Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Adaptação transcultural para o português de instrumentos de avaliação do estado nutricional em pacientes idosos em tratamento crônico de hemodiálise

O contingente de idosos iniciando tratamento de diálise vem aumentado de maneira importante desde o ano de 2000, conforme mostrado pelo United States Renal Data System. Dados nacionais demonstram que cerca de 31,5% dos pacientes em diálise tem idade acima de 65 anos, segundo o Censo Brasileiro de Diálise de 2011. Estes dados alertam para a importância no cuidado da saúde do idoso em diálise. O cuidado nutricional desse grupo merece especial atenção, uma vez que já foi demonstrado que a prevalência de desnutrição energético-proteica nos pacientes idosos em diálise é significantemente maior do que a de adultos jovens em diálise. Nesse sentido, faz-se importante desenvolver estudos com instrumentos que avaliem o estado nutricional desse grupo. Os questionários de avaliação subjetiva global de 7 pontos (ASG-7p) e o malnutrition inflammation score (MIS) têm sido bastante empregados em estudos incluindo pacientes em diálise. Contudo, estes instrumentos estão originalmente na língua Inglesa, e para o seu uso em nosso meio, é necessário a tradução por meio da adaptação transcultural. Porém, até o momento, não há estudos que tenham realizado a tradução transcultural desses questionários para a língua Portuguesa. Deste modo, o objetivo deste estudo foi realizar a adaptação transcultural para o português de dois instrumentos de avaliação do estado nutricional em pacientes idosos em tratamento crônico de hemodiálise (HD). O estudo é do tipo observacional e seccional. A adaptação transcultural consistiu na tradução para a língua Portuguesa da ASG-7p e MIS pelo método da retrotradução, avaliação da equivalência semântica, confiabilidade e validade de construto. Para tanto, 101 pacientes idosos em HD foram avaliados. Ambos questionários apresentaram alto grau de similaridade semântica. A consistência interna apresentou um valor de α de Cronbach para a ASG-7p de 0,72 (satisfatório) e para o MIS de 0,53 (não satisfatório). A ASG-7p apresentou discreta reprodutibilidade intra-avaliador e moderada reprodutibilidade interavaliador; e para o MIS tanto a reprodutibilidade inter quanto intra-avaliador foi indicativo de forte reprodutibilidade. Referente à validade de construto, ao avaliar o estado nutricional pela ASG-7p notou-se que os pacientes classificados como bem nutridos apresentaram medidas de peso corporal, adequação da dobra cutânea tricipital, percentual de gordura corporal, circunferência da panturrilha e creatinina sérica significantemente maiores do que de pacientes desnutridos. Para o MIS, ao comparar os grupo de bem nutridos com o de desnutridos, a albumina sérica, ângulo de fase, percentual de gordura corporal, a adequação da força de preensão manual e da dobra cutânea tricipital e a circunferência da panturrilha apresentaram diferença significante entre os grupos. Em conclusão, os questionários ASG-7p e MIS traduzidos para o português podem ser utilizados na população de idosos em HD.

Effect of feeding three different formulated feeds having different protein levels on the growth of angel fish (Pterophyllum scalare) juveniles

Experiment was conducted to study the effect of dietary protein level on growth and nutrient utilization by angel fish (Pterophyllum scalare) juveniles. Fifty-four juveniles (average wt. 2-2.5 g) were equally divided in three treatments with each of three replicates. Three formulated diets with graded protein levels, T1 (35% CP), T2 (40% CP) and T3 (45% CP) were fed to juveniles for 45 days. A trend of higher weight gain %, SGR, FER and PER was found with the increased CP level in the feed. Feed intake was similar in all the groups. T3 group fed with 45% CP registered highest weight gain % (43.26 ± 2.07), SGR (0.78 ± 0.04), FER (0.29 ± 0.01), which were significantly higher (P<0.05) than the T1 and T2 groups. Protein digestibility of T2 and T3 groups was significantly higher than the T1 group. Survival was similar in all the experimental groups. Diet with 45% CP with protein energy ratio of 112.62 mg protein/K cal. is ideal for juvenile angel fish for indoor rearing.

First-passage time distribution and non-Markovian diffusion dynamics of protein folding

We study the kinetics of protein folding via statistical energy landscape theory. We concentrate on the local-connectivity case, where the configurational changes can only occur among neighboring states, with the folding progress described in terms of an order parameter given by the fraction of native conformations. The non-Markovian diffusion dynamics is analyzed in detail and an expression for the mean first-passage time (MFPT) from non-native unfolded states to native folded state is obtained. It was found that the MFPT has a V-shaped dependence on the temperature. We also find that the MFPT is shortened as one increases the gap between the energy of the native and average non-native folded states relative to the fluctuations of the energy landscape. The second- and higher-order moments are studied to infer the first-passage time distribution. At high temperature, the distribution becomes close to a Poisson distribution, while at low temperatures the distribution becomes a Levy-type distribution with power-law tails, indicating a nonself-averaging intermittent behavior of folding dynamics. We note the likely relevance of this result to single-molecule dynamics experiments, where a power law (Levy) distribution of the relaxation time of the underlined protein energy landscape is observed.

Leucine supplementation favors liver protein status but does not reduce body fat in rats during 1 week of food restriction

An important role in protein-energy metabolism has been attributed to leucine because of its long-term effects on body fat reduction and on the improvement of some indicators of protein status in rodents. The present study investigated the influence of leucine supplementation on the body composition and protein status of rats during the early phase of weight loss, which is characterized by a rapid loss of body weight. Thirty adult male Wistar rats were divided into 2 groups, a control and a leucine group (diet supplemented with 0.59% L-leucine), and were submitted to 1 week of 50% food restriction. The following parameters were evaluated: chemical carcass composition, protein and RNA content in liver and gastrocnemius muscle, and serum concentrations of insulin-like growth factor-1 and corticosterone. A higher liver weight and liver protein content were observed in the supplemented group (p < 0.05). However, no difference in body fat was found between groups (p > 0.05). The results indicate that low-dose leucine supplementation favors liver protein status but does not reduce body fat in rats during the early phase of rapid weight loss.

Treatment with supplementary arginine, vitamin C and zinc in patients with pressure ulcers: A randomised controlled trial

Background & Aims
Nutrients putatively implicated in pressure ulcer healing were evaluated in a clinical setting.

Methods
Sixteen inpatients with a stage 2, 3 or 4 pressure ulcer randomised to receive daily a standard hospital diet; a standard diet plus two high-protein/energy supplements; or a standard diet plus two high-protein/energy supplements containing additional arginine (9 g), vitamin C (500 mg) and zinc (30 mg). Nutritional status measurements (dietary, anthropometric and biochemical) and pressure ulcer size and severity (by PUSH tool; Pressure Ulcer Scale for Healing; 0=completely healed, 17=greatest severity) were measured weekly for 3 weeks.

Results
Patients’ age and BMI ranges were 37–92 years and 16.4–28.1 kg/m2, respectively. Baseline PUSH scores were similar between groups (8.7±0.5). Only patients receiving additional arginine, vitamin C and zinc demonstrated a clinically significant improvement in pressure ulcer healing (9.4±1.2 vs. 2.6±0.6; baseline and week 3, respectively; P<0.01). All patient groups presented with low serum albumin and zinc and elevated C-reactive protein. There were no significant changes in biochemical markers, oral dietary intake or weight in any group.

Conclusions
In this small set of patients, supplementary arginine, vitamin C and zinc significantly improved the rate of pressure ulcer healing. The results need to be confirmed in a larger study.

The effect of exercise and nutrition on the mechanostat

In this review, we discuss the effect of increased and decreased loading and nutrition deficiency on muscle and bone mass and strength (and bone length and architecture) independently and combined. Both exercise and nutrition are integral components of the mechanostat model but both have distinctly different roles. Mechanical strain imparted by muscle action is responsible for the development of the external size and shape of the bone and subsequently the bone strength. In contrast, immobilization during growth results in reduced growth in bone length and a loss of bone strength due to large losses in bone mass (a result of endosteal resorption in cortical bone and trabecular thinning) and changes in geometry (bone shafts do not develop their characteristic shape but rather develop a rounded default shape). The use of surrogate measures for peak muscle forces acting on bone (muscle strength, size, or mass) limits our ability to confirm a cause-and-effect relationship between peak muscle force acting on bone and changes in bone strength. However, the examples presented in this review support the notion that under adequate nutrition, exercise has the potential to increase peak muscle forces acting on bone and thus can lead to a proportional increase in bone strength. In contrast, nutrition alone does not influence muscle or bone in a dose-dependent manner. Muscle and bone are only influenced when there is nutritional deficiency – and in this case the effect is profound. Similar to immobilization, the immediate effect of malnutrition is a reduction in longitudinal growth. More specifically, protein and energy malnutrition results in massive bone loss due to endosteal resorption in cortical bone and trabecular thinning. Unlike loading however, there is indirect evidence that severe malnutrition when associated with menstrual dysfunction can shift the mechanostat set point upward, thus leading to less bone accrual for a given amount of bone strain.

Digestibility and performance of pacu (Piaractus mesopotamicus) juveniles - fed diets containing different protein, lipid and carbohydrate levels

Due to lack of information on the use of non-protein energy sources in diets for pacu (Piaractus mesopotamicus), a 2 x 2 x 3 factorial experiment was conducted to evaluate the performance and digestibility of 12 diets containing approximately two crude protein (CP; 220 and 250 g kg(-1)), two lipid (40 and 80 g kg(-1)) and three carbohydrate levels (410, 460 and 500 g kg(-1)). The pacu juveniles-fed diets containing 220 g kg(-1) CP did not respond (P > 0.05) to increased dietary lipid and carbohydrate levels, but the fish-fed diets containing 250 g kg(-1) CP showed a better feed conversion ratio. There were interactions in weight gain (WG), specific growth rate (SGR), crude protein intake (CPI) and feed conversion rate (FCR) dependent on dietary carbohydrate and lipid levels, showing positive effects of increasing carbohydrate levels only for fish-fed diets containing 80 g kg(-1) lipid level. However, when the diets contained 40 g kg(-1) lipid, the best energy productive value (EPV) results were obtained at 460 g kg(-1) carbohydrate. A higher usage of lipids (80 g kg(-1)) reduced CPI and was detrimental to protein [apparent digestibility coefficient (ADC)(CP)] and energy (ADC(GE)), but did not affect growth. The ADC(GE) improved proportionally as dietary carbohydrate levels increased (P < 0.05), increasing the concentration of digestible energy. In addition, the WG, CPI, ADC(GE) results showed best use of the energy from carbohydrates when dietary protein level was 250 g kg(-1) CP. The utilization of 250 g kg(-1) CP in feeds for juvenile pacu for optimal growth is suggested. Therefore, the optimum dietary lipid and carbohydrate levels depend on their combinations. It can be stated that pacu uses carbohydrates as effectively as lipids in the maximization of protein usage, as long as it is not lower than 250 g kg(-1) CP or approximately 230 g kg(-1) digestible protein.

Growth and metabolism of pacu (Piaractus mesopotamicus Holmberg 1887) juveniles fed diets containing different protein, lipid and carbohydrate levels

To verify the potential of lipids and carbohydrates to spare dietary protein and to understand the intermediary metabolism of interaction of these nutrients in pacu juveniles, an experiment was carried out to evaluate pacu physiological and performance parameters. The experimental design was completely randomized with 12 treatments in a 2 x 2 x 3 factorial arrangement, consisting of diets containing two digestible protein levels (200 and 230 g kg(-1) PD), two lipid levels (40 and 80 g kg(-1)) and three carbohydrate levels (410, 460 and 500 g kg(-1)). Fish-fed 230 g kg(-1) digestable protein (DP) showed increased glycaemia, decreased hepatic glycogen, as well as a smaller intake index and better feed conversion ratio. The higher dietary lipid level (80 g kg(-1)) reduced protein intake and serum protein concentration, increased liver and body fat content, but did not affect growth. At a lipid level of 80 g kg(-1), the increase in dietary carbohydrate levels promoted greater weight gain (WG), crude protein intake (CPI) and better feed conversion ratio (FCR). For fish fed diets containing 40 g kg(-1) lipid, the best energy-productive values (EPV) were obtained at 460 g kg(-1) carbohydrate. Increased levels of the main nutrients in the diets reduced the levels of serum triglycerides, while the increase in energy concentration increased the hepatosomatic (HSI) and glycaemia index values. Pacu used lipids as effectively as carbohydrates in the maximization of protein usage, as long as dietary protein was at a level of 230 g kg(-1) DP. The physiological parameters indicated that the best balance between the DP, dietary lipid and carbohydrate levels within the ranged this trial was obtained at 230, 40 and 460 g kg(-1), respectively, without lower growth.

Antropometria de atletas culturistas em relacao a referencia populacional

Body builders have as their training goals the maximum muscle hypertrophy with minimum adiposity. However, the scarcity of specific standards implies often in framing wrongly those athletes either as overweight (by their BMI) or energy malnourished (by their fat stores). The objective of this study was to compare the body composition of body builders with population standards. Thirty-six adults, 26 male (27.2 ± 7.2 years) and 10 female (30 ± 6.1 years) nationwide competitive body builders, were assessed considering weight, height, body mass index, adiposity, arm and leg circumferences and skinfolds. The data were referred either as percentile or standard deviations (Z score) of population standards. Body weight and height were among the closest values from the populational mean whereas upper arm muscle circumference (for men) and body adiposity (for women) were the farterest. By using fat parameters as indicators of their protein-energy status, the undernourishment was found in 88.5% of men and 100.0% of women. Thus, it seems that body builders deserve their own anthropometric standards to avoid nutritional status misplacements.

Dietary restriction abrogates antibody production induced by a DNA vaccine encoding the mycobacterial 65 kDa heat shock protein

Background: Protein-calorie malnutrition (PCM) is the most common type of malnutrition. PCM leads to immunodeficiency and consequent increased susceptibility to infectious agents. In addition, responses to prophylactic vaccines depend on nutritional status. This study aims to evaluate the ability of undernourished mice to mount an immune response to a genetic vaccine (pVAXhsp65) against tuberculosis, containing the gene coding for the heat shock protein 65 from mycobacteria. Methods: Young adult female BALB/c mice were fed ad libitum or with 80% of the amount of food consumed by a normal diet group. We initially characterized a mice model of dietary restriction by determining body and spleen weights, hematological parameters and histopathological changes in lymphoid organs. The ability of splenic cells to produce IFN-gamma and IL-4 upon in vitro stimulation with LPS or S. aureus and the serum titer of specific IgG1 and IgG2a anti-hsp65 antibodies after intramuscular immunization with pVAXhsp65 was then tested. Results: Dietary restriction significantly decreased body and spleen weights and also the total lymphocyte count in blood. This restriction also determined a striking atrophy in lymphoid organs as spleen, thymus and lymphoid tissue associated with the small intestine. Specific antibodies were not detected in mice submitted to dietary restriction whereas the well nourished animals produced significant levels of both, IgG1 and IgG2a anti-hsp65. Conclusion: 20% restriction in food intake deeply compromised humoral immunity induced by a genetic vaccine, alerting, therefore, for the relevance of the nutritional condition in vaccination programs based on these kinds of constructs. © 2009 Ishikawa et al; licensee BioMed Central Ltd.

Circulating thyroid hormone levels in young pregnant rats and their fetuses: Effect of malnutrition

In order to evaluate some factors likely to be involved in the maternal and fetal growth impairment due to alimentary protein deficiency, the circulating levels of triiodothyronine (T 3) and thyroxine (T 4) were studied in 4 young (45-day-old) female rat groups: control and malnourished, both nonpregnant and pregnant; similarly schedules groups were studied using adult (100-day-old) rats. Circulating levels of T 4 were higher in nonpregnant, malnourished young rats in their corresponding controls. T 3 levels were higher in young malnourished animals and lower in adult malnourished animals, nonpregnant or pregnant, as compared to controls. Pups from young malnourished mothers showed significantly lower birth weights than those from controls. The present results suggest that there are age differences in thyroid function, as affected by protein-calorie malnutrition in pregnant and non-pregnant rats. On the other hand, the circulating thyroid hormone levels were not importantly affected by the mother dietary protein restriction under our experimental conditions.

Prediction of culture performance of juvenile Litopenaeus vannamei by in vitro (pH-stat) degree of feed protein hydrolysis with species-specific enzymes

Rapid in vitro methods for measuring digestibility may be useful in analysing aqua feeds if the extent and limits of their application are clearly defined. The pH-stat protein digestibility routine with shrimp hepatopancreas enzymes was previously related to apparent protein digestibility with juvenile Litopenaeus vannamei fed diets containing different protein ingredients. The potential of the method to predict culture performance of shrimp fed six commercial feeds (T3, T4, T5, T6, T7 and T8) with 350 g kg(-1) declared crude-protein content was assessed. The consistency of results obtained using hepatopancreas enzyme extracts from either pond or clear water-raised shrimp was further verified in terms of reproducibility and possible diet history effects upon in vitro outputs. Shrimps were previously acclimated and then maintained over 56 days (initial mean weight 3.28 g) on each diet in 500-L tanks at 114 ind m(-2), clear water closed system with continuous renewal and mechanical filtering (50 mu m), with four replicates per treatment. Feeds were offered four times daily (six days a week) delivered in trays at feeding rates ranging from 4.0% to 7.0% of stocked shrimp biomass. Feed was accessible to shrimp 4 h daily for 1-h feeding period after which uneaten feed was recovered. Growth and survival were determined every 14 days from a sample of 16 individuals per tank. Water quality was monitored daily (pH, temperature and salinity) and managed by water back flushing filter cleaning every 7-10 days. Feeds were analysed for crude protein, gross energy, amino acids and pepsin digestibility. In vitro pH-stat degree of protein hydrolysis (DH%) was determined for each feed using hepatopancreas enzyme extracts from experimental (clear water) or pond-raised shrimp. Feeds resulted in significant differences in shrimp performance (P < 0.05) as seen by the differences in growth rates (0.56-0.98 g week(-1)), final weight and feed conversion ratio (FCR). Shrimp performance and in vitro DH% with pond-raised shrimp enzymes showed significant correlation (P < 0.05) for yield (R-2 = 0.72), growth rates (R-2 = 0.72-0.80) and FCR (R-2 = -0.67). Other feed attributes (protein : energy ratio, amino acids, true protein, non-protein nitrogen contents and in vitro pepsin digestibility) showed none or limited correlation with shrimp culture performance. Additional correlations were found between growth rates and methionine (R-2 = 0.73), FCR and histidine (R-2 = -0.60), and DH% and methionine or methionine+cystine feed contents (R-2 = 0.67-0.92). pH-stat assays with shrimp enzymes generated reproducible DH% results with either pond (CV <= 6.5%) or clear water (CV <= 8.5%) hepatopancreas enzyme sources. Moreover, correlations between shrimp growth rates and feed DH% were significant regardless of the enzyme origin (pond or clear water-raised shrimp) and showed consistent R-2 values. Results suggest the feasibility of using standardized hepatopancreas enzyme extracts for in vitro protein digestibility.

Dietary restriction abrogates antibody production induced by a DNA vaccine encoding the mycobacterial 65 kDa heat shock protein

Abstract Background Protein-calorie malnutrition (PCM) is the most common type of malnutrition. PCM leads to immunodeficiency and consequent increased susceptibility to infectious agents. In addition, responses to prophylactic vaccines depend on nutritional status. This study aims to evaluate the ability of undernourished mice to mount an immune response to a genetic vaccine (pVAXhsp65) against tuberculosis, containing the gene coding for the heat shock protein 65 from mycobacteria. Methods Young adult female BALB/c mice were fed ad libitum or with 80% of the amount of food consumed by a normal diet group. We initially characterized a mice model of dietary restriction by determining body and spleen weights, hematological parameters and histopathological changes in lymphoid organs. The ability of splenic cells to produce IFN-gamma and IL-4 upon in vitro stimulation with LPS or S. aureus and the serum titer of specific IgG1 and IgG2a anti-hsp65 antibodies after intramuscular immunization with pVAXhsp65 was then tested. Results Dietary restriction significantly decreased body and spleen weights and also the total lymphocyte count in blood. This restriction also determined a striking atrophy in lymphoid organs as spleen, thymus and lymphoid tissue associated with the small intestine. Specific antibodies were not detected in mice submitted to dietary restriction whereas the well nourished animals produced significant levels of both, IgG1 and IgG2a anti-hsp65. Conclusion 20% restriction in food intake deeply compromised humoral immunity induced by a genetic vaccine, alerting, therefore, for the relevance of the nutritional condition in vaccination programs based on these kinds of constructs.

Digestibility and performance of pacu (Piaractus mesopotamicus) juveniles - fed diets containing different protein, lipid and carbohydrate levels

Due to lack of information on the use of non-protein energy sources in diets for pacu (Piaractus mesopotamicus), a 2 x 2 x 3 factorial experiment was conducted to evaluate the performance and digestibility of 12 diets containing approximately two crude protein (CP; 220 and 250 g kg(-1)), two lipid (40 and 80 g kg(-1)) and three carbohydrate levels (410, 460 and 500 g kg(-1)). The pacu juveniles-fed diets containing 220 g kg(-1) CP did not respond (P > 0.05) to increased dietary lipid and carbohydrate levels, but the fish-fed diets containing 250 g kg(-1) CP showed a better feed conversion ratio. There were interactions in weight gain (WG), specific growth rate (SGR), crude protein intake (CPI) and feed conversion rate (FCR) dependent on dietary carbohydrate and lipid levels, showing positive effects of increasing carbohydrate levels only for fish-fed diets containing 80 g kg(-1) lipid level. However, when the diets contained 40 g kg(-1) lipid, the best energy productive value (EPV) results were obtained at 460 g kg(-1) carbohydrate. A higher usage of lipids (80 g kg(-1)) reduced CPI and was detrimental to protein [apparent digestibility coefficient (ADC)(CP)] and energy (ADC(GE)), but did not affect growth. The ADC(GE) improved proportionally as dietary carbohydrate levels increased (P < 0.05), increasing the concentration of digestible energy. In addition, the WG, CPI, ADC(GE) results showed best use of the energy from carbohydrates when dietary protein level was 250 g kg(-1) CP. The utilization of 250 g kg(-1) CP in feeds for juvenile pacu for optimal growth is suggested. Therefore, the optimum dietary lipid and carbohydrate levels depend on their combinations. It can be stated that pacu uses carbohydrates as effectively as lipids in the maximization of protein usage, as long as it is not lower than 250 g kg(-1) CP or approximately 230 g kg(-1) digestible protein.