Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis

A significant proportion of enzymes display cooperativity in binding ligand molecules, and such effects have an important impact on metabolic regulation. This is easiest to understand in the case of positive cooperativity. Sharp responses to changes in metabolite concentrations can allow organisms to better respond to environmental changes and maintain metabolic homeostasis. However, despite the fact that negative cooperativity is almost as common as positive, it has been harder to imagine what advantages it provides. Here we use computational models to explore the utility of negative cooperativity in one particular context: that of an inhibitor binding to an enzyme. We identify several factors which may contribute, and show that acting together they can make negative cooperativity advantageous.     

Salinity and hormone interactions in affecting growth,transpiration and ionic relations ofPhaseolus vulgaris

Addition of either abscisic acid (ABA) or kinetin at 10⁻⁶ M to salinized media (20–120mM NaCl) induced remarkable effects on growth ofPhaseolus vulgaris plants. Whereas ABA inhibited the plant growth and the rate of transpiration, kinetin induced stimulation of both parameters. Moreover, ABA increased proline and phosphorus concentrations in the salinized plants whilst kinetin decreased them. ABA induced stimulation of the transport of K, Ca and Cl from root to shoot, accumulation of K, Na and Cl in root cells and inhibits the transport of Na and accumulation of Ca. Kinetin appeared to inhibit the transport and accumulation of Na and Cl, transport of K, and stimulates the accumulation of K and Ca as well as the transport of Ca. The highest influence of both ABA and kinetin was mostly observed when these hormones were used in combination with the highest concentration of NaCl (120 mM) in the medium.     

Effects of salinity on growth and metabolism ofPhaseolus vulgaris

Increasing salinity induced a marked reduction in the plant growth, thoughPhaseolus seedlings tolerated salinity up to 120 mM NaCI. A great reduction in sugar and protein contents occurred with increasing salinity, whereas soluble nitrogen compounds and the relative contents of the photosynthetic pigments were increased in the treated plants. Increasing Ca concentration in the salinized medium appeared to improve the plant growth and to increase the contents of saccharides and proteins in the NaCl-treated plants. This suggests that Ca could be added to salinized media to overcome the deleterious effects of salinity on the growth and productivity of leguminous crop plants.     

Plastid development in germinating wheat (Triticum aestivum) is enhanced by gibberellic acid and delayed by gabaculine

Etioplast development and protochlorophyllide (Pchlide) accumulation was studied in wheat seedlings ( Triticum aestivum L. cv. Walde, Weibull) grown in darkness on gibberellic acid (GA₃), gabaculine (3-amino-2,3-dihydrobenzoic acid), or on a combination of the two. The results were compared with the features of seedlings grown on water only. GA₃ enhanced shoot growth and promoted etioplast development. A correlation was observed between the appearance of prolamellar bodies (PLBs) and of phototransformable Pchlide. Gabaculine, a known tetrapyrrole biosynthesis inhibitor, delayed growth, slowed down the rate of PLB formation and caused structural alterations of the etioplasts up to 48 h of germination. Gabaculine also delayed the formation of phototransformable Pchlide as well as overall Pchlide biosynthesis, as determined by low-temperature fluorescence emission in vivo. The spectral blue-shift of newly formed chlorophyllide (Chlide) was delayed in irradiated dark-grown gabaculine-grown seedlings, indicating an inhibited dissociation of Chlide and NADPH-Pchlide oxidoreductase (Pchlide reductase: EC 1.3.1.33). Thus there is a close correlation between accumulation of Pchlide and etioplast development, also under conditions when development is enhanced or delayed.     

Conformation and activity of chloroplast coupling factor exposed to low chemical potential of water in cells.

(1) Photophosphorylation, Ca2+-ATPase and Mg2+-ATPase activities of isolated chloroplasts were inhibited 55--65% when the chemical potential of water was decreased by dehydrating leaves to water potentials (psi w) of --25 bars before isolation of the plastids. The inhibition could be reversed in vivo by rehydrating the leaves. (2) These losses in activity were reflected in coupling factor (CF1) isolated from the leaves, since CF1 from leaves with low psi w had less Ca2+-ATPase activity than control CF1 and did not recouple phosphorylation in CF1-deficient chloroplasts. In contrast, CF1 from leaves having high psi w only partially recoupled phosphorylation by CF1-deficient chloroplasts from leaves havig low psi w. This indicated that low psi w affected chloroplast membranes as well as CF1 itself. (3) Coupling factor from leaves having low psi w had the same number of subunits, and the same electrophoretic mobility, and could be obtained with the same yields as CF1 from control leaves. However, direct measurements of fluorescence polarization, ultraviolet absorption, and circular dichroism showed that CF1 from leaves having low psi w differed from control CF1. The CF1 from leaves having low psi w also had decreased ability to bind fluorescent nucleotides (epsilon-ATP and epsilon-ADP). (4) Exposure of isolated CF1 to low psi w in vitro by preincubation in sucrose-containing media inhibited the Ca2+-ATPase activity of the protein in subsequent assays without sucrose. Inclusion of 5 or 10 mM Mg2+ in the preincubation medium markedly inhibited Ca2+-ATPase activity. (5) These results show that CF1 undergoes changes in cells which alter its phosphorylating ability. Since low cell psi w changed the spectroscopic properties but not other protein properties of CF1, the changes were most likely caused by altered confurn, photophosphorylation. The inhibition of ATPase activity in CF1 in vitro at low psi w and high ion concentration mimicked the change in activity seen in vivo.     

Nitrogen metabolism in tomato seedlings

Tomato seedlings absorbed increasing amounts of nitrate-N. The total uptake was doubled as the concentration of nitrate was quadruplicated. NO₃?N absorption seemed to be accompanied by efflux of OH^? ions which shift the pH of the media to the alkaline side. A minor fraction of the absorbed nitrate accumulated in the tissues while the major part was assimilated into peptides and proteins. The dry matter gain was by the end of experiment relatively higher than the control samples raised on nitrogen-free nutrient solution. Nitrate assimilation seemed to involve its reduction down to ammonia level. Since neither nitrite nor ammonia was recovered in the tissue-medium system, it was postulated that the rate of reduction was slower than the rate of product assimilation. The first step in nitrate reduction (nitrate→nitrate) appeared to be limiting while further reduction steps occurred rapidly and accompanied by simultaneous assimilation of ammonia. The enzyme responsible for the first step of nitrate reduction,i.e., nitrate reductase, was extracted from tomato shoots and roots. The activity in root extract amounted to about 30% of that of the shoot. This may suggest the localization of nitrate reduction in the leaves and realizes the relation between nitrate metabolism and photosynthesis.     

In-Silico Analyses of Nonsynonymous Variants in the BRCA1 Gene

BReast CAncer gene 1 (BRCA1)—a tumor suppressor gene plays an important role in the DNA repair mechanism. Several BRCA1 variants perturb its structure and function, including synonymous and nonsynonymous single nucleotide polymorphisms (SNPs). In the present study, we performed in-silico analyses of nonsynonymous SNPs (nsSNPs) of the BRCA1 gene. In total, 122 nsSNPs were retrieved from the NCBI SNP database and in-silico analyses were performed using computational prediction tools: SIFT, PROVEAN, Mutation Taster, PolyPhen-2, MutPred, and ConSurf. Of these tools, SIFT, PROVEAN, and Mutation Taster predicted 61 out of 122 nsSNPs as “damaging”, based on structural homology analysis. PolyPhen-2 classified 22 nsSNPs as “probably damaging”. These nsSNPs were further analyzed by MutPred to predict basic molecular mechanisms of amino acid alteration. ConSurf analysis predicted eleven conserved amino acid residues with structural and functional consequences. We identified five amino acid residues in the RING finger domain (L22, C39, H41, C44, and C47) and two in the BRCT domain (P1771 and I1707) with the potential to deter the BRCA1 protein function. This study provides insights into the effect of nsSNPs and amino acid substitutions in BRCA1.

     

Quest for Novel Preventive and Therapeutic Options Against Multidrug-Resistant Pseudomonas aeruginosa

International Journal of Peptide Research and Therapeutics - Pseudomonas aeruginosa (P. aeruginosa) is a critical healthcare challenge due to its ability to cause persistent infections and the...     

Impact of Dietary Organic Mineral Supplementation on Reproductive Performance,Egg Quality Characteristics,Lipid Oxidation,Ovarian Follicular Development,and Immune Response in Laying Hens Under High Ambient Temperature

Biological Trace Element Research - The objectives of this study were to investigate the impact of dietary organic mineral mixture (manganese, zinc, and copper) supplementation on reproductive...