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1.
Braz. arch. biol. technol ; 64: e21210007, 2021. tab, graf
Artigo em Inglês | LILACS | ID: biblio-1339314

RESUMO

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.


Assuntos
Estrutura Secundária de Proteína , Máquina de Vetores de Suporte , Inteligência Artificial , Biologia Computacional/métodos
2.
Clinics ; 70(5): 363-368, 05/2015. tab, graf
Artigo em Inglês | LILACS | ID: lil-748276

RESUMO

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 During the follow-up period, 40 patients were withdrawn from peritoneal dialysis.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, ...


Assuntos
Regulação da Expressão Gênica , Proteínas de Bactérias/química , Biologia Computacional , Cinética , Ligantes , Conformação de Ácido Nucleico , Nucleotídeos/química , Ligação Proteica , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , RNA , Termodinâmica
3.
Rev. bras. enferm ; 68(2): 219-227, Mar-Apr/2015. tab
Artigo em Espanhol | LILACS, BDENF - Enfermagem | ID: lil-752507

RESUMO

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. .


Assuntos
Humanos , DNA , Receptores de Glucocorticoides/química , Receptores de Mineralocorticoides/química , Sequência de Aminoácidos , Cristalografia por Raios X , DNA , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Dados de Sequência Molecular , Mutação , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/patologia , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Pseudo-Hipoaldosteronismo/genética , Pseudo-Hipoaldosteronismo/metabolismo , Pseudo-Hipoaldosteronismo/patologia , Receptores de Glucocorticoides/genética , Receptores de Glucocorticoides/metabolismo , Receptores de Mineralocorticoides/genética , Receptores de Mineralocorticoides/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia Estrutural de Proteína
4.
J. appl. oral sci ; 23(2): 135-144, Mar-Apr/2015. tab, graf
Artigo em Inglês | LILACS, BBO - Odontologia | ID: lil-746539

RESUMO

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. .


Assuntos
Animais , Camundongos , Anti-Inflamatórios não Esteroides/metabolismo , Ciclo-Oxigenase 1/metabolismo , /metabolismo , Inibidores de Ciclo-Oxigenase/metabolismo , Piroxicam/análogos & derivados , Tiazinas/metabolismo , Tiazóis/metabolismo , Substituição de Aminoácidos , Anti-Inflamatórios não Esteroides/química , Arginina/química , Arginina/genética , Arginina/metabolismo , Sítios de Ligação , Domínio Catalítico , Ciclo-Oxigenase 1/química , Ciclo-Oxigenase 1/genética , /química , /genética , Inibidores de Ciclo-Oxigenase/química , Ligação de Hidrogênio , Leucina/química , Leucina/genética , Leucina/metabolismo , Mutação , Piroxicam/química , Piroxicam/metabolismo , Estrutura Secundária de Proteína , Serina/química , Serina/genética , Serina/metabolismo , Tiazinas/química , Tiazóis/química , Tirosina/química , Tirosina/genética , Tirosina/metabolismo , Água
5.
Salud colect ; 11(1): 115-128, ene.-mar. 2015.
Artigo em Espanhol | LILACS | ID: lil-746688

RESUMO

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.


Assuntos
Proteínas de Bactérias/química , Biofísica/métodos , Proteínas de Ligação a DNA/química , Microscopia de Força Atômica/métodos , Ligação de Hidrogênio , Cinética , Modelos Moleculares , Modelos Estatísticos , Método de Monte Carlo , Peptostreptococcus/metabolismo , Conformação Proteica , Desnaturação Proteica , Dobramento de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas/química , Estresse Mecânico , Temperatura , Fatores de Tempo , Ubiquitina/química
6.
Rev. bras. epidemiol ; 18(1): 208-219, Jan-Mar/2015. tab, graf
Artigo em Português | LILACS | ID: lil-736434

RESUMO

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. .


Assuntos
Animais , Epiderme/metabolismo , beta-Queratinas/metabolismo , Sequência de Aminoácidos , Eletroforese em Gel Bidimensional , Queratinas/metabolismo , Modelos Anatômicos , Modelos Biológicos , Dados de Sequência Molecular , Processamento de Proteína Pós-Traducional , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteômica/métodos , Répteis , Homologia de Sequência de Aminoácidos
8.
Genet. mol. res. (Online) ; 6(2): 422-433, 2007. tab, graf
Artigo em Inglês | LILACS | ID: lil-482027

RESUMO

We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with alpha-helix segments. The candidates were selected based on an amphipathy coefficient value range and the minimum number of residues in a segment. We compared our results with the transmembrane segments previously identified in the PDB_TM database by the TMDET algorithm. We expected that the hydrophobic segments would be identified using only the primary structures of the proteins and the amphipathy scale. However, some of these hydrophobic segments may pertain to hydrophobic pockets not included in transmembrane regions. We found that our amphipathy scale could identify alpha-helix transmembrane regions with a probability of success of 76% when all segments were included and 90% when all membrane proteins were included.


Assuntos
Humanos , Animais , Proteínas/química , Proteômica/métodos , Aminoácidos/química , Análise de Sequência de Proteína , Bases de Dados de Proteínas , Conformação Proteica , Estrutura Secundária de Proteína , Genética , Proteínas/metabolismo , Simulação por Computador
9.
Genet. mol. res. (Online) ; 6(4): 946-963, 2007. ilus, tab
Artigo em Inglês | LILACS | ID: lil-520054

RESUMO

We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature.


Assuntos
Animais , Sequência de Aminoácidos , Bovinos/genética , Mapeamento de Interação de Proteínas , Serina Endopeptidases , Aprotinina , Sítios de Ligação , Análise por Conglomerados , Bases de Dados de Proteínas , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Dados de Sequência Molecular , Ligação Proteica , Estrutura Secundária de Proteína
10.
Genet. mol. res. (Online) ; 6(4): 923-936, 2007. ilus, tab
Artigo em Inglês | LILACS | ID: lil-520056

RESUMO

STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. BlueStar STING is available at http://www.cbi.cnptia.embrapa.br.


Assuntos
Aminoácidos/química , Bases de Dados de Proteínas , Modelos Químicos , Proteínas/química , Software , Reações Antígeno-Anticorpo , Estrutura Secundária de Proteína , Eletricidade Estática
11.
Genet. mol. res. (Online) ; 6(4): 911-922, 2007. ilus, graf
Artigo em Inglês | LILACS | ID: lil-520057

RESUMO

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one’s ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.


Assuntos
Biologia Computacional/métodos , Sistemas de Gerenciamento de Base de Dados , Bases de Dados de Proteínas , Proteínas/química , Estrutura Secundária de Proteína
12.
Genet. mol. res. (Online) ; 6(4): 901-910, 2007. ilus
Artigo em Inglês | LILACS | ID: lil-520058

RESUMO

The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three-alpha-helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-alpha-helix bundle.


Assuntos
Simulação por Computador , Modelos Moleculares , Proteínas/química , Sequência de Aminoácidos , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Solventes
13.
Genet. mol. res. (Online) ; 6(4): 799-820, 2007. ilus, tab, graf
Artigo em Inglês | LILACS | ID: lil-520064

RESUMO

The construction of a realistic theoretical model of proteins is determinant for improving the computational simulations of their structural and functional aspects. Modeling proteins as a network of non-covalent connections between the atoms of amino acid residues has shown valuable insights into these macromolecules. The energy-related properties of protein structures are known to be very important in molecular dynamics. However, these same properties have been neglected when the protein structures are modeled as networks of atoms and amino acid residues. A new approach for the construction of protein models based on a network of atoms is presented. This method, based on interatomic interaction, takes into account the energy and geometric aspects of the protein structures that were not employed before, such as atomic occlusion inside the protein, the use of solvation, protein modeling and analysis, and the use of energy potentials to estimate the energies of interatomic non-covalent contacts. As a result, we achieved a more realistic network model of proteins. This model has the virtue of being more robust in face of different unknown variables that usually are arbitrarily estimated. We were able to determine the most connected residues of all the proteins studied, so that we are now in a better condition to study their structural role.


Assuntos
Globinas/química , Proteínas/química , Termodinâmica , Sequência de Aminoácidos , Modelos Químicos , Dados de Sequência Molecular , Estrutura Secundária de Proteína
14.
Genet. mol. res. (Online) ; 5(1): 127-137, Mar. 31, 2006. ilus, graf
Artigo em Inglês | LILACS | ID: lil-449139

RESUMO

Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.


Assuntos
Humanos , Alinhamento de Sequência/métodos , Estrutura Secundária de Proteína/genética , Sequência Conservada/genética , Entropia , Modelos Genéticos , Sequência de Aminoácidos/genética
15.
Genet. mol. biol ; 29(4): 762-770, 2006. graf, tab
Artigo em Inglês | LILACS | ID: lil-450503

RESUMO

With the advent of structural genomics, the need for fast structural information about unknown proteins has increased. We describe a new methodology, based on 13C, 15N and ¹H chemical shift dispersion to predict the amount of secondary structure of unassigned proteins from their 15N- and/or 13C-edited heteronuclear single quantum coherence (HSQC) spectra. This methodology has been coded into a software called PASSNMR (Prediction of the Amount of Secondary Structure by Nuclear Magnetic Resonance), which can be accessed directly from the Internet. PASSNMR program is a powerful tool for screening proteins for proteomic or structural genomic investigations when used with recent methodologies that take advantage of the use of the antibiotic rifampicin to selectively label the heterologous proteins expressed in E. coli. PASSNMR analysis can be useful as a first approach to predict the amount of secondary structure in proteins to structural genomics. Information about the secondary structure of proteins can be obtained even before protein purification, with small quantities of protein, just by performing two simple nuclear magnetic resonance (NMR) experiments and using PASSNMR program.


Assuntos
Animais , Escherichia coli , Estrutura Secundária de Proteína , Software , Espectroscopia de Ressonância Magnética , Proteômica , Rifampina/farmacologia
16.
Rev. argent. microbiol ; 36(4): 151-157, Oct.-Dec. 2004. graf, tab
Artigo em Inglês | LILACS | ID: lil-634474

RESUMO

The gag gene of HIV-1 encodes a single open reading frame of 55 kDa that contains three subdomains: the matrix domain (p17), the capsid domain (p24) and the nucleocapsid domain (p15). The p24 and p17 proteins have a predominant a-helical structure and perform important functions throughout thevirallife-cycle. The determination of gag-specific antibodies is important because declining titers of these antibodies herald clinical deterioration.In this work we present the results obtained on immunoreactiviy of synthetic peptides that mimic immunogenic a-helical regions of p24 and p17. The influence on the immunoreactivity of structural modifications in native sequences, including the addition of non immunogenic side chains: AAAC- and -CAAA on both side of minimal epitopes was evaluated in indirect and competitive enzymeimmunoassays. The conformational characteristcs to the peptides were analysed by circular dichroism and these results were correlated with that obtained in the immunoassays. It was shown that the reactivity of peptides mimicking short a-helical regions of p24 and p17 is improved by adding short non immunogenic chains on both N- and C- terminus. These modifications enhanced the immobilization of the peptides onto the solid support and allowed more accesibility to the minimal epitopes byspecific antibodies, in solution.


El gen gag del VIH-1 codifica una región de 55kDA que contiene tres subdominios: matriz (p17), cápside (p24) y nucleocápside (p15). Las proteínas p24 y p17 tienen una estructura predominante helicoidal y cumplen un rol importante en el ciclo de vida del virus. En este trabajo presentamos los resultados de inmunorreactividad de péptidos sintéticos que imitan regiones helicoidales de p24 y p17. Utilizando enzimoinmunoensayos se evaluó la influencia de modificaciones en las secuencias nativas sobre la capacidad de reconocimiento de anticuerpos específicos en solución y en fase sólida, incluyendo el agregado de cadenas no inmunogénicas en ambos extremos de los epitopes mínimos. La conformación de los péptidos se determinó por dicroísmo circular y los resultados se correlacionaron con los de inmunorreactividad. Se observó que la capacidad de reconocimiento de anticuerpos por péptidos pequeños que imitan estructuras helicoidales de p24 y p17 mejoró con el agregado de cadenas no inmunogénicas en ambos extremos de los epitopes. Estas modificaciones mejoran la inmovilización sobre las superficies sólidas y permiten una mayor accesibilidad de los anticuerpos a los epitopes mínimos en solución.


Assuntos
Humanos , Reações Antígeno-Anticorpo , Ensaio de Imunoadsorção Enzimática/métodos , Produtos do Gene gag/imunologia , Anticorpos Anti-HIV/imunologia , Antígenos HIV/imunologia , /imunologia , HIV-1 , Mimetismo Molecular , Fragmentos de Peptídeos/imunologia , Proteínas Virais/imunologia , Sequência de Aminoácidos , Substituição de Aminoácidos , Dicroísmo Circular , Produtos do Gene gag do Vírus da Imunodeficiência Humana , Produtos do Gene gag/química , Anticorpos Anti-HIV/isolamento & purificação , Antígenos HIV/química , /química , Infecções por HIV/sangue , Infecções por HIV/imunologia , Epitopos Imunodominantes/química , Epitopos Imunodominantes/imunologia , Dados de Sequência Molecular , Ligação Proteica , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Fragmentos de Peptídeos/síntese química , Soluções , Proteínas Virais/química
17.
Electron. j. biotechnol ; 7(3): 04-05, Dec. 2004. ilus, graf, tab
Artigo em Inglês | LILACS | ID: lil-448761

RESUMO

Protein design is currently used for the creation of new proteins with desirable traits, which include a superior nutritional value. One of the challenges of protein design in this area is to achieve the production of stable native-like proteins that resist the proteolytic pressure of the organism used for its production (the bioreactor). We report here the identification of a specific peptide bond sensitive to E. coli proteolysis in the designer protein MB-1Trp. In an attempt to reduce proteolysis, we have created a MB-1TrpHis gene library in which the two amino acids surrounding the peptide bond, N44 and L45, were randomized using degenerated oligonucleotides. The initial characterization of MB-1TrpHis N44E/L45V and MB-1TrpHis N44E/L45M, 2 variants of the library that were more resistant than the parent protein, was performed in order to investigate the nature of the mutants' resistance. Our results suggest that the mutants behaved like MB-1Trp regarding folding and thermal stability, and that proteolytic resistance is due to the elimination of the protease recognition site.


Assuntos
Aminoácidos Essenciais/genética , Aminoácidos Essenciais/metabolismo , Engenharia de Proteínas/métodos , Proteínas na Dieta/metabolismo , Agroindústria , Reatores Biológicos , Biotecnologia , Dicroísmo Circular , Temperatura Alta , Mutação , Metionina/genética , Metionina/metabolismo , Desnaturação Proteica , Estrutura Secundária de Proteína
18.
Biol. Res ; 29(2): 213-25, 1996.
Artigo em Inglês | LILACS | ID: lil-228535

RESUMO

Several factors that may contribute to the stabilization of the helical structure in proteins, detected in studies made on short synthetic peptides, have been reported. Some of them are: presence of alanine or leucine, ionic-pair bonding, stabilization of the helical dipole moment by appropriate charges at the helix N- and C-caps, and aromatic interactions of amino acids located at positions i, i + 4. An analysis of 54 helical structures from 12 proteins showed that all these stabilizing factors were also present in proteins, but the influence of any of them had a different weight, according to the distribution of the hydrophobic and hydrophilic amino acid residues in the helical sequence. The role of non-sequence depending interactions in helical stability, such as presence of disulfide bridges, or bonding of helical residues to substrate and/or cofactors, was also analysed


Assuntos
Alanina/fisiologia , Aminoácidos/fisiologia , Estabilidade Enzimática/fisiologia , Leucina/fisiologia , Muramidase/ultraestrutura , Hormônios Pancreáticos/fisiologia , Estrutura Secundária de Proteína
19.
Biol. Res ; 29(1): 141-63, 1996.
Artigo em Inglês | LILACS | ID: lil-228545

RESUMO

Nuclear magnetic resonance (NMR) spectroscopy is emerging as a powerful tool for the study of enzyme structure and function. This article discusses the general principles of NMR and the potential information this technique can provide in the study of enzymes along with its limitations


Assuntos
Ativação Enzimática , Ligantes , Espectroscopia de Ressonância Magnética , Peptídeos , Conformação Proteica , Sítios de Ligação , Sequências Hélice-Volta-Hélice , Ligação Proteica , Estrutura Secundária de Proteína
20.
Biol. Res ; 29(1): 77-100, 1996.
Artigo em Inglês | LILACS | ID: lil-228551

RESUMO

Since the determination of the tertiary structure by X-ray crystallography has been achieved only for a limited number of proteins, alternative approaches are being sought. In this article, the use of secondary structure prediction and of molecular modeling is discussed. Several examples are analyzed in detail


Assuntos
Animais , Ativação Enzimática , Estrutura Secundária de Proteína , Sequência de Aminoácidos , Modelos Moleculares , Dados de Sequência Molecular , Raios X
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