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1.
Sci Rep ; 14(1): 6761, 2024 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-38514708

RESUMO

Voltage-gated sodium channels (NaV) are pivotal proteins responsible for initiating and transmitting action potentials. Emerging evidence suggests that proteolytic cleavage of sodium channels by calpains is pivotal in diverse physiological scenarios, including ischemia, brain injury, and neuropathic pain associated with diabetes. Despite this significance, the precise mechanism by which calpains recognize sodium channels, especially given the multiple calpain isoforms expressed in neurons, remains elusive. In this work, we show the interaction of Calpain-10 with NaV's C-terminus through a yeast 2-hybrid assay screening of a mouse brain cDNA library and in vitro by GST-pulldown. Later, we also obtained a structural and dynamic hypothesis of this interaction by modeling, docking, and molecular dynamics simulation. These results indicate that Calpain-10 interacts differentially with the C-terminus of NaV1.2 and NaV1.6. Calpain-10 interacts with NaV1.2 through domains III and T in a stable manner. In contrast, its interaction with NaV1.6 involves domains II and III, which could promote proteolysis through the Cys-catalytic site and C2 motifs.


Assuntos
Calpaína , Canais de Sódio Disparados por Voltagem , Animais , Camundongos , Potenciais de Ação , Calpaína/metabolismo , Neurônios/metabolismo , Isoformas de Proteínas/metabolismo , Canais de Sódio Disparados por Voltagem/metabolismo
2.
J Biomol Struct Dyn ; 41(13): 6074-6088, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-35869651

RESUMO

The interaction between the anti-apoptotic Bcl-2 protein and its antagonist Bax is essential to the regulation of the mitochondrial pathway of apoptosis. For this work, we built models by homology of Bcl-2 full-sequence length in monomeric form (apo-Bcl-2) and in complex with the BH3 domain of Bax (holo-Bcl-2). The Bcl-2 protein was analyzed with its transmembrane domain anchored to a lipidic bilayer of DPPC, imitating physiological conditions. We performed molecular dynamics (MD) simulations using the GROMACS program. Conformational changes showed that the flexible loop domain (FLD) tends to fold on itself and move towards the main core. Furthermore, the BH3 peptide of pro-apoptotic protein Bax, showed an allosteric stabilizing effect on FLD upon being bound to the hydrophobic cleft of the anti-apoptotic protein Bcl-2, causing a reduction in its structural flexibility. However, FLD is distal from the main core of Bcl-2. Principal component analysis (PCA) showed a weak correlation between FLD residues and BH3 peptide from Bax. Upon MD simulations, several new contacts appeared between FLD and some α-helices of the core of Bcl-2, which contribute to maintaining the stability of Bcl-2. This knowledge sheds light on the behavior of Bcl-2 in the cell's native environment.Communicated by Ramaswamy H. Sarma.


Assuntos
Proteínas Reguladoras de Apoptose , Simulação de Dinâmica Molecular , Proteínas Reguladoras de Apoptose/química , Proteína X Associada a bcl-2/química , Proteínas Proto-Oncogênicas c-bcl-2/química , Apoptose , Conformação Proteica
3.
Bioinformation ; 19(12): 1116-1123, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38250526

RESUMO

Human alpha-L-iduronidase (IDUA) is a 653 amino acid protein involved in the sequential degradation of glycos-amino-glycans (GAG), heparan sulfate (HS), and dermatan sulfate (DS). Some variants in the IDUA gene produce a deficient enzyme that causes un-degraded DS and HS to accumulate in multiple tissues, leading to an organ dysfunction known as muco-poly-saccharidosis type I (MPS I). Molecular and catalytic activity assays of new or rare variants of IDUA do not predict the phenotype that a patient will develop. Therefore, it is of interest to describe the molecular docking analysis, to locate binding regions of DS to IDUA to better understand the effect of a variant on MPS I development. The results presented herein demonstrate the presence of a polar/acidic catalytic site and a basic region in the putative binding site of DS to IDUA. Further, synthetic substrate docking with the enzyme could help in the predictions of the MPS I phenotype.

4.
J Mol Model ; 28(2): 43, 2022 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-35079869

RESUMO

The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short single-stranded DNA models and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the fragment molecular orbital (FMO) method, in terms of quantum descriptors (QDs) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than 1 eV in the ionization potential, global softness, electrophilicity index, and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.


Assuntos
Guanina/química , Modelos Químicos , Modelos Moleculares , Oligodesoxirribonucleotídeos/química , Prótons , Algoritmos , Conformação Molecular , Estrutura Molecular , Oligonucleotídeos/química , Eletricidade Estática
5.
Microb Pathog ; 162: 105349, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34864144

RESUMO

The heat shock response is a conserved mechanism that allows cells to respond and survive stress damage and is transcriptionally regulated by the heat shock factors and heat shock elements. The P-glycoprotein confer the multidrug resistance phenotype; Entamoeba histolytica has the largest multidrug resistance gene family described so far; one of these genes, the EhPgp5 gene, has an emetine-inducible expression. A functional heat shock element was localized in the EhPgp5 gene promoter, indicating transcriptional regulation by heat shock factors. In this work, we determined the oligomer state of EhHSTF7 and the recognition of the heat shock element of the EhPgp5 gene. The EhHSTF7 recombinant protein was obtained as monomer and oligomer. In silico molecular docking predicts protein-DNA binding between EhHSTF7 and 5'-GAA-3' complementary bases. The rEhHSTF7 protein specifically binds to the heat shock element of the EhPgp5 gene in gel shift assays. The competition assays with heat shock element mutants indicate that 5'-GAA-3' complementary bases are necessary for the rEhHSTF7 binding. Finally, the siRNA-mediated knockdown of Ehhstf7 expression causes downregulation of EhPgp5 expression, suggesting that EhHSTF7 is likely to play a key role in the E. histolytica multidrug resistance. This is the first report of a transcription factor that recognizes a heat shock element from a gene involved in drug resistance in parasites. However, further analysis needs to demonstrate the biological relevance of the EhHSTF7 and the rest of the heat shock factors of E. histolytica, to understand the underlying regulation of transcriptional control in response to stress.


Assuntos
Entamoeba histolytica , Parasitos , Animais , Entamoeba histolytica/genética , Resposta ao Choque Térmico , Simulação de Acoplamento Molecular , Fatores de Transcrição
6.
Biosci Biotechnol Biochem ; 85(9): 1971-1985, 2021 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-34232281

RESUMO

Cellulomonas uda produces Xyn11A, moderately thermostable xylanase, with optimal activity at 50 °C and pH 6.5. An improvement in the biochemical properties of Xyn11A was achieved by site-directed mutagenesis approach. Wild-type xylanase, Xyn11A-WT, and its mutant Xyn11A-N9Y were expressed in Escherichia coli, and then both enzymes were purified and characterized. Xyn11A-N9Y displayed optimal activity at 60 °C and pH 7.5, an upward shift of 10 °C in the optimum temperature and an upward shift of 1 unit in optimum pH; also, it manifested an 11-fold increase in thermal stability at 60 °C, compared to that displayed by Xyn11A-WT. Molecular dynamics simulations of Xyn11A-WT and Xyn11A-N9Y suggest that the substitution N9Y leads to an array of secondary structure changes at the N-terminal end and an increase in the number of hydrogen bonds in Xyn11A-N9Y. Based on the significant improvements, Xyn11A-N9Y may be considered as a candidate for several biotechnological applications.


Assuntos
Cellulomonas/enzimologia , Endo-1,4-beta-Xilanases/genética , Mutação , Sequência de Aminoácidos , Catálise , Endo-1,4-beta-Xilanases/química , Escherichia coli/genética , Simulação de Dinâmica Molecular , Conformação Proteica
7.
Nutr Neurosci ; 24(1): 1-12, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30822260

RESUMO

Background: Essential fatty acids (EFAs) and non-essential fatty acids (nEFAs) exert experimental and clinical neuroprotection in neurodegenerative diseases. The main EFAs, eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), nEFAs, and oleic acid (OA) contained in olive and fish oils are inserted into the cell membranes, but the exact mechanism through which they exert neuroprotection is still unknown. Objectives and Methods: In this study, we assessed the fatty acids content and membrane fluidity in striatal rat synaptosomes after fatty acid-rich diets (olive- or a fish-oil diet, 15% w/w). Then, we evaluated the effect of enriching striatum synaptosomes with fatty acids on the oxidative damage produced by the prooxidants ferrous sulfate (FeSO4) or quinolinic acid (QUIN). Results and Discussion: Lipid profile analysis in striatal synaptosomes showed that EPA content increased in the fish oil group in comparison with control and olive groups. Furthermore, we found that synaptosomes enriched with fatty acids and incubated with QUIN or FeSO4 showed a significant oxidative damage reduction. Results suggest that EFAs, particularly EPA, improve membrane fluidity and confer antioxidant effect.


Assuntos
Membrana Celular/metabolismo , Corpo Estriado/metabolismo , Ácidos Graxos/metabolismo , Estresse Oxidativo , Sinaptossomos/metabolismo , Animais , Membrana Celular/ultraestrutura , Corpo Estriado/efeitos dos fármacos , Corpo Estriado/ultraestrutura , Ácidos Graxos/administração & dosagem , Óleos de Peixe/administração & dosagem , Masculino , Óleos de Plantas/administração & dosagem , Ratos Wistar , Espécies Reativas de Oxigênio/metabolismo , Sinaptossomos/ultraestrutura
8.
J Mol Model ; 26(2): 24, 2020 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-31927634

RESUMO

Caspases are cysteine proteases that perform a wide variety of roles in lethal intracellular signaling and cell-death regulation. Caspase-9, the primary initiator caspase of the intrinsic apoptotic pathway, is produced as a scarcely active zymogen (Procaspase-9). Here, we describe, for the first time, at the atomistic level, conformational changes which might be correlated to the activation of Procaspase-9. Molecular dynamics simulations performed at two temperatures (310 and 410 K) provide insights about the conformational space and the time-course evolution of the geometrical and structural characteristics of Procaspase-9. At both temperatures studied, the extremal globular domains of the protein approach each other, contracting the disordered region. In both temperatures, the compact conformations hide more than 40 nm2 (about 20% of the total solvent-accessible surface area), and their radius of gyration are reduced by about 40% from the original values. At each temperature, the pathway of contraction is different, as well as the compact structures reached. In consequence, the network of stabilizing interactions at the final conformations is dissimilar. Both final conformations were evaluated in their structural compatibility with the activation models described so far. In this work, we describe mechanistically how and why the activation of Procaspase-9 is favored by apoptosome recruitment via the Caspase Activation Recruitment Domain (CARD), as it has been proposed recently by in vitro experiments.


Assuntos
Caspase 9/química , Simulação de Dinâmica Molecular , Ativação Enzimática , Humanos
9.
PPAR Res ; 2019: 1371758, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30863432

RESUMO

Rosiglitazone (RGZ), a peroxisome proliferator-activated receptor gamma (PPARγ) ligand, has been reported to act as insulin sensitizer and exert cardiovascular actions. In this work, we hypothesized that RGZ exerts a PPARγ-dependent regulation of blood pressure through modulation of angiotensin-converting enzyme (ACE)-type 2 (ACE2)/angiotensin-(1-7)/angiotensin II type-2 receptor (AT2R) axis in an experimental model of high blood pressure. We carried on experiments in normotensive (Sham) and aortic coarctation (AoCo)-induced hypertensive male Wistar rats. Both sham and AoCo rats were treated 7 days with vehicle (V), RGZ (5 mg/kg/day), or RGZ+BADGE (120 mg/kg/day) post-coarctation. We measured blood pressure and vascular reactivity on aortic rings, as well as the expression of renin-angiotensin system (RAS) proteins. We found that RGZ treatment in AoCo group decreases blood pressure values and improves vascular response to acetylcholine, both parameters dependent on PPARγ-stimulation. RGZ lowered serum angiotensin II (AngII) but increased Ang-(1-7) levels. It also decreased 8-hydroxy-2'-deoxyguanosine (8-OH-2dG), malondialdehyde (MDA), and improved the antioxidant capacity. Regarding protein expression of RAS, RGZ decreases ACE and angiotensin II type 1 receptor (AT1R) and improved ACE2, AT2R, and Mas receptor in AoCo rats. Additionally, an in silico analysis revealed that 5'UTR regions of RAS and PPARγ share motifs with a transcriptional regulatory role. We conclude that RGZ lowers blood pressure values by increasing the expression of RAS axis proteins ACE2 and AT2R, decreasing the levels of AngII and increasing levels of Ang-(1-7) in a PPARγ-dependent manner. The in silico analysis is a valuable tool to predict the interaction between PPARγ and RAS.

10.
J Mol Model ; 24(8): 202, 2018 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-30003410

RESUMO

The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) in Entamoeba histolytica, the protozoan causing human amoebiasis, and showed the relevance of conserved Leu135 and Tyr236 residues for RNA binding. We also identified the GUUG sequence as the recognition site of EhCFIm25. To understand the interactions network that allows the EhCFIm25 to maintain its three-dimensional structure and function, here we performed molecular dynamics simulations of wild-type (WT) and mutant proteins, alone or interacting with the GUUG molecule. Our results indicated that in the presence of the GUUG sequence, WT converged more quickly to lower RMSD values in comparison with mutant proteins. However, RMSF values showed that movements of amino acids of WT and EhCFIm25*L135 T were almost identical, interacting or not with the GUUG molecule. Interestingly, EhCFIm25*L135 T, which is the only mutant with a slight RNA binding activity experimentally, presents the same stabilization of bend structures and alpha helices as WT, notably in the C-terminus. Moreover, WT and EhCFIm25*L135 T presented almost the same number of contacts that mainly involve lysine residues interacting with the G4 nucleotide. Overall, our data proposed a clear description of the structural and mechanistic data that govern the RNA binding capacity of EhCFIm25.


Assuntos
Entamoeba histolytica/química , Leucina/química , Proteínas de Protozoários/química , RNA Bacteriano/química , RNA Mensageiro/química , Tirosina/química , Fatores de Poliadenilação e Clivagem de mRNA/química , Substituição de Aminoácidos , Sítios de Ligação , Cristalografia por Raios X , Entamoeba histolytica/genética , Entamoeba histolytica/metabolismo , Leucina/metabolismo , Simulação de Dinâmica Molecular , Mutação , Poli A/química , Poli A/genética , Poli A/metabolismo , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , RNA Bacteriano/genética , RNA Bacteriano/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Termodinâmica , Tirosina/metabolismo , Fatores de Poliadenilação e Clivagem de mRNA/genética , Fatores de Poliadenilação e Clivagem de mRNA/metabolismo
11.
Sci Rep ; 8(1): 5720, 2018 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-29632392

RESUMO

Messenger RNA 3'-end polyadenylation is an important regulator of gene expression in eukaryotic cells. In our search for new ways of treating parasitic infectious diseases, we looked at whether or not alterations in polyadenylation might control the survival of Entamoeba histolytica (the agent of amoebiasis in humans). We used molecular biology and computational tools to characterize the mRNA cleavage factor EhCFIm25, which is essential for polyadenylation in E. histolytica. By using a strategy based on the systematic evolution of ligands by exponential enrichment, we identified single-stranded RNA aptamers that target EhCFIm25. The results of RNA-protein binding assays showed that EhCFIm25 binds to the GUUG motif in vitro, which differs from the UGUA motif bound by the homologous human protein. Accordingly, docking experiments and molecular dynamic simulations confirmed that interaction with GUUG stabilizes EhCFIm25. Incubating E. histolytica trophozoites with selected aptamers inhibited parasite proliferation and rapidly led to cell death. Overall, our data indicate that targeting EhCFIm25 is an effective way of limiting the growth of E. histolytica in vitro. The present study is the first to have highlighted the potential value of RNA aptamers for controlling this human pathogen.


Assuntos
Antiprotozoários/farmacologia , Aptâmeros de Nucleotídeos/farmacologia , Entamoeba histolytica/crescimento & desenvolvimento , Fatores de Poliadenilação e Clivagem de mRNA/antagonistas & inibidores , Fatores de Poliadenilação e Clivagem de mRNA/química , Motivos de Aminoácidos , Antiprotozoários/química , Aptâmeros de Nucleotídeos/química , Sítios de Ligação , Biologia Computacional/métodos , Entamoeba histolytica/efeitos dos fármacos , Entamoeba histolytica/metabolismo , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , Proteínas de Protozoários/antagonistas & inibidores , Proteínas de Protozoários/química , RNA/farmacologia , Técnica de Seleção de Aptâmeros , Trofozoítos/efeitos dos fármacos , Trofozoítos/crescimento & desenvolvimento , Trofozoítos/metabolismo
12.
Nutr Neurosci ; 20(7): 388-395, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26928375

RESUMO

Essential fatty acids have an important effect on oxidative stress-related diseases. The Huntington's disease (HD) is a hereditary neurologic disorder in which oxidative stress caused by free radicals is an important damage mechanism. The HD experimental model induced by quinolinic acid (QUIN) has been widely used to evaluate therapeutic effects of antioxidant compounds. The aim of this study was to test whether the fatty acid content in olive- or fish-oil-rich diet prevents against QUIN-related oxidative damage in rats. Rats were fed during 20 days with an olive- or a fish-oil-rich diet (15% w/w). Posterior to diet period, rats were striatally microinjected with QUIN (240 nmol/µl) or saline solution. Then, we evaluated the neurological damage, oxidative status, and gamma isoform of the peroxisome proliferator-activated receptor (PPARγ) expression. Results showed that fatty acid-rich diet, mainly by fish oil, reduced circling behavior, prevented the fall in GABA levels, increased PPARγ expression, and prevented oxidative damage in striatal tissue. In addition none of the enriched diets exerted changes neither on triglycerides or cholesterol blood levels, nor or hepatic function. This study suggests that olive- and fish-oil-rich diets exert neuroprotective effects.


Assuntos
Corpo Estriado/efeitos dos fármacos , Ácidos Graxos Essenciais/farmacologia , Estresse Oxidativo/efeitos dos fármacos , Ácido Quinolínico/toxicidade , Animais , Peso Corporal , Colesterol/sangue , Corpo Estriado/metabolismo , Modelos Animais de Doenças , Óleos de Peixe/farmacologia , Doença de Huntington/tratamento farmacológico , Peroxidação de Lipídeos/efeitos dos fármacos , Masculino , Fármacos Neuroprotetores/farmacologia , Azeite de Oliva/farmacologia , Ratos , Ratos Wistar , Triglicerídeos/sangue , Ácido gama-Aminobutírico/metabolismo
13.
Braz. j. infect. dis ; 20(6): 610-618, Nov.-Dec. 2016. tab, graf
Artigo em Inglês | LILACS | ID: biblio-828160

RESUMO

ABSTRACT Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host-parasite interactions from "omics" data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of "aptasensors" for parasite diagnosis, and "intramers" targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.


Assuntos
Humanos , Doenças Parasitárias/diagnóstico , Doenças Parasitárias/terapia , Aptâmeros de Nucleotídeos/genética , Técnica de Seleção de Aptâmeros/métodos , Terapia de Alvo Molecular/métodos , Doenças Parasitárias/prevenção & controle , Biomarcadores/análise
14.
Braz J Infect Dis ; 20(6): 610-618, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27755981

RESUMO

Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host-parasite interactions from "omics" data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of "aptasensors" for parasite diagnosis, and "intramers" targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.


Assuntos
Aptâmeros de Nucleotídeos/genética , Terapia de Alvo Molecular/métodos , Doenças Parasitárias/diagnóstico , Doenças Parasitárias/terapia , Técnica de Seleção de Aptâmeros/métodos , Biomarcadores/análise , Humanos , Doenças Parasitárias/prevenção & controle
15.
J Mol Model ; 22(4): 98, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27037822

RESUMO

Most of the B-cell lymphoma-2 (Bcl-2) protein structure has been elucidated; however, the conformation of its flexible loop domain (FLD) has not yet been experimentally predicted. Its high flexibility under physiological conditions is the reason. FLD behaves as an intrinsically disordered region (IDR) and can adopt regular structures in particular conditions associated with the control of Bcl-2's anti-apoptotic functions. In a previous contribution, we analyzed an engineered Bcl-2 construct (Bcl-2-Δ22Σ3) submitted to 25-ns MD and reported a disordered-to-helix transitions in a region of FLD (rFLD, residues 60-77). However, the conformational preferences in solution of rFLD in the nanosecond to microsecond scale were not analyzed. Herein, an average model was obtained for the native Bcl-2 protein by homology modeling and MD simulation techniques. From this, only the atomic coordinates corresponding to the rFLD were simulated for 1 µs by MD at 310 K. In concordance with previous studies, a disordered-to-helix transitions were exhibited, implying that this "interconversion of folding" in the rFLD suggest a possible set of conformations encoded in its sequence. Principal component analysis (PCA) showed that most of the conformational fluctuation of Bcl-2 is provided by rFLD. Dihedral PCA (dPCA) offered information about all the conformations of rFLD in the µs of the simulation, characterizing a dPCA-based free energy landscape of rFLD, and a conformational ensemble of fast interconverting conformations as other IDRs. Furthermore, despite the conformational heterogeneity of rFLD, the analysis of the dihedral angles (Φ, Ψ) showed that this region does not randomly explore the conformational space in solution.

16.
J Theor Biol ; 385: 90-101, 2015 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-26342543

RESUMO

Leptin is a hormone that regulates energy homeostasis, inflammation, hematopoiesis and immune response, among other functions (Houseknecht et al., 1998; Zhang et al., 1995; Paz-Filho et al., 2010). To obtain its crystallographic structure, it was necessary to substitute a tryptophan for a glutamic acid at position 100, thus creating a mutant leptin that has been reported to have biological activity comparable to the activity of the wild type but that crystallizes more readily. Here, we report a comparative study of the conformational space of WT and W100E leptin using molecular dynamics simulations performed at 300, 400, and 500 K. We detected differences between the interactions of the two proteins with local and distal effects, resulting in changes in the conformation, accessible surface area, compactness, electrostatic potential and dynamic behavior. Additionally, the series of unfolding events that occur when leptin is subjected to high temperature differs for the two constructs. We observed that both proteins are mostly unstructured after 20 ns of MD simulation at 500 K. However, WT leptin maintains a significant amount of secondary structure in helix α2, while the most stable region of W100E leptin is helix α3. Furthermore, we found that the region between residues 25 and 42 might adopt interconverting secondary structures ranging from α-helices and random coils to ß-strand structures. Thus, this region can be considered an intrinsically disordered region. This atomistic description supports our understanding of leptin signaling and consequently might facilitate the use of leptin in treatments for the pathophysiologies in which it is implicated.


Assuntos
Leptina/química , Simulação de Dinâmica Molecular , Humanos , Proteínas Intrinsicamente Desordenadas/química , Modelos Moleculares , Conformação Proteica , Estrutura Secundária de Proteína , Desdobramento de Proteína , Relação Quantitativa Estrutura-Atividade , Eletricidade Estática , Temperatura
17.
Biochimie ; 115: 44-51, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25941172

RESUMO

Pre-mRNA 3' end processing in the nucleus is essential for mRNA stability, efficient nuclear transport, and translation in eukaryotic cells. In Human, the cleavage/polyadenylation machinery contains the 25 kDa subunit of the Cleavage Factor Im (CFIm25), which specifically recognizes two UGUA elements and regulates the assembly of polyadenylation factors, poly(A) site selection and polyadenylation. In Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, EhCFIm25 has been reported as a RNA binding protein that interacts with the Poly(A) Polymerase. Here, we follow-up with the study of EhCFIm25 to characterize its interaction with RNA. Using in silico strategy, we identified Leu135 and Tyr236 in EhCFIm25 as conserved amino acids among CFIm25 homologues. We therefore generated mutant EhCFIm25 proteins to investigate the role of these residues for RNA interaction. Results showed that RNA binding activity was totally abrogated when Leu135 and Tyr236 were replaced with Ala residue, and Tyr236 was changed for Phe. In contrast, RNA binding activity was less affected when Leu135 was substituted by Thr. Our data revealed for the first time -until we know-the functional relevance of the conserved Leu135 and Tyr236 in EhCFIm25 for RNA binding activity. They also gave some insights about the possible chemical groups that could be interacting with the RNA molecule.


Assuntos
Entamoeba histolytica , Leucina , Proteínas de Protozoários/química , Proteínas de Protozoários/metabolismo , RNA/metabolismo , Tirosina , Sequência de Aminoácidos , Animais , Sequência de Bases , Simulação por Computador , Sequência Conservada , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Conformação Proteica , Proteínas de Protozoários/genética
18.
J Mol Recognit ; 28(9): 553-64, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25788327

RESUMO

Computational identification of potential epitopes with an immunogenic capacity challenges immunological research. Several methods show considerable success, and together with experimental studies, the efficiency of the algorithms to identify potential peptides with biological activity has improved. Herein, an epitope was designed by combining bioinformatics, docking, and molecular dynamics simulations. The hemagglutinin protein of the H1N1 influenza pandemic strain served as a template, owing to the interest of obtaining a scheme of immunization. Afterward, we performed enzyme-linked immunosorbent assay (ELISA) using the epitope to analyze if any antibodies in human sera before and after the influenza outbreak in 2009 recognize this peptide. Also, a plaque reduction neutralization test induced by virus-neutralizing antibodies and the IgG determination showed the biological activity of this computationally designed peptide. The results of the ELISAs demonstrated that the serum of both prepandemic and pandemic recognized the epitope. Moreover, the plaque reduction neutralization test evidenced the capacity of the designed peptide to neutralize influenza virus in Madin-Darby canine cells.


Assuntos
Epitopos/metabolismo , Glicoproteínas de Hemaglutininação de Vírus da Influenza/metabolismo , Influenza Humana/metabolismo , Peptídeos/metabolismo , Animais , Anticorpos/imunologia , Linhagem Celular , Biologia Computacional , Cães , Glicoproteínas de Hemaglutininação de Vírus da Influenza/química , Humanos , Influenza Humana/imunologia , Simulação de Dinâmica Molecular , Peptídeos/química , Coelhos
19.
J Res Med Sci ; 19(7): 610-6, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25364359

RESUMO

BACKGROUND: Obesity is a major health problem worldwide for which conventional therapy efficacy is limited. Traditional Chinese medicine, particularly body acupoint stimulation, provides an alternative, effective, and safe therapy for this medical challenge. The present study was designed to compare the effects of distinct methods to stimulate the same set of acupoints, on anthropometric and biochemical parameters in obese women. MATERIALS AND METHODS: Ninety-nine obese women were randomly assigned to six groups of treatment: Acupuncture with moxibustion, long needle acupuncture with moxibustion, electroacupuncture (EA), EA with moxibustion, embedded catgut with moxibustion (CGM) and sham acupuncture as control. Obesity-related parameters, including body weight, body mass index (BMI), waist and hip circumferences, waist/hip ratio, biochemical parameters (triglycerides, cholesterol, glucose, insulin) and homeostasis model of assessment - insulin resistance (HOMA-IR) index, were determined before and after each treatment. RESULTS: Body weight and BMI were significantly reduced in response to all treatments. Interestingly, acupoint catgut embedding therapy combined with moxibustion was the only treatment that produced a significant reduction in body weight (3.1 ± 0.2 kg, P < 0.001), BMI (1.3 ± 0.1 kg/m(2), P < 0.001), insulin (3.5 ± 0.8 mcU/ml, P < 0.1) and HOMA-IR (1.4 ± 0.2 units, P < 0.01) in comparison with sham group. Furthermore, this treatment was able to bring back obese women to a state of insulin sensitivity, indicating that acupoint catgut embedding therapy combined with moxibustion could be useful as a complementary therapy to reduce the risk of diabetes associated to obesity in women. CONCLUSION: Overall, our results confirmed the effectiveness of acupoints stimulation to assist in the control of body weight in women. They also highlighted the more favorable effects of embedded catgut-moxibustion combination that may be due to the extended and consistent stimulation of acupoints.

20.
Parasite ; 21: 7, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24534563

RESUMO

Entamoeba histolytica, the protozoan responsible for human amoebiasis, exhibits a great genome plasticity that is probably related to homologous recombination events. It contains the RAD52 epistasis group genes, including Ehrad51 and Ehrad54, and the Ehblm gene, which are key homologous recombination factors in other organisms. Ehrad51 and Ehrad54 genes are differentially transcribed in trophozoites when DNA double-strand breaks are induced by ultraviolet-C irradiation. Moreover, the EhRAD51 recombinase is overexpressed at 30 min in the nucleus. Here, we extend our analysis of the homologous recombination mechanism in E. histolytica by studying EhRAD51, EhRAD54, and EhBLM expression in response to DNA damage. Bioinformatic analyses show that EhRAD54 has the molecular features of homologous proteins, indicating that it may have similar functions. Western blot assays evidence the differential expression of EhRAD51, EhRAD54, and EhBLM at different times after DNA damage, suggesting their potential roles in the different steps of homologous recombination in this protozoan.


Assuntos
Reparo do DNA , Entamoeba histolytica/metabolismo , Recombinação Homóloga , Proteínas de Protozoários/fisiologia , Sequência de Aminoácidos , Animais , Núcleo Celular/química , Sequência Consenso , Citoplasma/química , Quebras de DNA de Cadeia Dupla , DNA Helicases/química , DNA Helicases/genética , DNA Helicases/fisiologia , Reparo do DNA/genética , DNA de Protozoário/genética , DNA de Protozoário/efeitos da radiação , Entamoeba histolytica/genética , Entamoeba histolytica/efeitos da radiação , Genes de Protozoários , Recombinação Homóloga/genética , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Proteínas de Protozoários/química , Proteínas de Protozoários/genética , Rad51 Recombinase/genética , Rad51 Recombinase/fisiologia , RecQ Helicases/genética , RecQ Helicases/fisiologia , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Fatores de Tempo , Raios Ultravioleta
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