Shapes of curves of pH-dependence of reactions.
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ABSTRACT:
SUBMITTER: Dixon HB
PROVIDER: S-EPMC1177448 | biostudies-other | 1973 Jan
REPOSITORIES: biostudies-other
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Project description:1. The pH-dependence of the pepsin-catalysed hydrolysis of three peptide substrates was studied by using a method for the continuous monitoring of the formation of ninhydrin-positive products. 2. Two peptide acid substrates, N-acetyl-l-phenylalanyl-l-phenylalanine and N-acetyl-l-phenylalanyl-l-phenylalanyl-glycine, show apparent pK(a) values of 1.1 and 3.5 in the plots of k(0)/K(m) versus pH. By contrast a neutral substrate, N-acetyl-l-phenylalanyl-l-phenylalanine amide, shows apparent pK(a) values of 1.0 and 4.7. 3. Together with the data of the preceding paper (Knowles, Sharp & Greenwell, 1969), these results are taken to indicate that the rate of pepsin-catalysed hydrolysis is controlled by the ionization of two groups, which on the free enzyme have apparent pK(a) values of 1.0 and 4.7. It is apparent that the anions of peptide acid substrates are not perceptibly bound to the enzyme, resulting in apparent pK(a) values of 3.5 for the dependence of k(0)/K(m) for these materials.
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Project description:A reaction in which the hydron [International Union of Pure and Applied Chemistry (1986) Chem. Int. 8 (4), 21] is a reactant will have a more acidic pH optimum than the reverse reaction in which it is a product. Simple mechanistic models, made by postulating various ways in which the hydron is supplied for the forward reaction, lead to the prediction that the pK that characterizes the fall in activity on the alkaline side for the forward reaction will be equal to that characterizing the fall on the acid side for the reverse reaction. It is not possible to identify what is responsible for this pK without additional information; as is well known, different possible dispositions of hydrons in transition states cannot usually be distinguished solely by kinetics.
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Project description:An acid, HnA, with n ionizing groups is known to have the same titration curve as an equimolar mixture of n hypothetical monobasic acids, whose dissociation constants are known as the 'titration constants' of the real acid. We show that the pH-dependence of any property of HnA is also represented by the sum of one-site titration curves, characterized by these same titration constants. Since one such property is the degree of dissociation of one of the dissociating groups, a fraction of each group shows each of the various titration pK values, so that the group partitions among them. The n groups therefore share the same n titration pK values but differ in the fractions belonging to each. The one H+ ion per molecule that titrates with each pK is thus made up of the fractions, one from each group, that share this pK value. A group may possess a single pK value, in that it contributes virtually all of this pK and almost nothing to the others, only if either (1) in titrates in a different pH range from the other groups or (2) its affinity for H+ is unaffected by their ionization state.
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Project description:As a means of making chitosan more useful in biotechnological applications, it was hydrolyzed using pepsin, chitosanase and ?-amylase. The enzymolysis behavior of these enzymes was further systematically studied for its effectiveness in the production of low-molecular-weight chitosans (LMWCs) and other derivatives. The study showed that these enzymes depend on ion hydronium (H3O+), thus on pH with a pH dependence fitting R2 value of 0.99. In y = 1.484[H^+] + 0.114, the equation of pH dependence, when [H^+] increases by one, y (k_0/k_m) increases by 1.484. From the temperature dependence study, the activation energy (Ea) and pre-exponential factor (A) were almost identical for two of the enzymes, but a considerable difference was observed in comparison with the third enzyme. Chitosanase and pepsin had nearly identical Ea, but ?-amylase was significantly lower. This serves as evidence that the hydrolysis reaction of ?-amylase relies on low-barrier hydrogen bonds (LBHBs), which explains its low Ea in actual conditions. The confirmation of this phenomenon was further derived from a similarly considerable difference in the order magnitudes of A between ?-amylase and the other two enzymes, which was more than five. Variation of the rate constants of the enzymatic hydrolysis of chitosan with temperature follows the Arrhenius equation.
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Project description:Most population dynamics studies assume that individuals use space uniformly, and thus mix well spatially. In numerous species, however, individuals do not move randomly, but use spatial memory to visit renewable resource patches repeatedly. To understand the extent to which memory-based foraging movement may affect density-dependent population dynamics through its impact on competition, we developed a spatially explicit, individual-based movement model where reproduction and death are functions of foraging efficiency. We compared the dynamics of populations of with- and without-memory individuals. We showed that memory-based movement leads to a higher population size at equilibrium, to a higher depletion of the environment, to a marked discrepancy between the global (i.e. measured at the population level) and local (i.e. measured at the individual level) intensities of competition, and to a nonlinear density dependence. These results call for a deeper investigation of the impact of individual movement strategies and cognitive abilities on population dynamics.
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Project description:BackgroundThe availability of genome sequences, and inferred protein coding genes, has led to several proteome-wide studies of isoelectric points. Generally, isoelectric points are distributed following variations on a biomodal theme that originates from the predominant acid and base amino acid sidechain pKas. The relative populations of the peaks in such distributions may correlate with environment, either for a whole organism or for subcellular compartments. There is also a tendency for isoelectric points averaged over a subcellular location to not coincide with the local pH, which could be related to solubility. We now calculate the correlation of other pH-dependent properties, calculated from 3D structure, with subcellular pH.ResultsFor proteins with known structure and subcellular annotation, the predicted pH at which a protein is most stable, averaged over a location, gives a significantly better correlation with subcellular pH than does isoelectric point. This observation relates to the cumulative properties of proteins, since maximal stability for individual proteins follows the bimodal isoelectric point distribution. Histidine residue location underlies the correlation, a conclusion that is tested against a background of proteins randomised with respect to this feature, and for which the observed correlation drops substantially.ConclusionThere exists a constraint on protein pH-dependence, in relation to the local pH, that is manifested in the pKa distribution of histidine sub-proteomes. This is discussed in terms of protein stability, pH homeostasis, and fluctuations in proton concentration.
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Project description:DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensitivity in vitro. Together, these data suggest that DksA responds to changes in pH by shifting between alternate conformations, in which competing interactions between the N- and C-terminal regions modify the protein activity.
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Project description:Despite more than a century of biological research on the evolution and maintenance of mimetic signals, the relative frequencies of models and mimics necessary to establish and maintain Batesian mimicry in natural populations remain understudied. Here we investigate the frequency-dependent dynamics of imperfect Batesian mimicry, using predation experiments involving artificial butterfly models. We use two geographically distinct populations of Adelpha butterflies that vary in their relative frequencies of a putatively defended model (Adelpha iphiclus) and Batesian mimic (Adelpha serpa). We found that in Costa Rica, where both species share similar abundances, Batesian mimicry breaks down, and predators more readily attack artificial butterfly models of the presumed mimic, A. serpa By contrast, in Ecuador, where A. iphiclus (model) is significantly more abundant than A. serpa (mimic), both species are equally protected from predation. Our results provide compelling experimental evidence that imperfect Batesian mimicry is frequency-dependent on the relative abundance of models and mimics in natural populations, and contribute to the growing body of evidence that complex dynamics, such as seasonality or the availability of alternative prey, influence the evolution of mimetic traits.
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Project description:Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
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