Functional evolution of two subtly different (similar) folds

BACKGROUND: The function of proteins is a direct consequence of their three-dimensional structure. The structural classification of proteins describes the ways of folding patterns all proteins could adopt. Although, the protein folds were described in many ways the functional properties of individual folds were not studied. RESULTS: We have analyzed two β-barrel folds generally adopted by small proteins to be looking similar but have different topology. On the basis of the topology they could be divided into two different folds named SH3-fold and OB-fold. There was no sequence homology between any of the proteins considered. The sequence diversity and loop variability was found to be important for various binding functions. CONCLUSIONS: The function of Oligonucleotide/oligosaccharide-binding (OB) fold proteins was restricted to either DNA/RNA binding or sugar binding whereas the Src homology 3 (SH3) domain like proteins bind to a variety of ligands through loop modulations. A question was raised whether the evolution of these two folds was through DNA shuffling

Redox biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide

<p>Abstract</p> <p>Background</p> <p><it>Mycobacterium tuberculosis</it>, an intracellular pathogen encounters redox stress throughout its life inside the host. In order to protect itself from the redox onslaughts of host immune system, <it>M. tuberculosis </it>appears to have developed accessory thioredoxin-like proteins which are represented by ORFs encoding WhiB-like proteins. We have earlier reported that WhiB1/Rv3219 is a thioredoxin like protein of <it>M. tuberculosis </it>and functions as a protein disulfide reductase. Generally thioredoxins have many substrate proteins. The current study aims to identify the substrate protein(s) of <it>M. tuberculosis </it>WhiB1.</p> <p>Results</p> <p>Using yeast two-hybrid screen, we identified alpha (1,4)-glucan branching enzyme (GlgB) of <it>M. tuberculosis </it>as a interaction partner of WhiB1. <it>In vitro </it>GST pull down assay confirmed the direct physical interaction between GlgB and WhiB1. Both mass spectrometry data of tryptic digests and <it>in vitro </it>labeling of cysteine residues with 4-acetamido-4' maleimidyl-stilbene-2, 2'-disulfonic acid showed that in GlgB, C⁹⁵and C⁶⁵⁸are free but C¹⁹³and C⁶¹⁷form an intra-molecular disulfide bond. WhiB1 has a C³⁷XXC⁴⁰motif thus a C⁴⁰S mutation renders C³⁷to exist as a free thiol to form a hetero-disulfide bond with the cysteine residue of substrate protein. A disulfide mediated binary complex formation between GlgB and WhiB1C⁴⁰S was shown by both in-solution protein-protein interaction and thioredoxin affinity chromatography. Finally, transfer of reducing equivalent from WhiB1 to GlgB disulfide was confirmed by 4-acetamido-4' maleimidyl-stilbene-2, 2'-disulfonic acid trapping by the reduced disulfide of GlgB. Two different thioredoxins, TrxB/Rv1471 and TrxC/Rv3914 of <it>M. tuberculosis </it>could not perform this reaction suggesting that the reduction of GlgB by WhiB1 is specific.</p> <p>Conclusion</p> <p>We conclude that <it>M. tuberculosis </it>GlgB has one intra-molecular disulfide bond which is formed between C¹⁹³and C⁶¹⁷. WhiB1, a thioredoxin like protein interacts with GlgB and transfers its electrons to the disulfide thus reduces the intra-molecular disulfide bond of GlgB. For the first time, we report that GlgB is one of the <it>in vivo </it>substrate of <it>M. tuberculosis </it>WhiB1.</p

Associations between diet, physical activity and body fat distribution: a cross sectional study in an Indian population.

BACKGROUND: Obesity is a growing health problem in India and worldwide, due to changes in lifestyle. This study aimed to explore the independent associations between dietary and physical activity exposure variables and total body fat and distribution in an Indian setting. METHODS: Individuals who had participated in the Indian Migration Study (IMS) or the Andhra Pradesh Children And Parents' Study (APCAPS), were invited to participate in the Hyderabad DXA Study. Total and abdominal body fat of study participants was measured using DXA scans. Diet and physical activity (PA) levels were measured using questionnaires. RESULTS: Data on 2208 participants was available for analysis; mean age was 49 yrs in IMS, 21 yrs in APCAPS. Total energy intake was positively associated with total body fat in the APCAPS sample: a 100 kcal higher energy intake was associated with 45 g higher body fat (95% CI 22, 68). In the IMS sample no association was found with total energy intake, but there was a positive association with percent protein intake (1% higher proportion of energy from protein associated with 509 g (95% CI 138,880) higher total body fat). Broadly the same pattern of associations was found with proportion of fat in the abdominal region as the outcome. PA was inversely associated with total body fat in both populations (in APCAPS, one MET-hour higher activity was associated with 46 g (95% CI 12, 81) less body fat; in the IMS it was associated with 145 g less body fat (95% CI 73, 218)). An inverse association was observed between PA and percentage abdominal fat in the IMS but no association was seen in the APCAPS population. CONCLUSIONS: In this Indian population, there was an inverse association between PA and body fat. Associations between body fat and dietary variables differed between the younger APCAPS population and older IMS population. Further longitudinal research is needed to elucidate causality and directions of these associations across the life course

Development and evaluation of the Andhra Pradesh Children and Parent Study Physical Activity Questionnaire (APCAPS-PAQ): a cross-sectional study.

BACKGROUND: There is limited availability of context-specific physical activity questionnaires in low and middle income countries. The aim of this study was to develop and examine the validity of a new Indian physical activity questionnaire, the Andhra Pradesh Children and Parent Study Physical Activity Questionnaire (APCAPS-PAQ). METHODS: The current study was conducted with the cohort from the Hyderabad DXA Study (n = 2321), recruited in 2009-2010. Criterion validity (n = 245) was examined by comparing the APCAPS-PAQ to a combined heart rate and motion sensor worn for 8 days. Construct validity (n = 2321) was assessed with linear regression, comparing APCAPS-PAQ against BMI, percent body fat, and pulse rate. RESULTS: The APCAPS-PAQ criterion validity was variable depending on the PA intensity groups (ρ = 0.26, 0.07, 0.39; к = 0.14, 0.04, 0.16 for sedentary, light, moderate/vigorous physical activity (MVPA) respectively). Sedentary and light intensity activities from the questionnaire were underestimated when compared to the criterion data while MVPA in APCAPS-PAQ was overestimated. Higher time spent in sedentary activity in APCAPS-PAQ was associated with higher BMI and percent body fat, suggesting construct validity. CONCLUSIONS: The APCAPS-PAQ validity is comparable to other physical activity questionnaires. This tool is able to assess sedentary behavior, moderate/vigorous activity and physical activity energy expenditure on a group level with reasonable validity. This new questionnaire may be used for ranking individuals according to their sedentary time and physical activity in southern India

Socio-economic patterning of cardiometabolic risk factors in rural and peri-urban India: Andhra Pradesh children and parents study (APCAPS).

AIM: To assess the prevalence of cardiometabolic risk factors by socio-economic position (SEP) in rural and peri-urban Indian population. SUBJECTS AND METHODS: Cross-sectional survey of 3,948 adults (1,154 households) from Telangana (2010-2012) was conducted to collect questionnaire-based data, physical measurements and fasting blood samples. We compared the prevalence of risk factors and their clustering by SEP adjusting for age using the Mantel Hansel test. RESULTS: Men and women with no education had higher prevalence of increased waist circumference (men: 8 vs. 6.4 %, P < 0.001; women: 20.9 vs. 12.0 %, P = 0.01), waist-hip ratio (men: 46.5 vs. 25.8 %, P = 0.003; women: 58.8 vs. 29.2 %, P = 0.04) and regular alcohol intake (61.7 vs. 32.5 %, P < 0.001; women: 25.7 vs. 3.8 %, P < 0.001) than educated participants. Unskilled participants had higher prevalence of regular alcohol intake (men: 57.7 vs. 38.7 %, P = 0.001; women: 28.3 vs. 7.3 %, P < 0.001). In contrast, participants with a higher standard of living index had higher prevalence of diabetes (top third vs. bottom third: men 5.2 vs. 3.5 %, P = 0.004; women 5.5 vs. 2.4 %, P = 0.003), hyperinsulinemia (men 29.5 vs. 16.3 %, P = 0.002; women 31.1 vs. 14.3 %, P < 0.001), obesity (men 23.3 vs. 10.6 %, P < 0.001; women 25.9 vs. 12.8 %, P < 0.001), and raised LDL (men 16.8 vs. 11.4 %, P = 0.001; women 21.3 vs. 14.0 %, P < 0.001). CONCLUSIONS: Cardiometabolic risk factors are common in rural India but do not show a consistent association with SEP except for higher prevalence of smoking and regular alcohol intake in lower SEP group. Strategies to address the growing burden of cardiometabolic diseases in urbanizing rural India should be assessed for their potential impact on social inequalities in health

Cohort profile: Andhra Pradesh Children and Parents Study (APCAPS).

The Andhra Pradesh Children and Parents Study (APCAPS) was originally established to study the long-term effects of early-life undernutrition on risk of cardiovascular disease. Its aims were subsequently expanded to include trans-generational influences of other environmental and genetic factors on chronic diseases in rural India. It builds on the Hyderabad Nutrition Trial (HNT) conducted in 1987-90 to compare the effects on birthweight of a protein-calorie supplement for pregnant women and children. The index children of HNT and their mothers were retraced and examined in 2003-05, and the children re-examined as young adults aged 18-21 years in 2009-10. The cohort was expanded to include both parents and siblings of the index children in a recently completed follow-up conducted in 2010-12 (N=∼6225 out of 10,213 participants). Recruitment of the remaining residents of these 29 villages (N=∼55,000) in Ranga Reddy district of Andhra Pradesh is now under way. Extensive data on socio-demographic, lifestyle, medical, anthropometric, physiological, vascular and body composition measures, DNA, stored plasma, and assays of lipids and inflammatory markers on APCAPS participants are available. Details of how to access these data are available from the corresponding author

Is increasing urbanicity associated with changes in breastfeeding duration in rural India? An analysis of cross-sectional household data from the Andhra Pradesh children and parents study.

OBJECTIVE: To investigate whether village-level urbanicity and lower level socioeconomic factors are associated with breastfeeding practices in transitioning rural communities in India. SETTING: 29 villages in Ranga Reddy district, southern India between 2011 and 2014. PARTICIPANTS: 7848 children under 6 years identified via a cross-sectional household survey conducted as part of the Andhra Pradesh Children and Parents Study. OUTCOME MEASURES: Two key indicators of optimal breastfeeding: termination of exclusive breastfeeding before 6 months and discontinuation of breastfeeding by 24 months. Village urbanicity was classified as low, medium or high according to satellite assessed night-light intensity. RESULTS: Breastfeeding initiation was almost universal, and approximately two in three children were exclusively breastfed to 6 months and a similar proportion breastfed to 24 months. Using multilevel logistic regression, increasing urbanicity was associated with breastfeeding discontinuation before 24 months (medium urbanicity OR 1.45, 95% CI 0.71 to 2.96; high urbanicity OR 2.96, 95% CI 1.45 to 6.05) but not with early (<6 months) termination of exclusive breastfeeding. Increased maternal education was independently associated with both measures of suboptimal breastfeeding, and higher household socioeconomic position was associated with early termination of exclusive breastfeeding. CONCLUSION: In this transitional Indian rural community, early stage urbanicity was associated with a shorter duration of breastfeeding. Closer surveillance of changes in breastfeeding practices alongside appropriate intervention strategies are recommended for emerging economies

Water-Dependent Domain Motion and Flexibility in Ribonuclease A and the Invariant Features in its Hydration Shell. An X-ray Study of Two Low-Humidity Crystal Forms of the Enzyme

The crystal structures of 88 and 79% relative humidity forms of ribonuclease A, resulting from water-mediated transformations, have been refined employing the restrained least-squares method using X-ray data collected on an area detector to R = 0.173 for 15 326 observed reflections in the 10-1.5 ,~ resolution shell and R = 0.176 for 8534 observed reflections in the 10-1.8 ,~, shell, respectively. The comparison of these structures with those of the native, the phosphate-bound and the sulfate-bound forms demonstrates that the mobility of the ribonuclease A molecule involves hinge-bending movement of the two domains and local flexibility within them, particularly at the termini of regular secondary structures and in loops. The comparison also leads to the identification of 31 invariant water molecules in the hydration shell of the enzyme, many of which are involved in holding different parts of the molecule together and in stabilizing local structure. The conformational changes that accompany the partial removal of the surrounding water, particularly those observed in the 79% form, could be similar to those that occur during enzyme action

Automated IMT estimation and BMI correlation using a low-quality carotid ultrasound image database from India.

This paper presents AtheroEdgeLowRes (AELR), an extention of AtheroEdge™ from AtheroPoint™, and a solution to carotid ultrasound IMT measurement in low-resolution and overall low quality images. The images were collected using a low-end ultrasound machine during a screening study in India. We aim to demonstrate the accuracy and reproducibility of the AELR system by benchmarking it against an expert Reader's manual tracing and to show the correlation between the automatically measured intima media thickness (IMT) and the subjects' cardiovascular risk factors (i.e. body mass index--BMI). We introduced an innovative penalty function (PF) to our dual-snake segmentation technique, necessary due to the low image resolution. We processed 512 images from 256 patients, and correlated the AELR IMT values with the patients' age and BMI. AELR processed all 512 images, and the IMT measurement error was 0.011±0.099 mm with the PF correction and 0.173±0.127 mm without. AELR IMT values correlated with the Reader's values (r = 0.883) and also correlated with the subject's BMI and age. The AELR system showed accuracy and reproducibility levels that make it suitable to be used in large epidemiological and screening studies in emerging countries