Template‐free protein structure prediction and quality assessment with an all‐atom free‐energy model

Biophysical forcefields have contributed less than originally anticipated to recent progress in protein structure prediction. Here, we have investigated the selectivity of a recently developed all‐atom free‐energy forcefield for protein structure prediction and quality assessment (QA). Using a heuristic method, but excluding homology, we generated decoy‐sets for all targets of the CASP7 protein structure prediction assessment with <150 amino acids. The decoys in each set were then ranked by energy in short relaxation simulations and the best low‐energy cluster was submitted as a prediction. For four of nine template‐free targets, this approach generated high‐ranking predictions within the top 10 models submitted in CASP7 for the respective targets. For these targets, our de‐novo predictions had an average GDT_S score of 42.81, significantly above the average of all groups. The refinement protocol has difficulty for oligomeric targets and when no near‐native decoys are generated in the decoy library. For targets with high‐quality decoy sets the refinement approach was highly selective. Motivated by this observation, we rescored all server submissions up to 200 amino acids using a similar refinement protocol, but using no clustering, in a QA exercise. We found an excellent correlation between the best server models and those with the lowest energy in the forcefield. The free‐energy refinement protocol may thus be an efficient tool for relative QA and protein structure prediction. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Prediction of Proteins Putatively Involved in the Thiol: Disulfide Redox Metabolism of a Bacterium (Listeria): The CXXC Motif as Query Sequence

Thiol:disulfide redox metabolism (TDRM) is a central metabolic network in all living cells. However, numerous proteins with different biochemical functions and several structural domains are involved, making it not trivial to identify and annotate its constituents in sequenced genomes. We developed an uncomplicated approach to solve the problem using existing web-based tools and public databases with the gram-positive bacterium Listeria monocytogenes EGD-e as a model organism. A pattern search for the Cys-Xaa-Xaa-Cys (CXXC) motif - a hallmark of TDRM proteins - in the genome sequence of the bacterium yielded 156 proteins. After initial refinement by protein and domain analysis, 14 candidate proteins remained. Subsequent detailed analyses, supported by modeling of 3D structures and data integration yielded 6 thioredoxin-like proteins plus thioredoxin reductase, glutaredoxin, one redox-sensitive regulator, one peptide methionine reductase - all typical TDRM constituents - and three putative novel components of the TDRM. For all 14 proteins orthologues were found in other Listeria species. Homology searches and phylogenetic analyses showed that related proteins are present mainly in other Firmicutes. This fast approach required minimal resources. It is immediately applicable to any genome with appropriate modifications and should be practicable also for other conserved, functionally important amino acid motifs.     

Decreased sarcolipin protein expression and enhanced sarco(endo)plasmic reticulum Ca2+ uptake in human atrial fibrillation

Sarcolipin (SLN), a key regulator of cardiac sarco(endo)plasmic reticulum (SR) Ca(2+) ATPase, is predominantly expressed in atria and mediates β-adrenergic responses. Studies have shown that SLN mRNA expression is decreased in human chronic atrial fibrillation (AF) and in aortic banded mouse atria; however, SLN protein expression in human atrial pathology and its role in atrial SR Ca(2+) uptake are not yet elucidated. In the present study, we determined the expression of major SR Ca(2+) handling proteins in atria of human AF patients and in human and in a mouse model of heart failure (HF). We found that the expression of SR Ca(2+) uptake and Ca(2+) release channel proteins are significantly decreased in atria but not in the ventricles of pressure-overload induced HF in mice. In human AF and HF, the expression of SLN protein was significantly decreased; whereas the expressions of other major SR Ca(2+) handling proteins were not altered. Further, we found that the SR Ca(2+) uptake was significantly increased in human AF. The selective downregulation of SLN and enhanced SR Ca(2+) uptake in human AF suggest that SLN downregulation could play an important role in abnormal intracellular Ca(2+) cycling in atrial pathology.     

Impact of social class on body fatness among rural pre-school Bengalee Hindu children of Arambagh, West Bengal, India

Body composition is a useful marker for assessing the adiposity of an individual. The amount of body fat (BF) differs with age, sex, environmental conditions and genotype, and is a good indicator of the health and nutritional status of a community. As the subcutaneous fat serves as a reservoir for energy during nutritional deprivation, lower BF in comparison with other studies indicates a lower energy intake by those children, who are affected by their lower socio-economic status. The objective of the present study was to evaluate the impact of socio-economic class, after allowing for sex and age, on body fatness among rural pre-school children of Bengalee Hindu ethnicity of Arambagh, West Bengal, India. The present study was undertaken at 20 Integrated Child Development Services (ICDS) scheme centers in Bali Gram Panchayat, Arambagh, Hooghly District of West Bengal, India. A total of 1012 boys and girls (aged 2-6 years) living in these areas were studied. The children were classified into two groups based on their social class: Schedule Castes (SC) and Non-Schedule Castes (NSC). In general, SC comprise socio-economically and educationally deprived individuals. Three-way analysis of variance was used to assess the effect of ethnicity on mid-upper arm circumference (MUAC) and sum of skinfolds (SS), allowing for age and sex. There was an increasing age trend in both these variables in both sexes in the two groups. All three factors had a significant effect on MUAC, whereas only age and social class had a significant impact on SS. In the case of MUAC, only one second order interaction (sex-age) was significant. In conclusion, we found that after controlling for age and sex, children belonging to the SC group had lower body fatness. These results implied that they were under more nutritional stress. There was also some evidence that at the early ages, girls belonging to the SC group probably received inadequate nutrition and as a result had lower body fat.     

Blood-based detection of radiation exposure in humans based on novel phospho-Smc1 ELISA

The structural maintenance of chromosome 1 (Smc1) protein is a member of the highly conserved cohesin complex and is involved in sister chromatid cohesion. In response to ionizing radiation, Smc1 is phosphorylated at two sites, Ser-957 and Ser-966, and these phosphorylation events are dependent on the ATM protein kinase. In this study, we describe the generation of two novel ELISAs for quantifying phospho-Smc1(Ser-957) and phospho-Smc1(Ser-966). Using these novel assays, we quantify the kinetic and biodosimetric responses of human cells of hematological origin, including immortalized cells, as well as both quiescent and cycling primary human PBMC. Additionally, we demonstrate a robust in vivo response for phospho-Smc1(Ser-957) and phospho-Smc1(Ser-966) in lymphocytes of human patients after therapeutic exposure to ionizing radiation, including total-body irradiation, partial-body irradiation, and internal exposure to (131)I. These assays are useful for quantifying the DNA damage response in experimental systems and potentially for the identification of individuals exposed to radiation after a radiological incident.     

Elevated CO2 increases water use efficiency by sustaining photosynthesis of water-limited maize and sorghum

Maize and grain sorghum seeds were sown in pots and grown for 39 days in sunlit controlled-environment chambers at 360 (ambient) and 720 (double-ambient, elevated) μmol mol⁻¹ carbon dioxide concentrations [CO₂]. Canopy net photosynthesis (PS) and evapotranspiration (TR) was measured throughout and summarized daily from 08:00 to 17:00 h Eastern Standard Time. Irrigation was withheld from matched pairs of treatments starting on 26 days after sowing (DAS). By 35 DAS, cumulative PS of drought-stress maize, compared to well-watered plants, was 41% lower under ambient [CO₂] but only 13% lower under elevated [CO₂]. In contrast, by 35 DAS, cumulative PS of drought-stress grain sorghum, compared to well-watered plants, was only 9% lower under ambient [CO₂] and 7% lower under elevated [CO₂]. During the 27-35 DAS drought period, water use efficiency (WUE, mol CO₂ Kmol⁻¹ H₂O), was 3.99, 3.88, 5.50, and 8.65 for maize and 3.75, 4.43, 5.26, and 9.94 for grain sorghum, for ambient-[CO₂] well-watered, ambient-[CO₂] stressed, elevated-[CO₂] well-watered and elevated-[CO₂] stressed plants, respectively. Young plants of maize and sorghum used water more efficiently at elevated [CO₂] than at ambient [CO₂], especially under drought. Reductions in biomass by drought for young maize and grain sorghum plants were 42 and 36% at ambient [CO₂], compared to 18 and 14% at elevated [CO₂], respectively. Results of our water stress experiment demonstrated that maintenance of relatively high canopy photosynthetic rates in the face of decreased transpiration rates enhanced WUE in plants grown at elevated [CO₂]. This confirms experimental evidence and conceptual models that suggest that an increase of intercellular [CO₂] (or a sustained intercellular [CO₂]) in the face of decreased stomatal conductance results in relative increases of growth of C₄ plants. In short, drought stress in C₄ crop plants can be ameliorated at elevated [CO₂] as a result of lower stomatal conductance and sustaining intercellular [CO₂]. Furthermore, less water might be required for C₄ crops in future higher CO₂ atmospheres, assuming weather and climate similar to present conditions.     

Rediscovery of Lichen Genus Psorotheciopsis Rehm for India

The genus Psorotheciopsis Rehm recorded by Cunningham from Calcutta in 1879 has been rediscovered for India after a gap of 135 years. The taxonomic characters of Psorotheciopsis patellarioides (Rehm) Rolf Santesson are provided to facilitate the identification of the species. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)