on the biological activity of antimicrobial peptides and application in the molecular design, with the aim to provide a reference for the design and development of new antimicrobial peptides.


Subject(s)
Anti-Bacterial Agents/pharmacology , Anti-Infective Agents/pharmacology , Antimicrobial Cationic Peptides/pharmacology , Pore Forming Cytotoxic Proteins , Protein Structure, Secondary
2.
Chinese Journal of Biotechnology ; (12): 2890-2902, 2021.
Article in Chinese | WPRIM | ID: wpr-887851

ABSTRACT

The evolution, structure and antigenic epitopes prediction of Rana dybowskii antimicrobial peptide dybowskin-1ST were carried out using bioinformatics software available online. Its antibacterial mechanism and structural properties were analyzed, and its activity was verified by applying wound healing assay in mice and bacteriostatic assay in vitro. This provides the theoretical basis for the improvement of parental peptide and the development of novel derivative peptides. The software MEGA_X were used to conduct homology alignment and to construct a phylogenetic tree. The online software ProtParam, ProtScale, PeptideCutter, signal, TMHMM Server were respectively used to predict the physicochemical parameters, hydrophilia/hydrophobicity, shear sites, signal peptides, and transmembrane domains of dybowskin-1ST. The online software SOPMA, Jpred4, DNAstar Protean were used to predict the secondary structure of dybowskin-1ST, and SWISS-MODEL, I-TASSER were used to predict the tertiary structure. ABCpred and SYFPEITHI were respectively used to predict its B-and T-cell epitopes. The effect of dybowskin-1ST on the wound healing was observed on experimental mice. Kirby-Bauer method and dilution method were used to determine the bacteriostatic activity of dybowskin-1ST. The dybowskin-1ST consists of 59 amino acid residues, of which leucine accounts for 16.9%, with a molecular formula of C₃₁₈H₅₁₀N₈₀O₉₃S₂. Its theoretical isoelectric point is 5.10 and the charge is -2. The dybowskin-1ST and dybowskin-1CDYa are closely related phylogenetically. The secondary structure of dybowskin-1ST predicted by the three methods were similar, which consisted of α-helix (44.07%), extended strand (16.95%), β-turns (3.39%), and random coil (35.39%). The prediction of tertiary structure showed that dybowskin-1ST was mainly composed of α-helix, and it was regarded as a hydrophilic protein with signal peptide sequence. Subcellular localization analysis showed that the probability of secreting the mitochondrial targeted peptides was 0.944. Dybowskin-1ST is an extracellular protein with no transmembrane structure region, but contains seven phosphorylation sites, three T-cell epitopes and eight B-cell epitopes. The dybowskin-1ST promoted wound healing and effectively inhibited the growth of Escherichia coli and Staphylococcus aureus. However, it had limited antibacterial activity against fungi and drug-resistant bacteria. Although the structure of dybowskin-1ST is rich in α-helix, the verification experiments showed that its antibacterial ability needs to be enhanced. The reason may be that it is a negatively charged and hydrophilic protein, and amino acid modification with the aim of increasing the number of positive charges and changing the hydrophobicity may be used to obtain derived peptides with enhanced activity.


Subject(s)
Amino Acid Sequence , Animals , Mice , Phylogeny , Pore Forming Cytotoxic Proteins , Protein Structure, Secondary , Ranidae
3.
Braz. arch. biol. technol ; 64: e21210007, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339314

ABSTRACT

Abstract Improving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q3 accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSIPRED on the SCOPe test datasets and found that our method outperformed PSIPRED.


Subject(s)
Protein Structure, Secondary , Support Vector Machine , Artificial Intelligence , Computational Biology/methods
4.
Chinese Journal of Biotechnology ; (12): 750-762, 2020.
Article in Chinese | WPRIM | ID: wpr-826901

ABSTRACT

PEGylation is considered one of the most successful techniques to improve the characteristics of protein drugs including to increase the circulating half-life of proteins in blood and to decrease their immunogenicity and antigenicity. One known PEG modification method is to attach PEG to the free amino group, typically at lysine residues or at the N-terminal amino acid with no selectivity, resulting in a heterogeneous product mixture. This lack of selectivity can present problems when a therapeutic PEGylated protein is being developed, because predictability of activity and manufacturing reproducibility are needed for regulatory approval. Enzymatic PEGylation of proteins is one route to overcome this limitation. Transglutaminases (TGase) are enzyme candidates for site-specific PEGylation. We use human interferon alpha 2a (IFN α2a) as a test case, and predict that the potential modification residues are Gln101 by computational approach as it contains 12 potential PEGylation sites. IFN α2a was PEGylated by Y shaped PEG40k-NH2 mediated by microbial transglutaminase. Our results show that the microbial transglutaminase mediated PEGylation of IFN α2a was site-specific only at the site of Gln101 in IFN α2a, yielding the single mono-conjugate PEG-Gln101-IFN α2a with a mass of 59 374.66 Da. Circular dichroism studies showed that PEG-Gln101-IFN α2a preserved the same secondary structures as native IFN α2a. As expected, the bioactivity and pharmacokinetic profile in rats of PEG-Gln101-IFN α2a revealed a significant improvement to unmodified IFN α2a, and better than PEGASYS.


Subject(s)
Animals , Antiviral Agents , Humans , Interferon alpha-2 , Metabolism , Interferon-alpha , Pharmacokinetics , Polyethylene Glycols , Pharmacokinetics , Protein Structure, Secondary , Rats , Recombinant Proteins , Pharmacokinetics , Pharmacology , Reproducibility of Results , Transglutaminases , Metabolism
5.
Article in English | WPRIM | ID: wpr-773002

ABSTRACT

Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and learning patterns from complex data. The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical field. We first introduce the development of artificial neural network and deep learning. We then describe two main components of deep learning, i.e., deep learning architectures and model optimization. Subsequently, some examples are demonstrated for deep learning applications, including medical image classification, genomic sequence analysis, as well as protein structure classification and prediction. Finally, we offer our perspectives for the future directions in the field of deep learning.


Subject(s)
Algorithms , Computational Biology , Methods , Diagnostic Imaging , Genomics , Methods , Humans , Image Interpretation, Computer-Assisted , Methods , Machine Learning , Neural Networks, Computer , Protein Structure, Secondary , Proteins , Metabolism
6.
Article in Chinese | WPRIM | ID: wpr-771679

ABSTRACT

According to the previous results from transcriptome analysis of Ligustrum quihoui, a glycosyltransferase gene(xynzUGT) was cloned by rapid amplification of cDNA ends(RACE). The full length cDNA of xynzUGT was 1 598 bp, consisting of 66 bp 5'-UTR, 1 440 bp ORF and 92 bp 3'-UTR. The ORF encoded a 480 amino-acid protein(xynzUGT) with a molecular weight of 54 826.67 Da and isoelectric point of 5.82. The structure of enzyme was analyzed by using bioinformatics method, the results showed that the primary structure contained a highly conserved PSPG box of glycosyltransferase, the secondary structure included α helix(38%), sheet(12.1%) and random coil(49.9%), and tertiary structure was constructed by peptide chain folding to form two face-to-face domains(often referred to as a Rossmann domains), between which a substrate binding pocket is sandwiched. The phylogenetic tree analysis indicated that xynzUGT might catalyze glycosylation of phenylpropanoids, such as tyrosol. Further simulation experiment of molecular docking between enzyme and tyrosol showed that Gly138 and Ser285 located in the binding pocket interacted with tyrosol by hydrogen bonding. SDS-PAGE analysis exhibited that the prokaryotic expression system successfully expressed recombinant xynzUGT with molecular weight of 58 370.57 Da, but it exists in the form of non-soluble inclusion bodies. Using the molecular chaperone and enzyme co-expression method, the soluble expression was promoted to some extent. The above works laid the foundation for further studying on enzymatic reaction and clarifying the functional mechanism of enzyme.


Subject(s)
Cloning, Molecular , DNA, Complementary , Glycosyltransferases , Genetics , Ligustrum , Genetics , Molecular Docking Simulation , Phylogeny , Plant Proteins , Genetics , Protein Structure, Secondary , Protein Structure, Tertiary
7.
Article in Chinese | WPRIM | ID: wpr-771677

ABSTRACT

Chorismate synthase(CS, EC:4.2.3.5) catalyses 5-enolpyruvy-shikimate-3-phosphate to form chorismate, which is the essential enzyme for chorismate biosynthesis in organisms. The amino acid sequences of CS from 79 species of higher plants were reported in GenBank at present. 125 amino acid sequences of CS from Baphicacanthus cusia and other 78 species of plants were predicted and analyzed by using various bioinformatics software, including the composition of amino acid sequences, signal peptide, leader peptide, hydrophobic/hydrophilic, transmembrane structure, coiled-coil domain, protein secondary structure, tertiary structure and functional domains. The phylogenetic tree of CS protein family was constructed and divided into eight groups by phylogenetic analysis. The homology comparison indicated that B. cusia shared a high homology with several plants such as Sesamum indicum, Nicotiana tabacum, Solanum tuberosum and so on. The open reading frame(ORF) of all samples is about 1 300 bp, the molecular weight is about 50 kDa, the isoelectric point(pI) is 5.0-8.0 which illustrated that CS protein is slightly basic. The ORF of CS we cloned in B. cusia is 1 326 bp, the amino acid residues are 442, the molecular weight is 47 kDa and pI is 8.11. The CS in B.cusia showed obvious hydrophobicity area and hydrophilicity area, no signal peptide, and may exists transmembrane structure areas. The main secondary structures of CS protein are random coil and Alpha helix, also contain three main structural domains which are an active structural domain, a PLN02754 conserved domain and a FMN binding site. The acquired information in this study would provide certain scientific basis for further study on structure-activity relationship and structure modification of CS in plants in the future.


Subject(s)
Acanthaceae , Amino Acid Sequence , Computational Biology , Phosphorus-Oxygen Lyases , Chemistry , Phylogeny , Plant Proteins , Chemistry , Protein Structure, Secondary
8.
Protein & Cell ; (12): 3-14, 2018.
Article in English | WPRIM | ID: wpr-757007

ABSTRACT

Antibodies have proved to be a valuable mode of therapy for numerous diseases, mainly owing to their high target binding affinity and specificity. Unfortunately, antibodies are also limited in several respects, chief amongst those being the extremely high cost of manufacture. Therefore, non-antibody binding proteins have long been sought after as alternative therapies. New binding protein scaffolds are constantly being designed or discovered with some already approved for human use by the FDA. This review focuses on protein scaffolds that are either already being used in humans or are currently being evaluated in clinical trials. Although not all are expected to be approved, the significant benefits ensure that these molecules will continue to be investigated and developed as therapeutic alternatives to antibodies. Based on the location of the amino acids that mediate ligand binding, we place all the protein scaffolds under clinical development into two general categories: scaffolds with ligand-binding residues located in exposed flexible loops, and those with the binding residues located in protein secondary structures, such as α-helices. Scaffolds that fall under the first category include adnectins, anticalins, avimers, Fynomers, Kunitz domains, and knottins, while those belonging to the second category include affibodies, β-hairpin mimetics, and designed ankyrin repeat proteins (DARPins). Most of these scaffolds are thermostable and can be easily produced in microorganisms or completely synthesized chemically. In addition, many of these scaffolds derive from human proteins and thus possess very low immunogenic potential. Additional advantages and limitations of these protein scaffolds as therapeutics compared to antibodies will be discussed.


Subject(s)
Amino Acids , Metabolism , Animals , Antibodies , Therapeutic Uses , Humans , Ligands , Protein Engineering , Methods , Protein Structure, Secondary , Recombinant Proteins , Chemistry , Therapeutic Uses
9.
Chinese Journal of Biotechnology ; (12): 693-701, 2016.
Article in Chinese | WPRIM | ID: wpr-337430

ABSTRACT

The length of IGF1R 3'UTR is greater than 7 kb. The structure of IGF1R 3'UTR is complex, with multiple binding sites of miRNAs. IGF1R is involved in the regulation of MAPK and PI3K/AKT signaling pathways and theformation and development of tumors. Bioinformatics analysis can reveal the structure features of IGF1R, which provides ideas for further research. The analysis shows that the binding sites between IGF1R and miRNAs have the highest mutation rate in Neuroblastoma. We analyzed the structure of 3'UTR, miRNAs binding sites, physical and chemical properties, hydrophilic-hydrophobic property, glycosylation and phosphorylation sites, secondary structure and tertiary structure modeling of IGF1R. The locations and names of amino acids interacting in IGF1R and IGF1 were obtained by molecular docking. Therefore, if IGF1R 3'UTR is mutated, the capacity of IGF1R combined with miRNAs will reduce and the IGF1R expression will be up-regulated, and the function of miRNAs will be repressed. We can change the sites of IGF1R to combine with IGF1 to repress the function of IGF1R and IGF1. Then the function of IGF1R will be repressed.


Subject(s)
Binding Sites , Computational Biology , Humans , Insulin-Like Growth Factor I , MicroRNAs , Chemistry , Molecular Docking Simulation , Protein Structure, Secondary , Protein Structure, Tertiary , Receptor, IGF Type 1 , Chemistry , Signal Transduction
10.
Article in Chinese | WPRIM | ID: wpr-357835

ABSTRACT

This paper proposes a method based on quaternion for characterization a helix of proteins. The method defines the parameter called Quaternion Helix Axis Spherical Distance (QHASD) on the basis of mapping protein Cα frames' helical axis onto a unit sphere, and uses QHASD to characterize the a helix of the protein secondary structure. Application of this method has been verified based on the PDBselect database, with an a helix characterization accuracy of 91.7%. This method possesses significant advantages of high detection accuracy, low computation and clear geometric significance.


Subject(s)
Algorithms , Databases, Protein , Models, Molecular , Protein Structure, Secondary , Proteins , Chemistry
11.
Protein & Cell ; (12): 501-515, 2016.
Article in English | WPRIM | ID: wpr-757411

ABSTRACT

β/γ-Crystallins are predominant structural proteins in the cytoplasm of lens fiber cells and share a similar fold composing of four Greek-key motifs divided into two domains. Numerous cataract-causing mutations have been identified in various β/γ-crystallins, but the mechanisms underlying cataract caused by most mutations remains uncharacterized. The S228P mutation in βB1-crystallin has been linked to autosomal dominant congenital nuclear cataract. Here we found that the S228P mutant was prone to aggregate and degrade in both of the human and E. coli cells. The intracellular S228P aggregates could be redissolved by lanosterol. The S228P mutation modified the refolding pathway of βB1-crystallin by affecting the formation of the dimeric intermediate but not the monomeric intermediate. Compared with native βB1-crystallin, the refolded S228P protein had less packed structures, unquenched Trp fluorophores and increased hydrophobic exposure. The refolded S228P protein was prone to aggregate at the physiological temperature and decreased the protective effect of βB1-crystallin on βA3-crystallin. Molecular dynamic simulation studies indicated that the mutation decreased the subunit binding energy and modified the distribution of surface electrostatic potentials. More importantly, the mutation separated two interacting loops in the C-terminal domain, which shielded the hydrophobic core from solvent in native βB1-crystallin. These two interacting loops are highly conserved in both of the N- and C-terminal domains of all β/γ-crystallins. We propose that these two interacting loops play an important role in the folding and structural stability of β/γ-crystallin domains by protecting the hydrophobic core from solvent access.


Subject(s)
Amino Acid Substitution , Cataract , Genetics , Metabolism , HeLa Cells , Humans , Molecular Dynamics Simulation , Mutation, Missense , Protein Aggregation, Pathological , Genetics , Metabolism , Protein Domains , Protein Structure, Secondary , Proteolysis , beta-Crystallin B Chain , Chemistry , Genetics , Metabolism
12.
Protein & Cell ; (12): 673-683, 2016.
Article in English | WPRIM | ID: wpr-757406

ABSTRACT

Polyoxin is a group of structurally-related peptidyl nucleoside antibiotics bearing C-5 modifications on the nucleoside skeleton. Although the structural diversity and bioactivity preference of polyoxin are, to some extent, affected by such modifications, the biosynthetic logic for their occurence remains obscure. Here we report the identification of PolB in polyoxin pathway as an unusual UMP C-5 methylase with thymidylate synthase activity which is responsible for the C-5 methylation of the nucleoside skeleton. To probe its molecular mechanism, we determined the crystal structures of PolB alone and in complexes with 5-Br UMP and 5-Br dUMP at 2.15 Å, 1.76 Å and 2.28 Å resolutions, respectively. Loop 1 (residues 117-131), Loop 2 (residues 192-201) and the substrate recognition peptide (residues 94-102) of PolB exhibit considerable conformational flexibility and adopt distinct structures upon binding to different substrate analogs. Consistent with the structural findings, a PolB homolog that harbors an identical function from Streptomyces viridochromogenes DSM 40736 was identified. The discovery of UMP C5-methylase opens the way to rational pathway engineering for polyoxin component optimization, and will also enrich the toolbox for natural nucleotide chemistry.


Subject(s)
Bacterial Proteins , Chemistry , Crystallography, X-Ray , Methyltransferases , Chemistry , Protein Domains , Protein Structure, Secondary , Pyrimidine Nucleosides , Streptomyces
13.
Protein & Cell ; (12): 792-803, 2016.
Article in English | WPRIM | ID: wpr-757369

ABSTRACT

MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701). MRG701 forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.


Subject(s)
Amino Acid Sequence , Arabidopsis , Genetics , Metabolism , Arabidopsis Proteins , Chemistry , Genetics , Metabolism , Binding Sites , Chromosomal Proteins, Non-Histone , Chemistry , Genetics , Metabolism , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli , Genetics , Metabolism , Gene Expression , Histones , Chemistry , Genetics , Metabolism , Models, Molecular , Oryza , Genetics , Metabolism , Peptides , Chemistry , Genetics , Metabolism , Protein Binding , Protein Interaction Domains and Motifs , Protein Isoforms , Chemistry , Genetics , Metabolism , Protein Multimerization , Protein Structure, Secondary , Recombinant Proteins , Chemistry , Genetics , Metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Viridiplantae , Genetics , Metabolism
14.
Clinics ; 70(5): 363-368, 05/2015. tab, graf
Article in English | LILACS | ID: lil-748276

ABSTRACT

OBJECTIVES: To evaluate the clinical outcomes and identify the predictors of mortality in elderly patients undergoing peritoneal dialysis. METHODS: We conducted a retrospective study including all incident peritoneal dialysis cases in patients ≥65 years of age treated from 2001 to 2014. Demographic and clinical data on the initiation of peritoneal dialysis and the clinical events during the study period were collected. Infectious complications were recorded. Overall and technique survival rates were analyzed. RESULTS: Fifty-eight patients who began peritoneal dialysis during the study period were considered for analysis, and 50 of these patients were included in the final analysis. Peritoneal dialysis exchanges were performed by another person for 65% of the patients, whereas 79.9% of patients preferred to perform the peritoneal dialysis themselves. Peritonitis and catheter exit site/tunnel infection incidences were 20.4±16.3 and 24.6±17.4 patient-months, respectively. During the follow-up period, 40 patients were withdrawn from peritoneal dialysis. Causes of death included peritonitis and/or sepsis (50%) and cardiovascular events (30%). The mean patient survival time was 38.9±4.3 months, and the survival rates were 78.8%, 66.8%, 50.9% and 19.5% at 1, 2, 3 and 4 years after peritoneal dialysis initiation, respectively. Advanced age, the presence of additional diseases, increased episodes of peritonitis, the use of continuous ambulatory peritoneal dialysis, and low albumin levels and daily urine volumes (<100 ml) at the initiation of peritoneal dialysis were predictors of mortality. The mean technique survival duration was 61.7±5.2 months. The technique survival rates were 97.9%, 90.6%, 81.5% and 71% at 1, 2, 3 and 4 years, respectively. None of the factors analyzed were predictors of technique survival. CONCLUSIONS: Mortality was higher in elderly patients. Factors affecting mortality in elderly patients included advanced age, ...


Subject(s)
Gene Expression Regulation , Bacterial Proteins/chemistry , Computational Biology , Kinetics , Ligands , Nucleic Acid Conformation , Nucleotides/chemistry , Protein Binding , Protein Conformation , Protein Structure, Secondary , Protein Structure, Tertiary , RNA , Thermodynamics
15.
Rev. bras. enferm ; 68(2): 219-227, Mar-Apr/2015. tab
Article in Spanish | LILACS, BDENF | ID: lil-752507

ABSTRACT

RESUMEN Objetivo: estudio cualitativo que siguió los principios de la teoría fundamentada con el fin de analizar la identidad profesional de docentes de enfermería por medio del análisis de incidentes críticos que más las desestabilizaban. Método: entrevistas semi-estructuradas fueron realizadas a siete enfermeras que actúan como docentes e investigadoras en una universidad privada de Barcelona. Resultados: el material empírico resultante fue organizado en dos categorías: caracterización de los incidentes críticos y reacción de las enfermeras frente a ellos. Conclusión: se concluye que la identidad profesional de estas enfermeras en el campo académico está aún en construcción y que la inexperiencia es el mayor obstáculo que enfrentan para gestionar los incidentes críticos en el trabajo docente. .


RESUMO Objetivo: estudo qualitativo que seguiu os princípios da teoria fundamentada em dados com o objetivo de analisar a identidade profissional de docentes de enfermagem por meio da análise de incidentes críticos que mais as desestabilizaram. Método: entrevistas semiestruturadas foram realizadas com sete enfermeiras que atuam como docentes e pesquisadoras em uma universidade privada de Barcelona. Resultados: o material empírico resultante foi organizado em duas categorias: caracterização dos incidentes críticos e reação das enfermeiras frente a eles. Conclusão: concluiu-se que identidade profissional dessas enfermeiras no campo acadêmico está ainda em construção e a que inexperiência é o maior obstáculo que enfrentam para gerenciar incidentes críticos no trabalho docente. .


ABSTRACT Objective: a qualitative study that followed the principles of the grounded theory in order to analyze the professional identity of nursing academics through the analysis of the most disturbing critical incidents. Method: semi-structured interviews were conducted with seven nurses who worked as professors and researchers in a private university in Barcelona. Results: the resulting empirical material was organized into two categories: characterization of critical incidents and responsiveness to the incident. Conclusion: the professional identity of nurses regarding the academic area is still under construction and inexperience is the major obstacle in the management of critical incidents in the teaching career. .


Subject(s)
Humans , DNA , Receptors, Glucocorticoid/chemistry , Receptors, Mineralocorticoid/chemistry , Amino Acid Sequence , Crystallography, X-Ray , DNA , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Molecular Sequence Data , Mutation , Neoplasms/genetics , Neoplasms/metabolism , Neoplasms/pathology , Protein Structure, Secondary , Protein Structure, Tertiary , Pseudohypoaldosteronism/genetics , Pseudohypoaldosteronism/metabolism , Pseudohypoaldosteronism/pathology , Receptors, Glucocorticoid/genetics , Receptors, Glucocorticoid/metabolism , Receptors, Mineralocorticoid/genetics , Receptors, Mineralocorticoid/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Structural Homology, Protein
16.
J. appl. oral sci ; 23(2): 135-144, Mar-Apr/2015. tab, graf
Article in English | LILACS, BBO | ID: lil-746539

ABSTRACT

The mandible condylar process cartilage (CP) of Wistar rats is a secondary cartilage and acts as a mandibular growth site. This phenomenon depends on adequate proteins intake and hormone actions, including insulin. Objectives The present study evaluated the morphological aspects and the expression of the insulin receptor (IR) in the cartilage of the condylar process (CP) of rats subjected to protein undernourishment. Material and Methods The nourished group received a 20% casein diet, while the undernourished group (U) received a 5% casein diet. The re-nourished groups, R and RR, were used to assess the effects of re-nutrition during puberty and adulthood, respectively. CPs were processed and stained with picro-sirius red, safranin-O and azocarmine. Scanning electron microscopy and immunohistochemistry were also performed. Results The area of the CP cartilage and the number of cells in the chondroblastic layer decreased in the U group, as did the thickness of the CP layer in the joint and hypertrophic layer. Renourishment during the pubertal stage, but not during the adult phase, restored these parameters. The cell number was restored when re-nutrition occurred in the pubertal stage, but not in the adult phase. The extracellular matrix also decreased in the U group, but was restored by re-nutrition during the pubertal stage and further increased in the adult phase. IR expression was observed in all CPs, being higher in the chondroblastic and hypertrophic cartilage layers. The lowest expression was found in the U and RR groups. Conclusions Protein malnutrition altered the cellularity, the area, and the fibrous cartilage complex, as well as the expression of the IRs. .


Subject(s)
Animals , Mice , Anti-Inflammatory Agents, Non-Steroidal/metabolism , Cyclooxygenase 1/metabolism , /metabolism , Cyclooxygenase Inhibitors/metabolism , Piroxicam/analogs & derivatives , Thiazines/metabolism , Thiazoles/metabolism , Amino Acid Substitution , Anti-Inflammatory Agents, Non-Steroidal/chemistry , Arginine/chemistry , Arginine/genetics , Arginine/metabolism , Binding Sites , Catalytic Domain , Cyclooxygenase 1/chemistry , Cyclooxygenase 1/genetics , /chemistry , /genetics , Cyclooxygenase Inhibitors/chemistry , Hydrogen Bonding , Leucine/chemistry , Leucine/genetics , Leucine/metabolism , Mutation , Piroxicam/chemistry , Piroxicam/metabolism , Protein Structure, Secondary , Serine/chemistry , Serine/genetics , Serine/metabolism , Thiazines/chemistry , Thiazoles/chemistry , Tyrosine/chemistry , Tyrosine/genetics , Tyrosine/metabolism , Water
17.
Rev. bras. epidemiol ; 18(1): 208-219, Jan-Mar/2015. tab, graf
Article in Portuguese | LILACS | ID: lil-736434

ABSTRACT

INTRODUÇÃO: Apesar do consenso científico sobre os benefícios que a amamentação proporciona à mãe, à criança, à família e ao próprio meio ambiente, além da recomendação para que sua prática seja realizada de forma exclusiva nos seis primeiros meses de vida, essa conduta está longe de ser alcançada. OBJETIVO: Analisar os fatores associados à amamentação exclusiva (AME) por pelo menos seis meses, em contraponto ao desmame total até o segundo mês de vida no estado de Pernambuco. MÉTODO: Estudo caso-controle reunindo 124 casos (AME por pelo menos seis meses) pareados por idade e sexo com 248 controles (desmame total até o segundo mês). Casos e controles foram oriundos da III Pesquisa Estadual de Saúde e Nutrição. Foram selecionadas como variáveis de exposição: idade e escolaridade materna, renda familiar, zona de moradia, consultas pré-natais, tipo de parto e profissional que o assistiu e orientação sobre amamentação no pré-natal. Foi aplicada regressão logística nas variáveis que apresentaram um valor de p < 0,2 nas análises bivariadas, adotando para a inclusão no modelo final o nível de significância p < 0,05. RESULTADOS: Dos 8 agrupamentos de variáveis consideradas como possíveis preditoras do AME por pelo menos 6 meses, mantiveram-se como fatores associados a idade materna entre 20 - 35 anos, sendo a odds ratio (OR) 2,5 e o intervalo de confiança de 95% (IC95%) 1,4 - 4,5; e a escolaridade de 5 - 8 anos de estudo (OR 2,1; IC95% 1,2 - 3,6). CONCLUSÃO: O estudo mostra que ainda são necessárias mobilizações dos poderes públicos e estímulo às pesquisas em prol do sucesso do AME e da saúde materno-infantil. .


INTRODUCTION: Despite the scientific consensus on the benefits that breastfeeding provides for the mother, the baby, the family and the environment, and also the recommendation to breastfeed exclusively for six months, this practice is far from being achieved. OBJECTIVE: To analyze the factors associated with exclusive breastfeeding (EBF) for at least six month, as opposed to weaning up to the second month of life in the state of Pernambuco, Brazil. METHODS: A case-control study of 124 cases (EBF for at least six months) matched for age and sex with 248 controls (weaning up to the second month of life). Cases and controls were drawn from the III State Health and Nutrition Survey. The exposure variables selected were maternal age and education, per capita income, housing zone, prenatal consultations, type of delivery, professional who assisted the delivery, and prenatal breastfeeding guidance. Logistic regression was applied to variables that showed a p-value < 0.2 in the bivariate analysis, and the variables with p-value < 0.05 were included in the final model. RESULTS: Of the eight groups of variables considered as possible predictors of EBF for at least six months, two remained as associated factors: maternal age between 20 - 35 years old, with odds ratio (OR) 2.5 and 95% confidence interval 95%CI 1.4 - 4.5; and maternal education of 5 - 8 years of schooling (OR 2.1; 95%CI 1.2 - 3.6). CONCLUSION: The study shows that mobilization of the public sector and stimulus to research is still needed for the success of EBF and for mother and child health. .


Subject(s)
Animals , Epidermis/metabolism , beta-Keratins/metabolism , Amino Acid Sequence , Electrophoresis, Gel, Two-Dimensional , Keratins/metabolism , Models, Anatomic , Models, Biological , Molecular Sequence Data , Protein Processing, Post-Translational , Protein Structure, Secondary , Protein Structure, Tertiary , Proteomics/methods , Reptiles , Sequence Homology, Amino Acid
18.
Salud colect ; 11(1): 115-128, ene.-mar. 2015.
Article in Spanish | LILACS | ID: lil-746688

ABSTRACT

Los antipsicóticos no parecen revertir las causas de la esquizofrenia y, aunque son fármacos que pueden aliviar los síntomas a corto y mediano plazo, a largo plazo pueden no ser beneficiosos e incluso ser contraproducentes. Su empleo debería limitarse a situaciones agudas con agitación y tensión incapacitante. Presentan considerables efectos adversos y, ante la negativa de una persona a seguir tomándolos, adoptar una estrategia de reducción de daños apoyando y supervisando la retirada puede ser preferible a la coerción. Existen alternativas a los neurolépticos. Los prescriptores deberían estar más atentos y considerar las valoraciones que los usuarios hacen de sus efectos. El apego a las guías de tratamiento es escaso, seguramente por basarse en ensayos clinicos de calidad deficente, que deben mejorar y prolongarse en el tiempo. La raíz del problema probablemente se encuentra en la tautología sobre la etiología y naturaleza biológica de lo que llaman esquizofrenia, que realmente no parece ser más que un constructo ideológico-comercial.


Antipsychotic drugs do not appear to reverse the causes of schizophrenia, and although they can relieve symptoms in the short to medium term, in the long term they may not be beneficial and could even be counterproductive. Their use should be limited to acute situations in which agitation and tension is disabling. The drugs have significant adverse effects, and given the refusal of a person to continue taking them, a harm reduction strategy to support and monitor the withdrawal may be preferable to coercion. There are alternatives to neuroleptics. Prescribers should be more vigilant and consider the assessments of users regarding the drugs' effects. Adherence to treatment guidelines is low, probably because the guidelines are based on clinical trials of deficient quality which consequently should be improved and extended over a greater period of time. The root of the problem is likely the tautology on the etiology and biological nature of what is known as schizophrenia, which in fact does not seem to be more than a commercial and ideological construct.


Subject(s)
Bacterial Proteins/chemistry , Biophysics/methods , DNA-Binding Proteins/chemistry , Microscopy, Atomic Force/methods , Hydrogen Bonding , Kinetics , Models, Molecular , Models, Statistical , Monte Carlo Method , Protein Conformation , Protein Denaturation , Protein Folding , Protein Structure, Secondary , Protein Structure, Tertiary , Peptostreptococcus/metabolism , Proteins/chemistry , Stress, Mechanical , Temperature , Time Factors , Ubiquitin/chemistry
19.
Article in Chinese | WPRIM | ID: wpr-330220

ABSTRACT

To obtain the key genes for chlorogenic acid biosynthesis of Lonicera hypoglauca, four new genes ware obtained from the our dataset of L. hypoglauca. And we also predicted the structure and function of LHPAL4, LHHCT1 , LHHCT2 and LHHCT3 proteins. The phylogenetic tree showed that LHPAL4 was closely related with LHPAL1, LHHCT1 was closely related with LHHCT3, LHHCT2 clustered into a single group. By Real-time PCR to detect the gene expressed level in different organs of L. hypoglauca, we found that the transcripted level of LHPAL4, LHHCT1 and LHHCT3 was the highest in defeat flowers, and the transcripted level of LHHCT2 was the highest in leaves. These result provided a basis to further analysis the mechanism of active ingredients in different organs, as well as the element for in vitro biosynthesis of active ingredients.


Subject(s)
Chlorogenic Acid , Metabolism , Cloning, Molecular , Computational Biology , Gene Expression Regulation, Plant , Lonicera , Chemistry , Classification , Genetics , Metabolism , Molecular Sequence Data , Phylogeny , Plant Proteins , Chemistry , Genetics , Metabolism , Protein Structure, Secondary
20.
Article in English | WPRIM | ID: wpr-310880

ABSTRACT

<p><b>OBJECTIVE</b>To understand the druggability of the bioactive compounds from traditional herbal formulations "Nilavembu Kudineer" and "Swasthya Raksha Amruta Peya" to heal chikungunya virus (CHIKV) infection.</p><p><b>METHODS</b>The efficiency of twenty novel chemical entities from "Nilavembu Kudineer" and "Swasthya Raksha Amruta Peya" to inhibit CHIKV infection in silico were evaluated. Ligands were prepared using Ligprep module of Schrödinger. Active site was identified using SiteMap program. Grid box was generated using receptor grid generation wizard. Molecular docking was carried out using Grid Based Ligand Docking with Energetics (GLIDE) program.</p><p><b>RESULTS</b>Molecular docking studies showed that among twenty compounds, andrographoside, deoxyandrographoside, neoandrographolide, 14-deoxy-11-oxoandrographolide, butoxone and oleanolic acid showed GLIDE extra precision (XP) score of -9.10, -8.72, -8.25, -7.38, -7.28 and -7.01, respectively which were greater than or comparable with chloroquine (reference compound) XP score (-7.08) and were found to interact with the key residues GLU 1043, LYS 1045, GLY 1176, LEU 1203, HIS 1222 and LYS 1239 which were characteristic functional unit crucial for replication of CHIKV.</p><p><b>CONCLUSION</b>The binding affinity and the binding mode of chemical entities taken from herbal formulations with non-structural protein 2 protease were understood and our study provided a novel strategy in the development and design of drugs for CHIKV infection.</p>


Subject(s)
Antiviral Agents , Chemistry , Pharmacology , Catalytic Domain , Chikungunya virus , Chloroquine , Chemistry , Pharmacology , Complementary Therapies , Cysteine Endopeptidases , Chemistry , Drug Design , Hydrogen Bonding , Ligands , Molecular Docking Simulation , Phytochemicals , Chemistry , Protein Structure, Secondary
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