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1.
Prostate ; 84(2): 158-165, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37904330

RESUMO

BACKGROUND: Urinary incontinence (UI) can negatively impact quality of life (QoL) after robot-assisted radical prostatectomy (RARP). Pelvic floor muscle training (PFMT) and duloxetine are used to manage post-RARP UI, but their efficacy remains uncertain. We aimed to investigate the efficacy of PFMT and duloxetine in promoting urinary continence recovery (UCR) after RARP. METHODS: A randomized controlled trial involving patients with urine leakage after RARP from May 2015 to February 2018. Patients were randomized into 1 of 4 arms: (1) PFMT-biofeedback, (2) duloxetine, (3) combined PFMT-biofeedback and duloxetine, (4) control arm. PFMT consisted of pelvic muscle exercises conducted with electromyographic feedback weekly, for 3 months. Oral duloxetine was administered at bedtime for 3 months. The primary outcome was prevalence of continence at 6 months, defined as using ≤1 security pad. Urinary symptoms and QoL were assessed by using a visual analogue scale, and validated questionnaires. RESULTS: From the 240 patients included in the trial, 89% of patients completed 1 year of follow-up. Treatment compliance was observed in 88% (92/105) of patients receiving duloxetine, and in 97% (104/107) of patients scheduled to PFMT-biofeedback sessions. In the control group 96% of patients had achieved continence at 6 months, compared with 90% (p = 0.3) in the PMFT-biofeedback, 73% (p = 0.008) in the duloxetine, and 69% (p = 0.003) in the combined treatment arm. At 6 months, QoL was classified as uncomfortable or worse in 17% of patients in the control group, compared with 44% (p = 0.01), 45% (p = 0.008), and 34% (p = 0.07), respectively. Complete preservation of neurovascular bundles (NVB) (OR: 2.95; p = 0.048) was the only perioperative intervention found to improve early UCR. CONCLUSIONS: PFMT-biofeedback and duloxetine demonstrated limited impact in improving UCR after RP. Diligent NVB preservation, along with preoperative patient and disease characteristics, are the primary determinants for early UCR.


Assuntos
Qualidade de Vida , Incontinência Urinária , Masculino , Humanos , Cloridrato de Duloxetina/uso terapêutico , Diafragma da Pelve , Resultado do Tratamento , Incontinência Urinária/etiologia , Incontinência Urinária/terapia , Prostatectomia/efeitos adversos
2.
Eur J Pediatr ; 2024 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-39292275

RESUMO

Levetiracetam (LEV) and carbamazepine (CBZ) are effective monotherapies for focal epilepsy in children. However, the best drug remains controversial. Therefore, we performed a systematic review and meta-analysis comparing LEV and CBZ monotherapy in the management of pediatric focal epilepsy (PFE). We searched PubMed, Embase, and Cochrane databases for randomized controlled trials (RCTs) published until February 2024 comparing LEV and CBZ monotherapy in PFE. Statistical analysis was performed using R version 4.2.2, heterogeneity was assessed using I2 statistics, and the risk of bias was evaluated using the RoB-2 tool. Risk Ratios (RR) with p < 0.05 were considered significant. The outcomes of interest were seizure freedom, any adverse events, adverse events leading to treatment discontinuation, dermatologic adverse events, and the frequency of at least one seizure, defined as the proportion of patients experiencing one or more seizures during the treatment period. Four RCTs comprising 381 children with a mean age of 7.32 to 9.28 years were included, of whom 186 (48.8%) received LEV monotherapy. There was no significant difference between groups (RR: 1.15; 95% CI 0.88-1.50; p = 0.31; I2 = 90%) regarding seizure freedom. The frequency of at least one seizure (RR: 0.71; 95% CI 0.52-0.97; p = 0.03; I2 = 8%) and dermatologic adverse events (RR: 0.24; 95% CI 0.09-0.64; p < 0.01; I2 = 0%) were both significantly lower in the LEV group. There were no significant differences in the presence of any adverse events (RR: 0.58; 95% CI 0.33-1.01; p = 0.05; I2 = 36%) or adverse events leading to treatment discontinuation (RR: 0.67; 95% CI 0.13-3.42; p = 0.63; I2 = 30%).Conclusion: In monotherapy, LEV was more advantageous than CBZ for PFE, with a lower frequency of seizures and fewer dermatological adverse events. However, both drugs are equally effective in achieving seizure freedom, adverse events without specification, and those that lead to treatment discontinuation. Our findings have important implications for clinical practice and decision-making in this condition.

3.
Nucleic Acids Res ; 50(9): e50, 2022 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-35104880

RESUMO

Proteins isolated from natural sources can be composed of a mixture of isoforms with similar physicochemical properties that coexist in the final steps of purification. Yet, even where unverified, the assumed sequence is enforced throughout the structural studies. Herein, we propose a novel perspective to address the usually neglected sequence heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER. The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data, and the genetic information relating sequence conservation is integrated into this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MS de novo sequencing with genomic-based algorithms to detect point mutations. We calibrated SLIDER with Gallus gallus lysozyme, whose sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterize a metalloproteinase and a phospholipase A2-like protein from the venom of Bothrops moojeni and a crotoxin from Crotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural sources.


Assuntos
Misturas Complexas/química , Isoformas de Proteínas/análise , Software , Animais , Venenos de Crotalídeos/química , Venenos de Crotalídeos/genética , Crotalus/genética , Crotoxina/química , Crotoxina/genética , Fosfolipases A2/química
4.
Curr Opin Urol ; 32(3): 248-253, 2022 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-35552306

RESUMO

PURPOSE OF REVIEW: Although most studies focus on the tumour component of prostate cancer (PCa), increasing attention is being paid to the prostatic tumour microenvironment (TME) and its role in diagnosis, prognosis, and therapy development. Herein, we review the prognostic capability of tumour and nontumour derived biomarkers, the immunomodulatory effects of focal therapy (FT) on TME, and its potential as part of a multidisciplinary approach to PCa treatment. RECENT FINDINGS: Tumour cells have always been the natural candidates to explore new biomarkers, but recent evidence highlights the prognostic contribution of TME cell markers. TME plays a critical role in PCa progression and tumours may escape from the immune system by establishing a microenvironment that suppresses effective antitumour immunity. It has been demonstrated that FT has an immunomodulatory effect and may elicit an immune response that can either favour or inhibit tumorigenesis. TME shows to be an additional target to enhance oncological control. SUMMARY: A better understanding of TME has the potential to reliably elucidate PCa heterogeneity and assign a prognostic profile in accordance with prostate tumour foci. The joint contribution of biomarkers derived from both tumour and TME compartments may improve patient selection for FT by accurately stratifying disease aggressivity according to the characteristics of tumour foci. Preclinical studies have suggested that FT may act as a TME modulator, highlighting its promising role in multimodal therapeutic management.


Assuntos
Neoplasias da Próstata , Microambiente Tumoral , Carcinogênese , Humanos , Masculino , Prognóstico , Próstata , Neoplasias da Próstata/terapia
5.
J Urol ; 205(1): 129-136, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33119421

RESUMO

PURPOSE: Focal instead of whole gland ablation for prostate cancer has been proposed to decrease treatment morbidity. We sought to determine differences in erectile function and urinary continence after focal and whole gland ablation for prostate cancer. MATERIALS AND METHODS: From 2009 to 2018, 346 patients underwent high intensity focused ultrasound or cryotherapy for prostate cancer. Urinary continence was defined as use of no pads and sexual potency as enough erection for sexual penetration. Logistic regressions to treatment groups and covariates age, prostate specific antigen, International Society of Urological Pathology grading, prostate volume and energy modality were performed to access the effect of focal therapy in sexual potency and urinary continence after 3 and 12 months. IIEF-5 (International Index of Erectile Function) and I-PSS (International Prostate Symptom Score) questionnaires were evaluated. Propensity score matching was performed to adjust for potential baseline differences between groups. RESULTS: After exclusion, 195 post-focal therapy and 105 post-whole gland therapy patients were included in analysis. No significant difference was seen in baseline I-PSS and IIEF-5 scores. In multivariate models focal therapy was the most important factor related to sexual potency at 3 (OR 7.7) and 12 months (OR 3.9). Median IIEF-5 score at 3 months was 12 and 5 (p <0.001), and at 12 months was 13 and 9 (p=0.04) in focal therapy and whole gland therapy groups, respectively. Focal therapy was the only factor related to continence (OR 0.7, p <0.001). Results remained significant after propensity score matching. CONCLUSIONS: Focal ablation instead of whole gland therapy is the most important factor related to better sexual and urinary continence recovery after high intensity focused ultrasound and cryotherapy for prostate cancer.


Assuntos
Técnicas de Ablação/efeitos adversos , Criocirurgia/efeitos adversos , Disfunção Erétil/diagnóstico , Ablação por Ultrassom Focalizado de Alta Intensidade/efeitos adversos , Complicações Pós-Operatórias/diagnóstico , Neoplasias da Próstata/cirurgia , Incontinência Urinária/diagnóstico , Técnicas de Ablação/métodos , Idoso , Criocirurgia/métodos , Disfunção Erétil/epidemiologia , Disfunção Erétil/etiologia , Disfunção Erétil/prevenção & controle , Seguimentos , Ablação por Ultrassom Focalizado de Alta Intensidade/métodos , Humanos , Masculino , Pessoa de Meia-Idade , Complicações Pós-Operatórias/epidemiologia , Complicações Pós-Operatórias/etiologia , Complicações Pós-Operatórias/prevenção & controle , Próstata/patologia , Próstata/cirurgia , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/patologia , Índice de Gravidade de Doença , Resultado do Tratamento , Incontinência Urinária/epidemiologia , Incontinência Urinária/etiologia , Incontinência Urinária/prevenção & controle
6.
BMC Urol ; 19(1): 32, 2019 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-31060521

RESUMO

BACKGROUND: Post-radical prostatectomy urinary incontinence (PPI) negatively affects the quality of life of patients. Accurate identification of the problem by physicians is essential for adequate postoperative management. In this study we sought to access whether there is, for urinary incontinence, any discrepancy between medical reports and the perception of patients. METHODS: We performed a retrospective analysis of medical records of 337 patients subjected to radical retropubic prostatectomy (RRP) between 2005 and 2010. Sociodemographic variables were collected, as well as continence status over the course of treatment. Next, we contacted patients by phone to determine continence status at present and at time of their last appointment, as well as to apply ICIQ - SF questionnaire. Poisson regression model with robust variance was used to estimate the factors associated with discrepancy, using the stepwise backward strategy. Software used was Stata® (StataCorp, LC) version 11.0. RESULTS: There is discrepancy between medical reports and patients' perceptions in 42.2% of cases. This discrepancy was found in 56% of elderly patients and 52% of men with low schooling, with statistical significance in these groups (p = 0.069 and 0.0001, respectively), whereas in multivariate regression analysis the discrepancy rate was significantly higher in black men (discrepancy rate of 52.6%) with low schooling (p = 0.004 and 0.043, respectively). CONCLUSION: There is discrepancy between medical reports and the perception of black men with low schooling in respect to post-radical prostatectomy urinary incontinence and a need for more thorough investigation of this condition in patients that fit this risk profile.


Assuntos
Registros Eletrônicos de Saúde/normas , Satisfação do Paciente , Percepção , Complicações Pós-Operatórias/psicologia , Prostatectomia/efeitos adversos , Incontinência Urinária/psicologia , Adulto , Idoso , Humanos , Masculino , Pessoa de Meia-Idade , Papel do Médico/psicologia , Complicações Pós-Operatórias/diagnóstico , Complicações Pós-Operatórias/etiologia , Neoplasias da Próstata/psicologia , Neoplasias da Próstata/cirurgia , Qualidade de Vida/psicologia , Estudos Retrospectivos , Incontinência Urinária/diagnóstico , Incontinência Urinária/etiologia
7.
J Insect Sci ; 19(1)2019 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-30624704

RESUMO

The invasion of the spotted wing drosophila, Drosophila suzukii Matsumura, across the Americas and Europe has led to increased insecticide applications to protect fruit crops. This insecticide usage conflicts with integrated pest management programs, as well as harvest, export, and pollination services in the affected crops. A novel management tool was assessed against D. suzukii that may mitigate these conflicts. HOOK SWD, an attract-and-kill (A&K) formulation applied as a sprayable bait, was evaluated for three growing seasons in two berry crops in New Jersey and California. In blueberry crops treated with HOOK SWD, fruit infestations by D. suzukii were 2-8 times lower than in untreated crops. In trials in commercial raspberry fields, weekly or biweekly HOOK SWD applications combined with a single grower standard D. suzukii-targeted cover spray resulted in nearly 2-5 times fewer fruit infestations compared to the grower standard cover spray alone. Assays of the residual activity of HOOK SWD resulted in more than 78-93% adult D. suzukii mortality when exposed to raspberry leaves after the formulation had aged for 35 d in the field under plastic hoop houses. These results suggest that this A&K strategy can be integrated in D. suzukii management programs.


Assuntos
Drosophila , Controle de Insetos , Feromônios , Animais , Mirtilos Azuis (Planta)/crescimento & desenvolvimento , California , Produtos Agrícolas/crescimento & desenvolvimento , Feminino , Frutas/crescimento & desenvolvimento , Controle de Insetos/métodos , Masculino , New Jersey , Rubus/crescimento & desenvolvimento
8.
Biochim Biophys Acta Proteins Proteom ; 1866(3): 473-481, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29287778

RESUMO

The myotoxic mechanism for PLA2-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction caused by natural amino acid substitutions and an insertion. Herein, we present four crystal structures of MjTX-II, in its apo state and complexed with fatty acids of different lengths. Analyses of these structures revealed slightly different oligomeric conformations but with both MDoSs in an arrangement that resembles an active-state PLA2-like structure. To explore the structural transitions between apo protein and fatty-acid complexes, we performed Normal Mode Molecular Dynamics simulations, revealing that oligomeric conformations of MjTX-II/fatty acid complexes may be reached in solution by the apo structure. Similar simulations with typical PLA2-like structures demonstrated that this transition is not possible without the presence of fatty acids. Thus, we hypothesize that MjTX-II does not require fatty acids to be active, although these ligands may eventually help in its stabilization by the formation of hydrogen bonds. Therefore, these results complement previous findings for MjTX-II and help us understand its particular ligand-binding properties and, more importantly, its particular mechanism of action, with a possible impact on the design of structure-based inhibitors for PLA2-like toxins in general.


Assuntos
Ácidos Graxos/química , Simulação de Dinâmica Molecular , Fosfolipases A/química , Conformação Proteica , Multimerização Proteica , Animais , Bothrops/metabolismo , Biologia Computacional/métodos , Cristalografia por Raios X , Ácidos Graxos/metabolismo , Ligação de Hidrogênio , Ligantes , Fosfolipases A/metabolismo , Ligação Proteica
9.
Biochim Biophys Acta Gen Subj ; 1861(1 Pt A): 3199-3209, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27531710

RESUMO

BACKGROUND: One of the main challenges in snakebite envenomation treatment is the development of stable, versatile and efficient anti-venom therapies. Local myotoxicity in accidents involving snakes from the Bothrops genus is still a consequence of serum therapy inefficient neutralization that may lead to permanent sequelae in their victims. One of the classes of toxins that participate in muscle necrosis is the PLA2-like proteins. The aim of this work was to investigate the role of zinc ions in the inhibition of PLA2-like proteins and to advance the current knowledge of their action mechanism. METHODS: Myographic and electrophysiological techniques were used to evaluate the inhibitory effect of zinc ions, isothermal titration calorimetry assays were used to measure the affinity between zinc ions and the toxin and X-ray crystallography was used to reveal details of this interaction. RESULTS: We demonstrated that zinc ions can effectively inhibit the toxin by the interaction with two different sites, which are related to two different mechanism of inhibition: preventing membrane disruption and impairing the toxin state transition. Furthermore, structural study presented here included an additional step in the current myotoxic mechanism improving the comprehension of the allosteric transition that PLA2-like proteins undergo to exert their function. CONCLUSIONS: Our findings show that zinc ions are inhibitors of PLA2-like proteins and suggest two different mechanisms of inhibition for these ions. GENERAL SIGNIFICANCE: Zinc is a new candidate that can assist in anti-venom treatments and can promote the design of new and even more accurate structure-based inhibitors for PLA2-like proteins.


Assuntos
Venenos de Crotalídeos/toxicidade , Inibidores de Fosfolipase A2/farmacologia , Fosfolipases A2/toxicidade , Zinco/metabolismo , Animais , Bothrops , Calorimetria , Venenos de Crotalídeos/química , Cristalografia por Raios X , Diafragma/efeitos dos fármacos , Interações Hidrofóbicas e Hidrofílicas , Íons , Masculino , Potenciais da Membrana/efeitos dos fármacos , Camundongos , Modelos Moleculares , Fosfolipases A2/química , Nervo Frênico/efeitos dos fármacos
10.
Gynecol Endocrinol ; 33(5): 359-362, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28277134

RESUMO

OBJECTIVES: To evaluate Ki-67 antigen expression in mammary epithelium of female rats in persistent estrus treated with anastrozole. MATERIALS AND METHODS: Twenty-eight Wistar-Hanover female rats in persistent estrus induced by subcutaneous injection of 1.25 mg of testosterone propionate in the second day of life were randomly divided into two groups, control and experimental, with 14 animals each. The animals of control group received only the vehicle (propyleneglycol) and the animals of group experimental received 0.125 mg daily of anastrozole by gavage during 28 days. After 28 days of treatment, all animals were sacrificed and the first pair of abdominal-inguinal mammary glands was removed and fixed in 10% buffered formalin to investigate Ki-67 antigen expression by immunohistochemistry. RESULTS: The mean percentage of Ki-67-stained nuclei per 500 cells in the mammary epithelium was 76.97 ± 0.76 and 14.44 ± 2.02 [mean ± standard error of the mean (SEM)] in the control and experimental groups, respectively (p < 0.0001). CONCLUSIONS: Anastrozole treatment significantly reduced Ki-67 expression in the mammary epithelium of rats in persistent estrus.


Assuntos
Estro/efeitos dos fármacos , Antígeno Ki-67/metabolismo , Glândulas Mamárias Animais/efeitos dos fármacos , Glândulas Mamárias Animais/metabolismo , Nitrilas/farmacologia , Triazóis/farmacologia , Anastrozol , Animais , Proliferação de Células/efeitos dos fármacos , Epitélio/efeitos dos fármacos , Epitélio/metabolismo , Estro/metabolismo , Feminino , Ratos , Ratos Wistar , Testosterona/farmacologia
11.
An Acad Bras Cienc ; 88(4): 2349-2356, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27925035

RESUMO

Insulin-like Growth Factor-1 (IGF-1) gene polymorphism has been associated with an increased risk for breast cancer. IGF-1 is a key regulator of proliferation, cell differentiation and apoptosis. It has important mitogenic and anti-apoptotic activities in normal cells and in breast cancer cells, acting synergistically with estrogen to increase neoplastic cell proliferation. This review aims to present the recent finds of IGF-1 gene polymorphism and its relationship with the risk of breast cancer through following the polymorphic dinucleotide repeat cytosine-adenine (CA) and single nucleotide polymorphisms (SNPs) by searching in the PubMed database publications focused studies published from 2010 to 2015 related to IGF-1 gene polymorphism and breast cancer risk. A growing number of studies support an association between IGF-1 gene polymorphism and breast cancer risk with conflicting results, nevertheless elucidation of the patterns of IGF-1 gene expression may permit characterization of women at high-risk for breast cancer, as well as the development of strategies for early diagnosis and efficient treatment against the disease.


Assuntos
Neoplasias da Mama/genética , Expressão Gênica , Fator de Crescimento Insulin-Like I/genética , Polimorfismo Genético , Alelos , Proliferação de Células , Repetições de Dinucleotídeos , Feminino , Humanos , Fatores de Risco
12.
Chaos ; 26(4): 043107, 2016 04.
Artigo em Inglês | MEDLINE | ID: mdl-27131486

RESUMO

We have studied the effects of perturbations on the cat's cerebral cortex. According to the literature, this cortex structure can be described by a clustered network. This way, we construct a clustered network with the same number of areas as in the cat matrix, where each area is described as a sub-network with a small-world property. We focus on the suppression of neuronal phase synchronisation considering different kinds of perturbations. Among the various controlling interventions, we choose three methods: delayed feedback control, external time-periodic driving, and activation of selected neurons. We simulate these interventions to provide a procedure to suppress undesired and pathological abnormal rhythms that can be associated with many forms of synchronisation. In our simulations, we have verified that the efficiency of synchronisation suppression by delayed feedback control is higher than external time-periodic driving and activation of selected neurons of the cat's cerebral cortex with the same coupling strengths.


Assuntos
Córtex Cerebral , Animais , Gatos , Neurônios
13.
Biochim Biophys Acta ; 1844(12): 2265-76, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25278377

RESUMO

Envenomation via snakebites is an important public health problem in many tropical and subtropical countries that, in addition to mortality, can result in permanent sequelae as a consequence of local tissue damage, which represents a major challenge to antivenom therapy. Venom phospholipases A2 (PLA2s) and PLA2-like proteins play a leading role in the complex pathogenesis of skeletal muscle necrosis, nevertheless their precise mechanism of action is only partially understood. Recently, detailed structural information has been obtained for more than twenty different members of the PLA2-like myotoxin subfamily. In this review, we integrate the available structural, biochemical and functional data on these toxins and present a comprehensive hypothesis for their myotoxic mechanism. This process involves an allosteric transition and the participation of two independent interaction sites for docking and disruption of the target membrane, respectively, leading to a five-step mechanism of action. Furthermore, recent functional and structural studies of these toxins complexed with ligands reveal diverse neutralization mechanisms that can be classified into at least three different groups. Therefore, the data summarized here for the PLA2-like myotoxins could provide a useful molecular basis for the search for novel neutralizing strategies to improve the treatment of envenomation by viperid snakes.

14.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 9): 1921-30, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26327382

RESUMO

ARCIMBOLDO solves the phase problem at resolutions of around 2 Šor better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Šis described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.


Assuntos
Computadores , Sistemas de Gerenciamento de Base de Dados , Proteínas/química , Sequência de Aminoácidos , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Software
15.
BMC Plant Biol ; 15: 198, 2015 08 14.
Artigo em Inglês | MEDLINE | ID: mdl-26268941

RESUMO

BACKGROUND: In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. RESULTS: We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. CONCLUSION: Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.


Assuntos
Eucalyptus/genética , Genoma de Planta , Proteínas de Plantas/genética , Retroelementos , Transcriptoma , Eucalyptus/metabolismo , Dados de Sequência Molecular , Mutagênese Insercional , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Estrutura Secundária de Proteína , Análise de Sequência de DNA , Sequências Repetidas Terminais
17.
Biochim Biophys Acta ; 1834(12): 2772-81, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24145104

RESUMO

Bothrops brazili is a snake found in the forests of the Amazonian region whose commercial therapeutic anti-bothropic serum has low efficacy for local myotoxic effects, resulting in an important public health problem in this area. Catalytically inactive phospholipases A2-like (Lys49-PLA2s) are among the main components from Bothrops genus venoms and are capable of causing drastic myonecrosis. Several studies have shown that the C-terminal region of these toxins, which includes a variable combination of positively charged and hydrophobic residues, is responsible for their activity. In this work we describe the crystal structures of two Lys49-PLA2s (BbTX-II and MTX-II) from B. brazili venom and a comprehensive structural comparison with several Lys49-PLA2s. Based on these results, two independent sites of interaction were identified between protein and membrane which leads to the proposition of a new myotoxic mechanism for bothropic Lys49-PLA2s composed of five different steps. This proposition is able to fully explain the action of these toxins and may be useful to develop efficient inhibitors to complement the conventional antivenom administration.


Assuntos
Bothrops , Venenos de Crotalídeos/química , Fosfolipases A2/química , Animais , Venenos de Crotalídeos/genética , Cristalografia por Raios X , Fosfolipases A2/genética , Estrutura Terciária de Proteína , Relação Estrutura-Atividade
18.
Protein Sci ; 33(9): e5136, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39150227

RESUMO

Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.


Assuntos
Modelos Moleculares , Proteínas , Proteínas/química , Cristalografia por Raios X , Conformação Proteica , Software
19.
Biochimie ; 218: 46-56, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37659716

RESUMO

In accidents involving Crotalus snakes, the crotoxin complex (CTX) plays lethal action due to its neurotoxic activity. On the other hand, CTX have potential biotechnological application due to its anti-tumoral, anti-inflammatory, antimicrobial, analgesic and immunomodulatory properties. CTX is a heterodimer composed of Crotoxin A (CA or crotapotin), the acidic nontoxic and non-enzymatic component and; Crotoxin B (CB), a basic, toxic and catalytic PLA2. Currently, there are two classes of CTX isoforms, whose differences in their biological activities have been attributed to features presented in CB isoforms. Here, we present the crystal structure of CB isolated from the Crotalus durissus collilineatus venom. It amino acid sequence was assigned using the SEQUENCE SLIDER software, which revealed that the crystal structure is a heterodimer composed of two new CB isoforms (colCB-A and colCB-B). Bioinformatic and biophysical analyses showed that the toxin forms a tetrameric assembly in solution similar to CB from Crotalus durissus terrificus venom, despite some differences observed at the dimeric interface. By the previously proposed classification, the colCB-B presents features of the class I isoforms while colCB-A cannot be classified into classes I and II based on its amino acid sequence. Due to similar features observed for other CB isoforms found in the NCBI database and the results obtained for colCB-A, we suggest that there are more than two classes of CTX and CB isoforms in crotalic venoms.


Assuntos
Venenos de Crotalídeos , Crotoxina , Serpentes Peçonhentas , Animais , Crotoxina/química , Fosfolipases A2/química , Crotalus/metabolismo , Venenos de Crotalídeos/química , Isoformas de Proteínas/metabolismo
20.
J Biomol Struct Dyn ; 42(5): 2616-2631, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37166375

RESUMO

The withanolides are naturally occurring steroidal lactones found mainly in plants of the Solanaceae family. The subtribe Withaninae includes species like Withania sominifera, which are a source of many bioactive withanolides. In this work, we selected and evaluate the ADMET-related properties of 91 withanolides found in species of the subtribe Withaninae computationally, to predict the relationship between their structures and their pharmacokinetic profiles. We also evaluated the interaction of these withanolides with known targets of Alzheimer's disease (AD) through molecular docking and molecular dynamics. Withanolides presented favorable pharmacokinetic properties, like high gastrointestinal absorption, lipophilicity (logP ≤ 5), good distribution and excretion parameters, and a favorable toxicity profile. The specie Withania aristata stood out as an interesting source of the promising withanolides classified as 5-ene with 16-ene or 17-ene. These withanolides presented a favourable pharmacokinetic profile and were also highlighted as the best candidates for inhibition of AD-related targets. Our results also suggest that withanolides are likely to act as cholinesterase inhibitors by interacting with the catalytic pocket in an energy favorable and stable way.Communicated by Ramaswamy H. Sarma.


Assuntos
Doença de Alzheimer , Withania , Vitanolídeos , Vitanolídeos/farmacologia , Simulação de Acoplamento Molecular , Doença de Alzheimer/tratamento farmacológico , Simulação de Dinâmica Molecular , Withania/química
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