Página 1 dos resultados de 464205 itens digitais encontrados em 0.116 segundos

Effects of a Low-Protein Diet on Plasma Amino Acid and Homocysteine Levels and Oxidative Status in Rats

DEMINICE, Rafael; PORTARI, Guilherme Vannucchi; MARCHINI, Julio Sergio; VANNUCCHI, Helio; JORDAO, Alceu Afonso
Fonte: KARGER Publicador: KARGER
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
35.82%
Background/Aims: Transmethylation reactions and antioxidant metabolism are linked by transsulfuration, where homocysteine (Hcy) is converted to cysteine and reduced glutathione (GSH). Low protein intake can modulate the balance of this metabolic reaction. The aim of the present investigation was to study the effect of a low-protein diet on Hcy metabolism by monitoring levels of the amino acids involved in these pathways, and relating these levels to GSH levels and lipid peroxidation in rats. Methods: Sixteen rats were divided into 2 groups: control (C; standard AIN-93 diet, 20% protein) and low-protein diet (LPD; 8% protein diet). Rats in both groups were placed on the diets for 28 days. Results: A significant reduction (p < 0.05) in plasma Hcy concentration was found in LPD rats (0.16 +/- 0.04 mu mol/mg protein) versus C rats (0.25 +/- 0.03 mu mol/mg protein). Methionine levels were not significantly different between the 2 groups (C: 1.24 +/- 0.22 mu mol/mg protein; LPD: 1.03 +/- 0.27 mu mol/mg protein). A significant reduction (p ! 0.05) in hepatic GSH concentrations (C: 44 8 10 mu mol/mg protein; LPD: 17.4 +/- 4.3 mu mol/mg protein) was accompanied by an increase in lipid peroxidation (C: 0.13 +/- 0.01 mu mol/mg protein; LPD: 0.17 +/- 0.02 mu mol/mg protein; r = -0.62...

Effects of dietary urea levels on milk protein fractions of Holstein cows

AQUINO, A. A.; LIMA, Yv. R.; BOTARO, B. G.; ALBERTO, C. S. S.; PEIXOTO JR., K. C.; SANTOS, M. V.
Fonte: ELSEVIER SCIENCE BV Publicador: ELSEVIER SCIENCE BV
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
35.83%
The aim of this study was to evaluate the effects of substituting soybean meal for urea on milk protein fractions (casein, whey protein and non-protein nitrogen) of dairy cows in three dietary levels. Nine mid-lactation Holstein cows were used in a 3 x 3 Latin square arrangement, composed of 3 treatments, 3 periods of 21 days each, and 3 squares. The treatments consisted of three different diets fed to lactating cows, which were randomly assigned to three groups of three animals: (A) no urea inclusion, providing 100% of crude protein (CP), rumen undegradable protein (RUP) and rumen degradable protein (RDP) requirements, using soybean meal and sugarcane as roughage; (B) urea inclusion at 7.5 g/kg DM in partial substitution of soybean meal CP equivalent; (C) urea inclusion at 15 g/kg DM in partial substitution of soybean meal CP equivalent. Rations were isoenergetic and isonitrogenous-1 60 g/kg DM of crude protein and 6.40 MJ/kg DM of net energy for lactation. When the data were analyzed by simple polynomial regression, no differences were observed among treatments in relation to milk CP content, true protein, casein, whey protein, non-casein and non-protein nitrogen, or urea. The milk true protein:crude protein and casein:true protein ratios were not influenced by substituting soybean meal for urea in the diet. Based on the results it can be concluded that the addition of urea up to 15 g/kg of diet dry matter in substitution of soybean meal did not alter milk protein concentration casein...

Suplementação protéica, uso de subprodutos agroindustriais e processamento de milho em dietas para vacas leiteiras em confinamento.; Protein supplementation, by-products and corn processing for lactating dairy cows.

Imaizumi, Hugo
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 20/04/2005 PT
Relevância na Pesquisa
35.82%
Na intenção de avaliar o efeito da suplementação protéica, uso de subprodutos agroindustriais e o processamento de milho, foram conduzidos quatro experimentos. No experimento I, avaliou-se formas de processamento de milho (milho moído, M; e resíduo de pipoca doce, P) e fontes protéicas (farelo de soja, FS; uréia, U; ou farinha de peixe, FP), combinando-os para formar quatro tratamentos: MFS (M + FS); PFS (P + FS); PFP (P + FS + FP); PU (P + U). Comparado ao milho moído (MFS), o resíduo de pipoca doce (PFS) diminuiu os teores de gordura e proteína no leite. Em relação às fontes protéicas (PFS x PFP x PU), observou-se que a maior produção leiteira foi obtida no tratamento PFS. A farinha de peixe (PFP) levou ao menor teor de gordura no leite, mas aumentou o teor protéico no leite. No experimento II, avaliou-se os efeitos da inclusão de três teores (0,15 e 30% da MS) de farelo de algodão (FA) em substituição ao farelo de soja na dieta. O consumo de MS não foi afetado pelos tratamentos, contudo a inclusão de FA levou a efeitos lineares negativos sobre a produção de leite e teor e produção de proteína e efeitos lineares positivos sobre o teor e produção de gordura no leite. No experimento III, comparou-se os efeitos de uma dieta basal com 16% de PB contra duas outras com 17...

Efeito Hipocolesterolemizante da Proteína de Amaranto (Amaranthus cruentus BRS-Alegria) em Hamsters ; Cholesterol-lowering effect of amaranth protein (Amaranthus cruentus L. BRS-Alegria) in hamsters.

Mendonça, Simone
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 09/03/2006 PT
Relevância na Pesquisa
35.82%
Objetivo. Amaranto é considerado um alimento funcional devido às suas propriedades de redução de colesterol plasmático. Um possível componente do amaranto responsável por este efeito é a proteína.Métodos. Neste estudo, foi produzido isolado protéico de amaranto através da solubilização da proteína em pH 11 e precipitação em pH 5,7, obtendo-se o isolado com pureza de 96% de proteína. Este isolado protéico foi utilizado como fonte de proteínas em dietas experimentais para hamsters que tiveram hipercolesterolemia induzida, previamente, por dieta contendo 30% de caseína e 0,05% de colesterol, durante 3 semanas. Os animais foram, então, distribuídos em três grupos (n=11 animais/grupo) e foram alimentados com dietas contendo: (A) 20% caseína (controle), (B) 20% proteína de amaranto purificada (grupo substituição) e (C) 20% caseína + 10% proteína de amaranto purificada (grupo suplementação). Resultados. Comparando-se com a dieta controle, o grupo da suplementação e o da substituição tiveram dramáticas reduções do nível de colesterol plasmático, 30% (p<0,05) e 51% (p<0,05) respectivamente, enquanto o controle apresentou redução de apenas 7% após os 28 dias de dieta. Já na primeira semana este comportamento de redução para as duas dietas contendo amaranto foi percebido...

Efeito do feijão caupi (Vigna unguiculata L. Walp) e da proteína isolada no metabolismo lipídico em hamsters hipercolesterolemizados; Effect of the whole seed and protein isolate of cowpea (Vigna unguiculata L. Walp) on the lipid metabolism of hypercholesterolemic hamsters

Frota, Karoline de Macedo Gonçalves
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 05/06/2007 PT
Relevância na Pesquisa
35.82%
Introdução - A soja e outras leguminosas são consideradas como alimentos funcionais por apresentarem propriedades hipocolesterlemizantes. Esta propriedade, porém, ainda não foi relatada para o feijão caupi. Um possível componente deste grão responsável pelo feito redutor de colesterol é sua proteína. Objetivo - Produzir isolado protéico de feijão caupi e verificar a influência do grão integral e de sua proteína isolada no metabolismo lipídico de hamsters hipercolesterolemizados pela dieta. Métodos - O isolado protéico de feijão caupi foi produzido por precipitação isoelétrica, utilizando-se pH 8,5 para solubilização da proteína e 4,5 para a sua precipitação, obtendo-se um isolado com 92 % de proteína. O isolado protéico (IP) e o feijão caupi integral (FCI) foram utilizados como fonte protéica em dietas experimentais para hamsters que tiveram hipercolesterolemia induzida por dieta contendo 20 % de caseína, 13,5 % de gordura saturada e 0,1 % de colesterol, por 3 semanas. Os animais foram distribuídos em três grupos, recebendo cada grupo dieta com 20 % de caseína (controle), dieta com 20 % de proteína de isolado de feijão caupi e dieta com 20% de proteína de feijão caupi integral, por 4 semanas. Resultados - Comparando-se à dieta controle...

A proteína ligadora dos ácidos graxos Sm14 de Schistosoma mansoni: estrutura gênica, polimorfismo, expressão heteróloga em E. coli e significado estrutural e funcional das suas formas polimórficas e mutantes; The Sm14 Schistosoma mansoni fatty acid binding protein: gene structure, polymorphism, heterologus expression in E. coli and structure-functional study of her polymorphic and mutant forms

Ramos, Celso Raul Romero
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 26/03/2002 PT
Relevância na Pesquisa
35.82%
A esquistossomose é a mais importante das doenças helmínticas humanas em termos de morbidez e mortalidade. A proteína Sm14 de Schistosoma mansoni, que pertence à família de proteínas ligadoras de ácidos graxos (fatty acid-binding proteins, FABPs) (Moser et al., 1991), mostrou um bom nível de proteção (65%) contra a esquistossomose em animais experimentais (Tendler et al., 1996). No presente trabalho foram desenvolvidos sistemas de expressão que possibilitará a produção da proteína Sm14 em larga escala em E.coli. Com o intuito de conhecer a estrutura do gene da proteína Sm14, foi clonado um fragmento de DNA genômico de S. mansoni que contém a seqüência codificante da proteína Sm14. Como os outros membros da família gênica das FABP, o gene para a proteína Sm14 contém quatro "exons" separados por três "introns" de 674, 585 e 42 bp. Esta é a primeira descrição da estrutura gênica de um membro das FABP correspondente a um helminto. A Sm14 é uma proteína que pode ser potencialmente usada como vacina. Estudamos a existência de polimorfismo em duas linhagens de S. mansoni endêmicas do Brasil: LE e BH. Para a análise de polimorfismo, a ORF correspondente à proteína Sm14 foi amplificada por RT-PCR do RNA total de vermes adultos de S. mansoni. Os produtos de amplificação independentes foram clonados no vetor pGEM-T e seqüenciados. As análises de seqüências mostraram duas isoformas principais para a proteína Sm14: Sm14-M20...

Suplementação com aminoácios de cadeia ramificada atenua em proles os efeitos mediados pela dieta materna restrita em proteína; Branched-chain amino acids supplementation attenuates in offspring the effects mediated by maternal protein-restrict diet.

Teodoro, Gabriela Fullin Resende
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 12/08/2010 PT
Relevância na Pesquisa
35.82%
Estudos em animais mostram que a desnutrição proteica intrauterina pode acarretar redistribuição do fluxo sanguíneo intraútero, podendo promover modificações permanentes na estrutura e funcionalidade de alguns órgãos, o que ocasiona modificações no metabolismo. Além disso, a desnutrição intrauterina pode afetar a secreção de hormônios que atuam no crescimento fetal, podendo conduzir à restrição do crescimento intrauterino. Esse fenômeno pode parcialmente ser explicado pela hipótese da programação fetal, na qual é sugerido que ocorra uma adaptação metabólica e fisiológica do feto a uma condição intrauterina adversa, que pode induzir o desenvolvimento de doenças crônicas não transmissíveis na vida adulta. Neste contexto, pesquisas com suplementação de aminoácidos de cadeia ramificada (BCAA) têm verificado a capacidade desses nutrientes promoverem a síntese proteica mesmo em condições catabólicas, por meio da ativação de uma via bioquímica intracelular intercedida pela proteína quinase Alvo da Rapamicina em Mamíferos (mTOR), a qual está envolvida no estímulo à etapa de tradução proteica. Assim, o presente trabalho avaliou o efeito da suplementação de BCAA em proles submetidas à desnutrição proteica materna. Para tanto...

Serum and Urinary C-Reactive Protein Concentrations in Dogs with Leptospirosis

Oliveira, Simone Tostes de; Messick, Joanne Belle; Biondo, Alexander Welker; Santos, Andrea Pires dos; Guimarães, Ana Marcia Sá; Mohamed, Ahmed Sidi; Pires Neto, Jose Antonio Simoes; Dalmolin, Magnus Larruscaim; Diaz Gonzalez, Félix Hilário
Fonte: Universidade Federal do Rio Grande do Sul Publicador: Universidade Federal do Rio Grande do Sul
Tipo: Artigo de Revista Científica Formato: application/pdf
POR
Relevância na Pesquisa
35.82%
Background: Leptospirosis is a bacterial disease caused by pathogenic strains of Leptospira, which may affect human beings and a wide range of both domestic and wild animals. The disease in dogs is still a challenge for clinicians, since definitive diagnosis may be reached only few days after overt clinical signs. Besides that, dogs with leptospiruria have zoonotic risk, making development of rapid screening tests crucial for early diagnosis of disease. C-reactive protein is a positive acute phase protein, and in the dog a strong and fast response is expected after any tissue injury. The aim of this study was to evaluate serum and urinary C-reactive protein as potential early indicators of leptospirosis in dogs, and its association with clinical serum biochemistry, complete blood count (CBC) and clinical outcome. Materials, Methods & Results: A total of 62 dogs with risk factors and/or clinical signs of leptospirosis were prospectively obtained and included in this study. Definitive diagnosis was based on serology, using the microscopic agglutination test (MAT) against 13 serovars, and on a specific polymerase chain reaction (PCR) in blood or urine, using the primers sets G1/G2 and B64I/B64II, which amplify DNA of pathogenic leptospires. ( Continuation)Clinical serum biochemistry included creatinine...

Evaluation of a protein deficient diet in rats through blood oxidative stress biomarkers

Prada, F. J A; Macedo, D. V.; De Mello, Maria Alice Rostom
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 213-228
ENG
Relevância na Pesquisa
35.83%
Protein malnutrition leads to functional impairment in several organs, which is not fully restored with nutritional recovery. Little is known about the role of oxidative stress in the genesis of these alterations. This study was designed to assess the sensitivity of blood oxidative stress biomarkers to a dietary protein restriction. Male Wistar rats were divided into two groups, according to the diet fed from weaning (21 days) to 60 day old: normal protein (17% protein) and low protein (6% protein). Serum protein, albumin, free fatty acid and liver glycogen and lipids were evaluated to assess the nutritional status. Blood glutathione reductase (GR) and catalase (CAT) activities, plasma total sulfhydryl groups concentration (TSG) as well as plasma thiobarbituric acid reactive substances (TBARs) and reactive carbonyl derivatives (RCD) were measured as biomarkers of the antioxidant system and oxidative damage, respectively. The glucose metabolism in soleus muscle was also evaluated as an index of stress severity imposed to muscular mass by protein malnutrition. No difference was observed in muscle glucose metabolism or plasma RCD concentration between both groups. However, our results showed that the low protein group had higher plasma TBARs (62%) concentration and lower TSG (44%) concentration than control group...

Experimental mixture design as a tool for proteases production by Aspergillus niger and obtaining of protein hydrolysates with multiple functional and biological properties; Aplicação da ferramenta de planejamento experimental de misturas como estratégia para a produção de proteases por Aspergillus niger e obtenção de hidrolisados proteicos com múltiplas propriedades funcionais e biológicas

Ruann Janser Soares de Castro
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 02/03/2015 PT
Relevância na Pesquisa
35.83%
O presente trabalho teve como objetivo utilizar a técnica de delineamento experimental de misturas como estratégia para a produção de proteases por Aspergillus niger LBA02 em fermentação semissólida utilizando formulações contendo diferentes resíduos agroindustriais e produção de hidrolisados proteicos com atividades biológicas e funcionais utilizando a hidrólise enzimática simultânea de proteínas de diferentes fontes. Efeitos sinérgicos e significativos entre as misturas quaternárias de farelo de trigo, farelo de soja, farelo de algodão e casca de laranja foram observados durante a fermentação de A. niger LBA02, atingindo aumentos de 33,7, 7,6, 30,8 e 581,7%, respectivamente, na produção de proteases em comparação com os substratos utilizados de forma isolada. O estudo das características bioquímicas das preparações enzimáticas mostrou que a linhagem de A. niger LBA02 foi capaz de secretar diferentes tipos de proteases em resposta a cada substrato. De um modo geral, as proteases apresentaram atividade ótima a 50 °C e na faixa de pH de 3 a 4. As maiores diferenças entre as preparações de proteases foram observadas para os parâmetros cinéticos e termodinâmicos de ativação e inativação térmica. Na hidrólise enzimática de misturas contendo proteína isolada de soja...

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

Aguilar, Boris; Anandakrishnan, Ramu; Ruscio, Jory Z.; Onufriev, Alexey V.
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
Publicado em 03/03/2010 EN
Relevância na Pesquisa
35.83%
This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, protein, and nucleic acid), and distance from the binding region. Standard continuum solvent methodology is used to compute, on an equal footing, pK changes upon ligand binding for a total of 5899 ionizable residues in 20 protein-protein, 20 protein-small molecule, and 20 protein-nucleic acid high-resolution complexes. The size of the data set combined with an extensive error and sensitivity analysis allows us to make statistically justified and conservative conclusions: in 60% of all protein-small molecule, 90% of all protein-protein, and 85% of all protein-nucleic acid complexes there exists at least one ionizable residue that changes its charge state upon ligand binding at physiological conditions (pH = 6.5). Considering the most biologically relevant pH range of 4–8, the number of ionizable residues that experience substantial pK changes (ΔpK > 1.0) due to ligand binding is appreciable: on average, 6% of all ionizable residues in protein-small molecule complexes, 9% in protein-protein, and 12% in protein-nucleic acid complexes experience a substantial pK change upon ligand binding. These changes are safely above the statistical false-positive noise level. Most of the changes occur in the immediate binding interface region...

Eficácia alimentar e qualidade proteica de misturas de caseína com gelatina em dietas com baixos teores de proteína; Food and protein efficiency mixtures of gelatin with casein in diets with low levels of protein

BORDIN, Cláudia Cantelli Daud
Fonte: Universidade Federal de Goiás; BR; UFG; Mestrado em Nutricao e Saude; Ciencias da Saude Publicador: Universidade Federal de Goiás; BR; UFG; Mestrado em Nutricao e Saude; Ciencias da Saude
Tipo: Dissertação Formato: application/pdf
POR
Relevância na Pesquisa
35.83%
Gelatin is widely used in human feed, but has limited protein value. The composition in essential amino acids is quite atypical, since the levels of all the amino acids are below the benchmark of Food and Nutrition Board of the Institute of Medicine of the National Academy of Sciences of USA (FNB/IOM), with the aggravating not contain tryptophan in its composition. This study evaluated the effectiveness of food and the quality of protein mixtures of casein with gelatin (4:1 protein-based), in diets with low protein levels. An experimental study on animal model using 36 wealing male Wistar rats (21 to 23 days of age), divided into six groups of six animals each. The following were fed with diets: C10: 10% protein (casein); C8G2: 10% protein (8% casein; 2% gelatin); C12.5: 12.5% protein (casein); C10G2.5: 12.5% protein (10% casein; 2.5% gelatin); G10: 10% protein (gelatin); AP: protein-free. The duration of the experiment was 28 days for groups C10; C8G2; C12.5 e C10G2.5 and 14 days for groups G10 e AP. The effectiveness of food diets containing mixing casein:gelatin was influenced by the gelatin, according to the Food Conversion Ratio to protein level of 10% (C10 = 3.35 ± 0.19 versus C8G2 = 3.91 ± 0.34) and in supplementation with gelatin (C10 = 3.35 ± 0.19 versus C10G2.5 = 3.86 ± 0.32). The protein effectiveness was reduced in the protein level of 10% (C10 = 2.90 ± 0.17 versus C8G2 = 2.41 ± 0.22)...

The effect of higher protein human milk fortifier on growth in preterm infants.

Reid, Jessica
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2014
Relevância na Pesquisa
35.83%
Preterm infants are difficult to adequately nourish due to their immature organ systems and prematurity related illnesses. Human milk is accepted as the preferred feed for the preterm infant but needs to be supplemented with protein, carbohydrate, vitamins and minerals to meet the metabolic needs of the infant. Currently available commercial fortifiers do not meet the recommended protein intakes suggested in the literature. This thesis tested the hypothesis that preterm infants fed a human milk fortifier with a protein content of 1.8 grams protein per 100 ml expressed breast milk would experience greater weight gain than infants fed the current nursery practice amount – 1.0 grams protein per 100 ml expressed breast milk. Criteria for eligibility of infants in this study were birth at 28–32 weeks gestation and a planned breast milk diet. Power analysis indicated that to detect a clinically significant weight gain increase of 3.31 grams per day, 60 infants in total would be required. After parental consent was obtained, 60 infants were randomised into the study between February 2012 and February 2013, with 31 in the High protein group and 29 in the Standard group. Multiple births were randomised as individual infants. Infants in the High protein group received a human milk fortifier (FM-85...

Parallel and miniaturised Analysis of Protein-Protein Interactions in T-Cell Signal Transduction by Fluorescence Cross-Correlation Spectroscopy and Peptide Microarrays; Parallele und miniaturisierte Analyse von Protein-Protein-Interaktionen in der T-Zell-Signaltransduktion mittels Fluoreszenz-Kreuzkorrelations-Spektroskopie und Peptidmikroarrays

Stoevesandt, Oda
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
EN
Relevância na Pesquisa
35.83%
The aim of this thesis was to develop methods for the parallel analysis of complexes of endogenous proteins in T-cell signal transduction. We opted for detection in cell lysates, as the labelling of proteins in lysates is more versatile and more amenable to parallelisation compared to the labelling of proteins in life cells. Two approaches were developed, based on peptide microarrays and on fluorescence correlation and cross correlation spectroscopy (FCS / FCCS). It is shown that peptide microarrays provide a robust and quantitative means for detecting signalling-dependent changes of protein interactions. Recruitment of a protein into a complex leads to the masking of an otherwise exposed binding site. In cell lysates this masking can be detected by reduced binding to a microarray carrying a peptide corresponding to the binding motif of the respective interaction domain. This approach provides a significant shortcut to the detection of molecular interactions. It was first exemplified for the binding of ZAP70 to a bis-pY-motif of the activated T-cell receptor via its tandem SH2 domain. The activation-dependent recruitment of ZAP70 into signalling complexes reduced the microarray-bound signal, providing quantitative information on the change of the fraction of available binding sites. The concept was extended with microarrays comprising 24 peptides representing binding motifs for SH2...

Modeling Flexibility of Protein-DNA and Protein-Ligand Complexes using Molecular Dynamics; Modellierung der Flexibilität von Protein-DNA und Protein-Ligand Komplexen mit Hilfe von Molekulardynamischen Simulationen

Fischer, Nina M.
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
EN
Relevância na Pesquisa
35.83%
Molecular dynamics simulations provide valuable insights into the inherent flexibility of biomolecules and complement the static structures obtained from X-ray crystallography. Structural dynamics of proteins and alterations at protein-DNA and protein-ligand binding interfaces can thus be investigated. Regulation of gene expression plays a pivotal role in cellular processes and is modulated by special proteins binding to specific DNA sequences. WRKY proteins represent a large protein family in plants and are involved in the regulation of developmental processes, such as leaf senescence, as well as in the response to abiotic and biotic stress situations. The highly conserved WRKY DNA-binding domain recognizes predominantly the ‘TTGACC’ W-box consensus sequence. Since all WRKY proteins prefer this DNA sequence motif, it remains unclear so far how stimulus-specific responses are mediated. The W-box sequence might be more degenerate and yet undetected differences at the protein-DNA binding interface might exist. With molecular modeling and molecular dynamics simulations we constructed a first three-dimensional WRKY-DNA complex at atomic detail. Our modeling approach facilitates the investigation of structural differences and similarities of WRKY DNA-binding domains in complex with DNA while accounting for flexibility. Complexes of N- and C-terminal DNA-binding domains of AtWRKY33 with DNA and in silico binding free energy predictions gave a first indication that the N-terminal domain interacts with DNA in a similar way as the C-terminal domain. Additionally...

Resource for benchmarking the applicability of protein structure models

CARBAJO, DANIEL
Fonte: La Sapienza Universidade de Roma Publicador: La Sapienza Universidade de Roma
Tipo: Tese de Doutorado
EN
Relevância na Pesquisa
35.83%
The function of a protein is closely related to the structure it attains. The sequence of a protein is of limited biological relevance without some knowledge of both its structure and its function; protein structures provide a wealth of information that cannot be deduced from their primary sequence alone; therefore, we can get a complete understanding of protein roles by analyzing them in structural terms. Structure-based methodologies are consequently regarded as more robust than sequence-based ones. The limiting step for these structure-based methodologies is actually having the structure of a protein at hand. Due to the ever-increasing gap between known protein sequences and structures and the ever-growing number of protein structure prediction methods available, which are becoming more and more accurate over time, the use of protein structure models is mandatory. However, and in spite of progress in the field of protein structure prediction, computed models often contain structural inaccuracies in both backbone and side-chain spatial coordinates; instead of being discarded, these models can provide important insights into the function of the native counterpart; this, in turn, demands the existence of robust methods that can effectively make use of computed models in the midrange and low range of accuracy...

Pattern Discovery in Protein Structures and Interaction Networks

Ahmed, Hazem Radwan A.
Fonte: Quens University Publicador: Quens University
Tipo: Tese de Doutorado
EN; EN
Relevância na Pesquisa
35.83%
Pattern discovery in protein structures is a fundamental task in computational biology, with important applications in protein structure prediction, profiling and alignment. We propose a novel approach for pattern discovery in protein structures using Particle Swarm-based flying windows over potentially promising regions of the search space. Using a heuristic search, based on Particle Swarm Optimization (PSO) is, however, easily trapped in local optima due to the sparse nature of the problem search space. Thus, we introduce a novel fitness-based stagnation detection technique that effectively and efficiently restarts the search process to escape potential local optima. The proposed fitness-based method significantly outperforms the commonly-used distance-based method when tested on eight classical and advanced (shifted/rotated) benchmark functions, as well as on two other applications for proteomic pattern matching and discovery. The main idea is to make use of the already-calculated fitness values of swarm particles, instead of their pairwise distance values, to predict an imminent stagnation situation. That is, the proposed fitness-based method does not require any computational overhead of repeatedly calculating pairwise distances between all particles at each iteration. Moreover...

Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks

Tran, Duc T.
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação
Publicado em //2013
Relevância na Pesquisa
35.83%

The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of interactions such as binary and strong binding interactions. They also have high false-positive and false-negative rates. Described here is the development of and application of mass spectrometry-based proteomics metehods to detect and quantify the strength of protein-protein and protein-ligand interactions in the context of their interaction networks. Characterization of protein-protein and protein-ligand interactions can directly benefit diseased state analyses and drug discovery efforts.

The methodologies and protocols developed and applied in this work are all related to the Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX) and Stability of Protein from Rates of Oxidation (SPROX) techniques, which have been previously established for the thermodynamic analysis of protein folding reactions and protein-ligand binding interactions. The work in this thesis is comprised of four parts. Part I involves the development of a Histidine Slow H/D exchange protocol to facility SURPEX-like measurements on the proteomic scale. The Histidine Slow H/D exchange protocol is developed in the context of selected model protein systems and used to investigate the thermodynamic properties of proteins in a yeast cell lysate.

In Part II an isobaric mass tagging strategy is used in combination with SPROX (i.e....

Kinetic Characterization of the Coupled Folding and Binding Mechanism of Bacterial RNase P Protein: an Intrinsically Unstructured Protein

Chang, Yu-Chu
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação Formato: 32864628 bytes; application/pdf
Publicado em //2009 EN_US
Relevância na Pesquisa
35.83%

Understanding the interconversion between the thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was used as a model system to elucidate the general folding/unfolding of an intrinsically unstructured protein (IUP) both in the absence and presence of ligands.

P protein was previously characterized as an intrinsically unstructured protein, and it is predominantly unfolded in the absence of ligands. Addition of small anions can induce the protein to fold. Therefore, the folding and binding are tightly coupled. Trimethylamine-N oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic time courses at various final TMAO concentrations showed multiphase kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea to obtain a TMAO-urea titration surface of P protein. Both kinetic and equilibrium studies show evidence of an intermediate state in the P protein folding process. The intermediate state is significantly populated and the folding rate constants involved in the reaction are slow relative to similar size proteins.

NMR spectroscopy was used to characterize the structural properties of the folding intermediate of P protein. The results indicate that the N-terminal (residues 2-19) and C-terminal regions (residues 91-116...

Ineffectiveness of Nickel in augmenting the hepatotoxicity in protein deficient rats

Sidhu,P.; Garg,M. L.; Morgenstern,P.; Vogt,J.; Butz,T.; Dhawan,D. K.
Fonte: Nutrición Hospitalaria Publicador: Nutrición Hospitalaria
Tipo: info:eu-repo/semantics/article; journal article; info:eu-repo/semantics/publishedVersion Formato: text/html; application/pdf
Publicado em 01/12/2005 ENG
Relevância na Pesquisa
35.83%
This study was designed to determine the toxic effects of nickel sulfate on the biochemical and elemental profile of liver in protein deficient rats. Nickel sulfate in the dose of 800mg/l in drinking water was administrated to Sprauge Dawley (S.D) normal control as well as protein deficient rats for a total duration of eight weeks. The effects of nickel treatment and protein deficiency when given separately and in combination were studied on rat liver marker enzymes like Alkaline phosphatase (ALP),Glutamate oxaloacetate transaminase (GOT), Glutamate pyruvate transaminase (GPT) and also on the status of essential elements in rat liver. Protein deficient,Ni treated as well as combined protein deficient and nickel treated rats showed significant reductions in the body weight and hepatic protein contents as compared to normal control rats. Hepatic alkaline phosphatase activity and alanine aminotransferase showed a significant elevation in rats subjected to protein deficiency, nickel treatment and combined protein deficiency and nickel treatment.As regards to hepatic levels of aspartate aminotransferase a significant elevation was observed in protein deficient and nickel treated protein deficient animals. Nickel administration to normal and protein deficient rats has resulted in a significant increase in concentrations of nickel...