Estimation of intracellular pH in muscle of fishes from different thermal environments

A technique based on homogenisation of rapidly frozen tissue was used to investigate the regulation of intracellular pH (pH_i) in freshwater and marine fish from diverse environmental temperatures. The following species were held at ambient temperatures of ca. 1°C (Notothenia coriiceps; Antarctica), 5°C (Pleuronectes platessa, Myoxocephalus scorpius; North Sea), and 26°C (Oreochromis niloticus; African lakes). The effects of seasonal acclimatisation to 4, 11 and 18°C were also examined in rainbow trout in the winter, autumn and summer, respectively. Extracellular (whole blood) pH (pH_e) did not follow the constant relative alkalinity relationship, where pH⁺=pOH⁻ for any particular temperature, over a range of 1–26°C (overall δpH_e/δT=0.009±0.002 U °C⁻¹; P<0.001), apparently being regulated by ionic fluxes and ventilation. Intracellular pH (pH_i) was also regulated independently of pN(=0.5 pK water) in all species of fish examined. The inverse relationship between pH_i and environmental temperature gave an overall δpH_i/δT of −0.010±0.001 U °C⁻¹ (for both white and red muscle) and −0.004±0.003 U °C⁻¹ (cardiac muscle). However, between 1 and 11°C δpH_i/δT was much higher (P<0.001), −0.022±0.003 U °C⁻¹ (white muscle) and −0.022±0.004 U °C⁻¹ (red muscle). The possible adaptive roles for these different acid–base responses to environmental temperature variation among tissues and species, and the potential difficulties of estimating pH_i, are discussed.     

Effect of tetramethylammonium ions on conformational changes of DNA in the premelting temperature range

The reversible conformational change of DNAs and polydeoxyribonucleotides occurring before melting was followed by circular dichroism. Δθ/δT, the rate of change of ellipticity θ with temperature, was used mainly as a measure of this premelting phenomenon. If sodium ions were replaced by tetramethylammonium ions Δθ/δT decreased for poly (dA) poly (dT) and poly (dA.dT) poly (dT.dA), but increased for poly (dG.dC) poly (dC.dG). DNAs of different base composition showed no more premelting (Δθ/ΔT ~ 0) even at low molarities of TMACl provided the Na/TMA ratio was very small. For all cases studied the θ values at 0°C and at a given ionic strength were smaller in NaCl than in TMACl. When studying the series of ammonium ions from NH⁺₄ to (C₂H₅)₄,N⁺ the Δθ/ΔT values first decreased, going through zero with TMA⁺ io and then increased again. A tentative and qualitative explanation of our results can be given: (a) Hydration of the polymers increases in presence of TMA ions and their average stability decreases; locally, however, (AT) pairs are preferentially stabilized by TMA ions owing to a specific interaction at the level of O₂ of thymine. (b) In order to explain the different behaviour of (AT) polymers and DNA, it is assumed that only the B structure is able to accommodate TMA ions in the small groove of the double stranded helix.     

Binding of the Bovine and Porcine Pancreatic Secretory Trypsin Inhibitor (Kazal) To Human Leukocyte Elastase: A Thermodynamic Study

Abstract

The effect of pH and temperature on the apparent association equilibrium constant (K_a) for the binding of the bovine and porcine pancreatic secretory trypsin inhibitor (Kazal-type inhibitor, PSTI) to human leukocyte elastase has been investigated. At pH8.0, values of the apparent thermodynamic parameters for human leukocyte elastase: Kazal-type inhibitor complex formation are: bovine PSTT – K_a = 6.3 × 10⁴M^?1, δ5G° = -26.9kJ/mol, δH° = +11.7kJ/mol, and δS° = +1.3 × 10² entropy units; porcine PSTI –K_a = 7.0 × 10³M^?1,δG° = -21.5kJ/mol, δH° = +13.0kJ/mol, and δS° = +1.2 × 10² entropy units (values of K_a δG° and δS° were obtained at 21.0°C; values of δH° were temperature independent over the range (between 5.0°C and 45.0°C) explored). On increasing the pH from 4.5 to 9.5, values of K_a for bovine and porcine PSTI binding to human leukocyte elastase increase thus reflecting the acidic pK-shift of the His57 catalytic residue from ?7.0, in the free enzyme, to ?5.1, in the serine proteinase: inhibitor complexes. Thermodynamics of bovine and porcine PSTI binding to human leukocyte elastase has been analyzed in parallel with that of related serine (pro)enzyme/Kazal-type inhibitor systems. Considering the known molecular models, the observed binding behaviour of bovine and porcine PSTI to human leukocyte elastase was related to the inferred stereochemistry of the serine proteinase/inhibitor contact region(s).     

The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex—A Structural (NMR), Kinetic and Thermodynamic Study

Abstract

A single-point substitution of the O4′ oxygen by a CH₂ group at the sugar residue of A ⁶ (i.e. 2′-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5′- d(C¹G²C³G⁴A⁵A⁶T⁷T⁸C⁹G¹⁰C¹¹G¹²)₂ ^?3, has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A ⁶:T⁷ Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)→←(1B): K_eq = k₁/k_-1 = 0.56±0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k₁ (298K) = 3.9± 0.8 sec^?1; δH°? = 164±14 kJ/mol;-TδS°? (298K) = ?92 kJ/mol giving a δG₂₉₈°? of 72 kJ/mol. Ea (k1) = 167±14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0±0.6 sec-1, δH°? = 153±13 kJ/mol;-TδS°? (298K) = ?82 kJ/mol giving a δG₂₉₈°? of 71 kJ/mol. Ea (k-1) = 155±13 kJ/mol]. A comparison of δG₂₉₈°? of the forward (k1) and backward (k-1) conversions, (1A)→←(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A ⁶:T⁷ Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition, 55 NMR-derived backbone dihedral constraints per strand were used for both structures. The main effect of the Hoogsteen basepairs in (1B) on the overall structure is a narrowing of the minor groove and a corresponding widening of the major groove. The Hoogsteen basepairing at the central A ⁶:T⁷ basepairs in (1B) has enforced a syn conformation on the glycosyl torsion of the 2′- deoxyaristeromycin moiety, A ⁶, as a result of substitution of the endocyclic 4′-oxygen in the natural sugar with a methylene group in A ⁶. A comparison of the Watson-Crick basepaired duplex (1A) to the Hoogsteen basepaired duplex (1B) shows that only a few changes, mainly in α, σ and γ torsions, in the sugar-phosphate backbone seem to be necessary to accommodate the Hoogsteen basepair.     

Thermodynamic Parameters of Ligand-Receptor Interactions: Computation and Error Margins

Abstract

A semiempirical relationship describing the temperature function of ligand-receptor dissociation constants (K_d), derived from heat capacities of the system in equilibrium, is suggested for computation of the standard enthalpy (δH°) and standard entropy (δS°) changes in equilibrium. The use of the linear expression (called Gibbs-van't Hoff equation) may lead to inaccurate results when heat capacity C_p displays a considerable temperature dependence. The accuracy of K_d, δH° and δS° has been studied by simulation experiments. In the case of K_d, deviations of computed from “true” values are determined by both the accuracy of experimental data used for its estimation, and by the shape of the binding isotherm (for instance, by Hill coefficients or by the presence of low affinity sites). As a rule, if errors of bound ligand measurements are greater than 20 per cent, K_d estimates ought to be considered as less reliable. However, computations of δH° and δS° that use such K_d values, are more correct, probably due to an error compensation. The suggested nonlinear temperature function of K_d enables an estimate of the heat capacity of the system and its temperature dependence.     

A high-temperature water vapor equilibration method to determine non-exchangeable hydrogen isotope ratios of sugar,starch and cellulose

The analysis of the non-exchangeable hydrogen isotope ratio (δ²H_ne) in carbohydrates is mostly limited to the structural component cellulose, while simple high-throughput methods for δ²H_ne values of non-structural carbohydrates (NSC) such as sugar and starch do not yet exist. Here, we tested if the hot vapor equilibration method originally developed for cellulose is applicable for NSC, verified by comparison with the traditional nitration method. We set up a detailed analytical protocol and applied the method to plant extracts of leaves from species with different photosynthetic pathways (i.e., C₃, C₄ and CAM). δ²H_ne of commercial sugars and starch from different classes and sources, ranging from ?157.8 to +6.4‰, were reproducibly analysed with precision between 0.2‰ and 7.7‰. Mean δ²H_ne values of sugar are lowest in C₃ (?92.0‰), intermediate in C₄ (?32.5‰) and highest in CAM plants (6.0‰), with NSC being ²H-depleted compared to cellulose and sugar being generally more ²H-enriched than starch. Our results suggest that our method can be used in future studies to disentangle ²H-fractionation processes, for improving mechanistic δ²H_ne models for leaf and tree-ring cellulose and for further development of δ²H_ne in plant carbohydrates as a potential proxy for climate, hydrology, plant metabolism and physiology.     

Origins of irruptive migrations by Common Crossbills Loxia curvirostra into northwestern Europe revealed by stable isotope analysis

We used analyses of stable hydrogen isotope (δ²H) measurements in Common Crossbill feathers (δ²H_f) to infer the region of origin of Crossbills collected from different irruptions into Britain, Iceland and the Faeroes, comparing these values with those from birds sampled in breeding areas in Britain and elsewhere in the western Palaearctic. No differences in δ²H_f values were found between different species or sexes of Crossbills that could be presumed to have grown their feathers in the same region, but juveniles had lower δ²H_f values than adults that had grown their feathers in the same region. On the basis mainly of museum skins, immigrant birds were sampled from 30 different irruption years, spanning the period 1866–2009, with annual samples varying from one to 29 individuals. The variation in δ²H_f values within irruptions was substantially less than the variation between irruptions, indicating that irruptions in different years originated in different parts of the western Palaearctic boreal zone. Birds with lower δ²H_f values tended to arrive later in the migration season, which was consistent with the idea that they had travelled further. In 17 of the irruption years, the birds had mean δ²H_f values more than ?120‰, suggesting that they had originated somewhere in the region extending from northern Scandinavia to northwestern Russia. In these years the birds arrived early, in June and July. In 10 of the irruption years, the mean δ²H_f values were between ?120 and ?130‰, suggesting origins further east, in northern Russia, east of Archangel (about 40°E). In only three of the 30 years (1898, 2002, 2009) the mean δ²H_f values were even lower (< 130‰), and these birds arrived in late July, August and September. Birds in these three irruptions had probably come from Siberia, east of the Ural Mountains. In at least three irruption years (1898, 1927, 1985) the observed range of δ²H_f values suggested that birds had come from more than one of these regions, including east of the Urals in 1898 and 1927.     

The effect of bacterial strain and temperature changes on the nitrogenase activity of Lotus pedunculatus root nodules

After 40 days of growth at 25°C, Lotus pedunculatus cav., cv. Maku plants infected with Rhizobium loti strain NZP2037 displayed similar relative growth rates but had twice the nodule mass and only one third the whole plant dry weight of plants infected with Bradyrhizobium sp. (Lotus) strain CC814s. In the NZP2037 symbiosis, the rate of CO₂ evolution (per g dry weight of nodulated root) was 1.6 times as high as that in the CC814s symbiosis while the rate of C₂H₂ reduction (per g dry weight of nodule) was only 48% of that in the CC814s symbiosis. Studies of the effect of short term temperature changes on the gas exchange characteristics (CO₂ and H₂ evolution, C₂H₂ reduction) of these symbioses revealed wide differences in the optima for C₂H₂ reduction. Nodules infected with NZP2037 displayed maximal C₂H₂ reduction rates [157 μmol (g dry weight nodule)^?1 h^?1] at 12°C, whereas nodules infected with CC814s were optimal at 30°C [208 μmol (g dry weight nodule)^?1 h^?1]. These short term studies suggested that differences in temperature optima for N₂ may have partially accounted for the poorer effectivity, at 25°C, of strain NZP2037 when compared with strain CC-814s. The relative efficiency [RE = 1 – (H₂ evolution/C₂H₂ reduction)] of N₂ fixation varied widely with temperature in the two symbioses, but there was a general trend toward higher RE with lower temperatures. The ratio of CO₂ evolution: C₂H₂ reduction (mol/mol) in nodulated roots infected with CC814s was constant (ca 10 CO₂/C₂H₂) between 5°C and 30°C, whereas in plants infected with NZP2037 it reached a minimal value of 3.3 CO₂/C₂H₂ at 10°C and was 19 CO₂/C₂H₂ at the growing temperature (25°C).     

Microcalorimetric Investigation of DNA,poly(dA)poly(dT) and poly[d(A-C)]poly[d(G-T)] Melting in the Presence of Water Soluble (Meso tetra (4 N oxyethylpyridyl) Porphyrin) and its Zn Complex

Abstract

Thermodynamic parameters of melting process (δH_m, T_m, δT_m) of calf thymus DNA, poly(dA)poly(dT) and poly(d(A-C))·poly(d(G-T)) were determined in the presence of various concentrations of TOEPyP(4) and its Zn complex. The investigated porphyrins caused serious stabilization of calf thymus DNA and poly poly(dA)poly(dT), but not poly(d(A-C))poly(d(G-T)). It was shown that TOEpyp(4) revealed GC specificity, it increased T_m of satellite fraction by 24°C, but ZnTOEpyp(4), on the contrary, predominately bound with AT-rich sites and increased DNA main stage T_m by 18°C, and T_m of poly(dA)poly(dT) increased by 40 °C, in comparison with the same polymers without porphyrin. ZnTOEpyp(4) binds with DNA and poly(dA)poly(dT) in two modes—strong and weak ones. In the range of r from 0.005 to 0.08 both modes were fulfilled, and in the range of r from 0.165 to 0.25 only one mode—strong binding—took place. The weak binding is characterized with shifting of T_m by some grades, and for the strong binding T_m shifts by ～ 30–40°C. Invariability of ΔH_m of DNA and poly(dA)poly(dT), and sharp increase of T_m in the range of r from 0.08 to 0.25 for thymus DNA and 0.01–0.2 for poly(dA)poly(dT) we interpret as entropic character of these complexes melting. It was suggested that this entropic character of melting is connected with forcing out of H₂O molecules from AT sites by ZnTOEpyp(4) and with formation of outside stacking at the sites of binding. Four-fold decrease of calf thymus DNA melting range width ΔT_m caused by increase of added ZnTO- Epyp(4) concentration is explained by rapprochement of AT and GC pairs thermal stability, and it is in agreement with a well-known dependence, according to which ΔT～T_GC-T_AT for DNA obtained from higher organisms (L. V. Berestetskaya, M. D. Frank-Kamenetskii, and Yu. S. Lazurkin. Biopolymers 13, 193–205 (1974)). Poly (d(A-C))poly(d(G-T)) in the presence of ZnTOEpyp(4) gives only one mode of weak binding. The conclusion is that binding of ZnTOEpyp(4) with DNA depends on its nucleotide sequence.     

Daily variations in the thermoregulatory behaviors of naked neck broilers in an equatorial semi-arid environment

The aim of this study was to evaluate the daily variations in the thermoregulatory behavior of 4- to 6-week-old naked neck broilers (Label Rouge) in an equatorial semi-arid environment. A total of 220 birds were monitored for 5 days starting at 0600 hours and ending at 1800 hours. The period of observation was divided into classes of hours (C _H). The observed behaviors were as follows: feed and water intake, wing-spreading, sitting or lying, and beak-opening. A total of 14,300 behavioral data values were registered. In C _H 2 (0900 hours to 1100 hours) and 3 (1200 hours to 1500 hours), the greatest average body surface temperature was recorded (34.67?±?0.25 °C and 35.12?±?0.22 °C, respectively). The C _H had an effect on the exhibition of all behaviors with the exception of the water intake behavior. Feed intake was more frequent in C _H 1 (0600 hours to 0800 hours) and 4 (1600 hours to 1800 hours). In C _H 2 and 3, the highest frequency of sitting or lying behavior was observed. Beak-opening and wing-spreading behaviors occurred more frequently in C _H 3 where the body surface temperature (35.12?±?0.22 °C), radiant heat load (519.38?±?2.22 W m^?2), and enthalpy (82.74?±?0.36 kJ kg^?1 of dry air) reached maximum recorded averages. Thus, it can be concluded that naked neck broilers adjust their behavior in response to daily variations in the thermal environment. Wing-spreading and beak-opening behaviors are important adaptive responses to the thermal challenges posed by the equatorial semi-arid environment.     

Purification and Characterization of Lactobacillus bulgaricus Diaphorase

γ-Isomer of 1,2,3,4,5,6-hexachlorocyclohexane (BHC) showed greater decomposition on γ or UV irradiation of five isomers of BHC in crystalline state or in 2-propanol solution. The α- and δ-isomer of BHC and known la, 2a, 3e, 4e, 5e-pentachlorocyclohexane were separated from the irradiation product of crystalline γ-BHC. Four compounds were isolated from the irradiation product of γ-BHC in 2-propanol. Two compounds were tetrachloro-cyclohexenes (C₆H₆C1₄): γ-isomer (mp 86 ~87°C) and ?-isomer (mp 99 ~ 100°C). The other two were isomers of pentachlorocyclohexane (C₆H₇C1₅). One of them (mp 78 ~ 8.5°C) was consistent with known meso-1e,2a,3a,4a,5e isomer. The molecular structure of the other (mp 75°C) established by X-ray crystal structure analysis was 1α, 2α, 3α, 4β, 5α configuration or le 2a 3e 4e 5e conformation of CI atoms. A reaction mechanism was proposed that included a radical chain reaction and chlorine atom migration.     

Decomposition of water by cerium oxide of δ-phase

Reduced cerium dioxide (CeO_2?x) can reduce water, producing hydrogen at ?298 K. Kinetic studies were focused on the stoichiometric reaction of δ-phase cerium oxide (CeO_1.818) with water vapor. Different activation energies of 18.1 and 33.4 kJ mol^?1 were observed for the reactions at the temperature ranges above and below ca. 453 K, respectively. Rate equations observed in the two temperature ranges were also different. These results strongly suggest that the rate-determining steps are different between the two temperature ranges. Rapid oxygen exchange observed between H₂¹⁸O and lattice oxygen in cerium oxide of δ- phase at ? 298 K indicated that neither the adsorption of water molecules not the diffusion of oxygen ions in the bulk of the oxide can be the rate-determining step. H₂D₂ exchange occurred rapidly at 373 K compared to the rate of water decomposition, suggesting that the recombination of hydrogen atoms on the surface is not rate- determining either. A tentative reaction mechanism was proposed to explain the results of the kinetic studies. The rate-determining step at high temperatures (>453 K) is the reduction of OH^? by the six-coordinated Ce³⁺ which is present in the nonstoichiometric cerium oxide, while that at low temperatures (<453 K) is the subsequent reduction of H⁺ by the seven-coordinated Ce³⁺.     

Crystal structure of [chloro(diethyldithiocarbamato)butyl phenyl]tin(IV)

The crystal structure of the title compound, SnCl(C₆H₅)(C₄H₉)[S₂CN(C₂H₅)₂], was determined and refined to an R factor of 3.2% for 4876 reflections. The molecule contains five-coordinate tin in a distorted trigonal bipyramidal arrangement with the tin atom lying 0.20 Å below the equatorial plane formed by one of the sulphur atoms, S(1), and the donor carbons of the butyl and phenyl groups. The chlorine and the other sulphur atom, S(2), occupy axial sites, making a S(2)SnCl angle of 156.85(1)°. The SnS(2) bond is markedly elongated (2.764(1) Å) compared to the SnCl bond (2.449(1) Å) and the SnS(1) bond (2.454(1) Å). The structure resembles those of analogues such as (C₆H₅)₂Sn(glygly) in having both hydrocarbon ligands located in the equatorial plane. Crystal data: space group P$\text{1}$: a = 8.291(2) Å, b = 14.726(3) Å, c = 9.509(2) Å, α = 96.24(2)°, β = 107.02(3)°, γ = 116.70(2)°, Z = 2, R = 3.2% for 4876 independent reflections.     

Estimating stable carbon isotope values of microphytobenthos in the Arctic for application to food web studies

Most studies on Arctic food webs have neglected microphytobenthos as a potential food source because we currently lack robust measurements of δ¹³C values for microphytobenthos from this environment. As a result, the role of microphytobenthos in high latitude marine food webs is not well understood. We combined field measurements of the concentration of aqueous carbon dioxide and the stable carbon isotopic composition of dissolved inorganic carbon (δ¹³C_DIC) from bottom water in the Beaufort and Chukchi seas with a set of stable carbon isotopic fractionation factors reflecting differences in algal taxonomy and physiology to estimate the stable carbon isotope composition of microphytobenthos-derived total organic carbon (δ¹³C_p). The δ¹³C_p for Phaeodactylum tricornutum, a pennate diatom likely to be a dominant microphytobenthos taxon, was estimated to be ?23.9 ± 0.4 ‰ as compared to a centric diatom (Porosira glacialis, δ¹³C_p = ?20.0 ± 1.6 ‰) and a marine haptophyte (Emiliana huxleyi, δ¹³C_p = ?22.7 ± 0.5 ‰) at a growth rate (µ) of 0.1 divisions per day (d^?1). δ¹³C_p values increased by ~2.5 ‰ when µ increased from 0.1 to a maximum growth rate of 1.4 d^?1. We compared our estimates of δ¹³C_p values for microphytobenthos with published measurements for other carbon sources in the Arctic and sub-Arctic. We found that microphytobenthos values overlapped with pelagic sources, yet differed from riverine and ice-derived carbon sources. These model results provide valuable insight into the range of possible isotopic values for microphytobenthos from this region, but we remain cautious in regard to the conclusiveness of these findings given the paucity of field measurements currently available for model validation.     

Exon sequence requirements for excision in vivo of the bacterial group II intron RmInt1

Background

Group II intron splicing proceeds through two sequential transesterification reactions in which the 5' and 3'-exons are joined together and the lariat intron is released. The intron-encoded protein (IEP) assists the splicing of the intron in vivo and remains bound to the excised intron lariat RNA in a ribonucleoprotein particle (RNP) that promotes intron mobility. Exon recognition occurs through base-pairing interactions between two guide sequences on the ribozyme domain dI known as EBS1 and EBS2 and two stretches of sequence known as IBS1 and IBS2 on the 5' exon, whereas the 3' exon is recognized through interaction with the sequence immediately upstream from EBS1 [(δ-δ' interaction (subgroup IIA)] or with a nucleotide [(EBS3-IBS3 interaction (subgroup IIB and IIC))] located in the coordination-loop of dI. The δ nucleotide is involved in base pairing with another intron residue (δ') in subgroup IIB introns and this interaction facilitates base pairing between the 5' exon and the intron.

Results

In this study, we investigated nucleotide requirements in the distal 5'- and 3' exon regions, EBS-IBS interactions and δ-δ' pairing for excision of the group IIB intron RmInt1 in vivo. We found that the EBS1-IBS1 interaction was required and sufficient for RmInt1 excision. In addition, we provide evidence for the occurrence of canonical δ-δ' pairing and its importance for the intron excision in vivo.

Conclusions

The excision in vivo of the RmInt1 intron is a favored process, with very few constraints for sequence recognition in both the 5' and 3'-exons. Our results contribute to understand how group II introns spread in nature, and might facilitate the use of RmInt1 in gene targeting.     

Spatial configurations of polynucleotide chains. 3. Polydeoxyribonucleotides

The virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean-square end-to-end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C_2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C_3′–O_3′ bond of the deoxyribose residue in the C_2′-endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r²〉0/nl² calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C_3′-endo conformation and ≈21 with all residues in the C_2′-endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C_3′-endo and C_2′-endo conformational isomers present in a ratio of ～1 to 9.     

Calorimetric measurement of stepwise enthalpy changes for the binding of four oxygens to adult human hemoglobin

The successive enthalpy changes for the four steps of oxygen binding by diphosphoglycerate-free adult human hemoglobin have been measured by direct calorimetry at pH 7.4 and 6°. Average results in kcal/(mole O₂) are: ΔH₁ = ?25.1 ± 2.8; ΔH₂ = ?12.6 ± 3.0, ΔH₃ = ?12.5 ± 3.0, and ΔH₄ = ?10.1 ± 1.4. These results imply a substantial temperature dependence for the cooperativity of O₂ binding by the protein and generally resemble the van't Hoff results by Roughton $\text{et al}$. [Roy. Soc. of London Proc., $\text{B 144}$, 29 (1955)] for sheep hemoglobin at pH 9.1 and a temperature range of 2° to 19°.     

Chain length and oligonucleotide stability at high pressure

The effect of hydrostatic pressure on the helix-coil transition temperature (T_m) was measured for the DNA oligomers (dA)_n(dT)_n, where n = 11, 15, and 19, in 50 mM NaCl. The data were analyzed in light of previously published data for the polymer, poly(dA)·poly(dT) under the same conditions. As has been observed for DNA polymers, increasing the hydrostatic pressure led to an increase in the T_m of the oligomers; however, the effect of pressure diminished with decreasing chain length. The value of dT_m/dP decreased linearly with the inverse of the chain length varying from 3.15 × 10⁻²°C MPa⁻¹ for the polymer to 0.7 × 10⁻²°C MPa⁻¹ for the 11-mer. The two-state or van't Hoff enthalpy (ΔH_vH) of the helix-coil transition was obtained by analysis of the half-width of the thermal transition. As expected, ΔH_vH decreases with decreasing chain length. In contrast to the behavior of the polymer, poly(dA)·poly(dT), and (dA)₁₉(dT)₁₉, the ΔH_vH of the two shorter duplex oligonucleotides displayed a small pressure dependence dΔH_vH/dP≃−0.4 kJ MPa⁻¹ in both cases. The changes observed in the T_m and ΔH_vH were not sufficient to explain the magnitude of the chain-length dependence of the pressure effect. To interpret the large chain-length dependence of dT_m/dP, we propose that the terminal base pairs contribute a negative volume change to the helix-coil transition. Base pairs distant from the ends exhibit behavior characterized by the polymer where end effects are assumed to be negligible, i.e., a positive volume change for the helix-coil transition. The negative volume change of separating terminal bases may originate from the imperfect interactions these base pairs form with water due to the existence of several energetically equivalent conformations. This is reminiscent of one of the mechanisms proposed to be important in the pressure-induced dissociation of multimeric proteins into their constituent subunits. © 1996 John Wiley & Sons, Inc.     

Production,extraction, and thermodynamics protease partitioning from Aspergillus tamarii Kita UCP1279 using PEG/sodium citrate aqueous two-phase systems

Abstract

The protease from Aspergillus tamarii Kita UCP1279 extraction by aqueous two-phase PEG-Citrate (ATPS) systems, using a factorial design 2⁴, was investigated. Then, the variables studied were polyethylene glycol (PEG) molar mass (M_PEG), concentrations of PEG (C_PEG) and citrate (C_CIT), and pH. The responses analyzed were the partition coefficient (K), activity yield (Y) and purification factor (PF). The thermodynamic parameters of the ATPS partition were estimated as a function of temperature. ATPS was able to pre-purify the protease (PF = 1.6) and obtained 84% activity yield. The thermodynamic parameters ΔG°_m (?10.89?kJ mol^?1), ΔH_m (?5.0?kJ?mol^?1) and partition ΔS_m (19.74?J mol^?1 K^?1) showed that the preferential migration of almost all protein contaminants of the crude extract to the salt-rich phase, while the preferred protease was the PEG rich phase. The extracted enzyme presents optimum temperature and pH at range of 40–50?°C and 9.0–11.0, respectively. Moreover, the enzyme was identified as serine protease based on inhibition profile. ATPS showed the satisfactory performance as the first step for Aspergillus tamarii Kita UCP1279 protease pre-purification.