Binding thermodynamics of phosphorylated inhibitors to triosephosphate isomerase and the contribution of electrostatic interactions

Electrostatic interactions have a central role in some biological processes, such as recognition of charged ligands by proteins. We characterized the binding energetics of yeast triosephosphate isomerase (TIM) with phosphorylated inhibitors 2-phosphoglycollate (2PG) and phosphoglycolohydroxamate (PGH). We determined the thermodynamic parameters of the binding process (K_b, ΔG_b, ΔH_b, ΔS_b and ΔC_p) with different concentrations of NaCl, using fluorimetric and calorimetric titrations in the conventional mode of ITC and a novel method, multithermal titration calorimetry (MTC), which enabled us to measure ΔC_p in a single experiment. We ruled out specific interactions of Na⁺ and Cl^- with the native enzyme and did not detect significant linked protonation effects upon the binding of inhibitors. Increasing ionic strength (I) caused K_b, ΔG_b and ΔH_b to become less favorable, while ΔS_b became less unfavorable. From the variation of K_b with I, we determined the electrostatic contribution of TIM−2PG and TIM−PGH to ΔG_b at I = 0.06 M and 25 °C to be 36% and 26%, respectively. The greater affinity of PGH for TIM is due to a more favorable ΔH_b compared to 2PG (by 19-24 kJ mol^-1 at 25 °C). This difference is compatible with PGH establishing up to five more hydrogen bonds with TIM. Both binding ΔC_ps were negative, and less negative with increasing ionic strength. ΔC_ps at I = 0.06 M were much more negative than predicted by surface area models. Water molecules trapped in the interface when ligands bind to protein could explain the highly negative ΔCps. Thermodynamic binding functions for TIM−2PG changed more with ionic strength than those for TIM−PGH. This greater dependence is consistent with linked, but compensated, protonation equilibriums yielding the dianionic species of 2PG that binds to TIM, process that is not required for PGH.     

The stereodynamics of 1,2‐dipropyldiaziridines

N‐alkylated trans‐diaziridines are an intriguing class of compounds with two stereogenic nitrogen atoms which easily interconvert. In the course of our investigations of the nature of the interconversion process via nitrogen inversion or electrocyclic ring opening ring closure, we synthesized and characterized the three constitutionally isomeric diaziridines 1,2‐di‐n‐propyldiaziridine 1 , 1‐isopropyl‐2‐n‐propyldiaziridine 2 , and 1,2‐diisopropyldiaziridine 3 to study the influence of the substituents on the interconversion barriers. Enantiomer separation was achieved by enantioselective gas chromatography on the chiral stationary phase Chirasil‐β‐Dex with high separation factors α (1‐isopropyl‐2‐n‐propyldiaziridine: 1.18; 1, 2‐diisopropyldiaziridine: 1.24; 100°C 50 kPa He) for the isopropyl substituted diaziridines. These compounds showed pronounced plateau formation between 100 and 150°C, and peak coalescence at elevated temperatures. The enantiomerization barriers ΔG? and activation parameters ΔH? and ΔS? were determined by enantioselective dynamic gas chromatography (DGC) and direct evaluation of the elution profiles using the unified equation implemented in the software DCXplorer. Interestingly, 1‐isopropyl‐2‐n‐propyldiaziridine and 1,2‐diisopropyldiaziridine exhibit similar high interconversion barriers ΔG? (100°C) of 128.3 ± 0.4 kJ mol^?1 and 129.8 ± 0.4 kJ mol^?1, respectively, which indicates that two sterically demanding substituents do not substantially increase the barrier as expected for a distinct nitrogen inversion process. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Stereodynamics of tetramezine

The antidepressant drug tetramezine [1,2‐bis‐(3,3‐dimethyldiaziridin‐1‐yl)ethane] consists of two bridged diaziridine moieties with four stereogenic nitrogen centers, which are stereolabile and, therefore, are prone to interconversion. The adjacent substituents at the nitrogen atoms of the diaziridines moieties exist only in an antiperiplanar conformation, which results in a coupled interconversion. Therefore, three stereoisomers exist (meso form and two enantiomeric forms), which epimerize when the diaziridine moieties are regarded as stereogenic units due to the coupled interconversion. Here, we have investigated the epimerization between the meso and enantiomeric forms by dynamic gas chromatography. Temperature‐dependent measurements were performed, and reaction rate constants were determined using the unified equation of chromatography implemented in the software DCXplorer. The activation barriers of the epimerization were found to be ΔG^≠ = 100.7 kJ mol^?1 at 25°C and ΔG^≠ = 104.5 kJ mol^?1 at 37°C, respectively. The activation enthalpy and entropy were determined to be ΔH^≠ = 70.3 ± 0.4 kJ mol^?1 and ΔS^≠ = ?102 ± 2 J mol^?1 K^?1. Chirality, 2011. © 2010 Wiley‐Liss, Inc.     

Assessing the capacity for compensatory growth in growth‐hormone transgenic coho salmon Oncorhynchus kisutch

The effect of feed cycling (consisting of periods of starvation followed by periods of refeeding to satiation) on compensatory growth was evaluated in growth hormone transgenic and non‐transgenic wild‐type coho salmon Oncorhynchus kisutch. The specific growth rate (G_SR) of feed‐restricted non‐transgenic O. kisutch was not significantly different from the G_SR of fully‐fed non‐transgenic O. kisutch during two refeeding periods, whereas the G_SR of feed‐restricted transgenic O. kisutch was significantly higher in relation to the G_SR of fully‐fed transgenic O. kisutch during the second refeeding period, but not during the first, indicating that growth compensation mechanisms are different between non‐transgenic and growth‐hormone (GH)‐transgenic O. kisutch and may depend on life history (i.e. previous starvation). Despite the non‐significant growth rate compensation in non‐transgenic O. kisutch, these fish showed a level of body mass catch‐up growth not displayed by transgenic O. kisutch.     

Accelerating regrowth of temperate‐maritime forests due to environmental change

To understand how environmental changes have influenced forest productivity, stemwood biomass (B) dynamics were analyzed at 1267 permanent inventory plots, covering a combined 209 ha area of unmanaged temperate‐maritime forest in southwest British Columbia, Canada. Net stemwood production (ΔB) was derived from periodic remeasurements of B collected over a 40‐year measurement period (1959–1998) in stands ranging from 20 to 150 years old. Comparison between the integrated age response of net stemwood production, ΔB(A), and the age response of stemwood biomass, B(A), suggested a 58 ± 11% increase in ΔB between the first 40 years of the chronosequence period (1859–1898) and the measurement period. To estimate extrinsic forcing on ΔB, several different candidate models were developed to remove variation explained by intrinsic factors. All models exhibited temporal bias, with positive trends in (observed minus predicted) residual ΔB ranging between of 0.40 and 0.64% yr^?1. Applying the same methods to stemwood growth (G) indicated residual increases ranging from 0.43 and 0.67% yr^?1. Higher trend estimates corresponded with models that included site index (SI) as a predictor, which may reflect exaggeration of the age‐decline in SI tables. Choosing a model that excluded SI, suggested that ΔB increased by 0.40 ± 0.18% yr^?1, while G increased by 0.43 ± 0.12% yr^?1 over the measurement period. Residual G was significantly correlated with atmospheric carbon dioxide (CO₂), temperature (T), and climate moisture index (CMI). However, models driven with climate and CO₂, alone, could not simultaneously explain long‐term and measurement‐period trends without additional representation of indirect effects, perhaps reflecting compound interest on direct physiological responses to environmental change. Evidence of accelerating forest regrowth highlights the value of permanent inventories to detect and understand systematic changes in forest productivity caused by environmental change.     

Effects of salts on the interaction of 8-anilinonaphthalene 1-sulphonate and thermolysin

Neutral salts activate and stabilize thermolysin. In this study, to explore the mechanism, we analyzed the interaction of 8-anilinonaphthalene 1-sulphonate (ANS) and thermolysin by ANS fluorescence. At pH 7.5, the fluorescence of ANS increased and blue-shifted with increasing concentrations (0–2.0?μM) of thermolysin, indicating that the anilinonaphthalene group of ANS binds with thermolysin through hydrophobic interaction. ANS did not alter thermolysin activity. The dissociation constants (K_d) of the complex between ANS and thermolysin was 33?±?2?μM at 0?M NaCl at pH 7.5, decreased with increasing NaCl concentrations, and reached 9?±?3?μM at 4?M NaCl. The K_d values were not varied (31?34?μM) in a pH range of 5.5?8.5. This suggests that at high NaCl concentrations, Na⁺ and/or Cl^– ions bind with thermolysin and affect the binding of ANS with thermolysin. Our results also suggest that the activation and stabilization of thermolysin by NaCl are partially brought about by the binding of Na⁺ and/or Cl^– ions with thermolysin.     

Urea interactions with protein groups: A volumetric study

We determined the partial molar volumes and adiabatic compressibilities of N‐acetyl amino acid amides, N‐acetyl amino acid methylamides, N‐acetyl amino acids, and short oligoglycines as a function of urea concentration. We analyze these data within the framework of a statistical thermodynamic formalism to determine the association constants for the reaction in which urea binds to the glycyl unit and each of the naturally occurring amino acid side chains replacing two waters of hydration. Our determined association constants, k, range from 0.04 to 0.39M. We derive a general equation that links k with changes in free energy, ΔG_tr, accompanying the transfer of functional groups from water to urea. In this equation, ΔG_tr is the sum of a change in the free energy of cavity formation, ΔΔG_C, and the differential free energy of solute–solvent interactions, ΔΔG_I, in urea and water. The observed range of affinity coefficients, k, corresponds to the values of ΔΔG_I ranging from highly favorable to slightly unfavorable. Taken together, our data support a direct interaction model in which urea denatures a protein by concerted action via favorable interactions with a wide range of protein groups. Our derived equation linking k to ΔG_tr suggests that ΔΔG_I and, hence, the net transfer free energy, ΔG_tr, are both strongly influenced by the concentration of a solute used in the experiment. We emphasize the need to exercise caution when two solutes differing in solubility are compared to determine the ΔG_tr contribution of a particular functional group. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 866–879, 2010.     

First-principles study of phase stability and elastic properties in metastable Ti-Mo alloys with cluster structure

This paper provided a novel approach for evaluating phase stability and elastic properties in metastable Ti–Mo alloys with low Mo content by first-principles combined with cluster structure. In 54-atom body-centered-cubic supercell by substituting Ti atoms with 2–7 Mo atoms (7.1–23.0?wt% Mo), individual cluster structure of β-phase was constructed by ‘-Mo-Ti-Mo-’ cluster unit having the lowest cohesive energy. The distorted supercell was more stable than undistorted one at a low Mo content. With increasing Mo content, the density of state at Fermi level decreased, and bonding electron number increased, indicating β-phase stability was gradually promoted. Tetragonal shear elastic constant (C′?=?(C₁₁?–?C₁₂)/2), shear modulus (G₁₁₁) and anisotropy factor (A?=?C₄₄/C′) exhibited a fluctuation with Mo addition, while the change trend of A was opposite to C′ and G₁₁₁. Calculated Young’s modulus exhibited similar changing trend to the C′, implying that the softening of C′ resulted in low Young’s modulus of β-phase. Measured Young’s modulus exhibited significant difference from calculated one, which was mainly caused by formation of α″-martensite and ω-phase. The values of C′, G₁₁₁ and A were considered to associate with not only elastic properties of β-phase itself but also transition from β-phase to α″-martensite and/or ω-phase.     

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method

A multibaric‐multithermal molecular dynamics (MD) simulation of a 10‐residue protein, chignolin, was performed. All‐atom model with the Amber parm99SB force field was used for the protein and the TIP3P model was used for the explicit water molecules. This MD simulation covered wide ranges of temperature between 260 and 560 K and pressure between 0.1 and 600 MPa and sampled many conformations without getting trapped in local‐minimum free‐energy states. Folding events to the native β‐hairpin structure occurred five times and unfolding events were observed four times. As the temperature and/or pressure increases, fraction of folded chignolin decreases. The partial molar enthalpy change ΔH and partial molar volume change ΔV of unfolding were calculated as ΔH = 24.1 ± 4.9 kJ/mol and ΔV = ?5.6 ± 1.5 cm³/mol, respectively. These values agree well with recent experimental results. Illustrating typical local‐minimum free‐energy conformations, folding and unfolding pathways were revealed. When chignolin unfolds from the β‐hairpin structure, only the C terminus or both C and N termini open first. It may undergo an α‐helix or 3₁₀‐helix structure and finally unfolds to the extended structure. Difference of the mechanism between temperature denaturation and pressure denaturation is also discussed. Temperature denaturation is caused by making the protein transferred to a higher entropy state and making it move around more with larger space. The reason for pressure denaturation is that water molecules approach the hydrophobic residues, which are not well hydrated at the folded state, and some hydrophobic contacts are broken. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

Design of Peptides Using α,β-Dehydro-residues: Synthesis,Crystal Structure and Molecular Conformation of N-Boc-L-Val-ΔPhe–ΔPhe-L-Ala-OCH3

To obtain general rules of peptide design using α,β-dehydro-residues, a sequence with two consecutive ΔPhe-residues, Boc-L -Val-ΔPhe–ΔPhe- L -Ala-OCH₃, was synthesized by azlactone method in solution phase. The peptide was crystallized from its solution in an acetone/water mixture (70:30) in space group P6₁ with a=b=14.912(3) Å, c= 25.548(5) Å, V=4912.0(6) ų. The structure was determined by direct methods and refined by a full matrix least-squares procedure to an R value of 0.079 for 2891 observed [I?3σ(I)] reflections. The backbone torsion angles ?₁=?54(1)°, ψ₁= 129(1)°, ω₁=?177(1)°, ?₂ =57(1)°, ψ₂=15(1)°, ω₂ =?170(1)°, ?₃=80(1)°, ψ₃ =7(2)°, ω₃=?177(1)°, ?₄ =?108(1)° and ψ^T₄=?34 (1)° suggest that the peptide adopts a folded conformation with two overlapping β-turns of types II and III′. These turns are stabilized by two intramolecular hydrogen bonds between the CO of the Boc group and the NH of ΔPhe³ and the CO of Val¹ and the NH of Ala⁴. The torsion angles of ΔPhe² and ΔPhe³ side chains are similar and indicate that the two ΔPhe residues are essentially planar. The folded molecules form head-to- tail intermolecular hydrogen bonds giving rise to continuous helical columns which run parallel to the c-axis. This structure established the formation of two β-turns of types II and III′ respectively for sequences containing two consecutive ΔPhe residues at (i+2) and (i+3) positions with a branched β-carbon residue at one end of the tetrapeptide.     

Dimeric chlorite dismutase from the nitrogen‐fixing cyanobacterium Cyanothece sp. PCC7425

It is demonstrated that cyanobacteria (both azotrophic and non‐azotrophic) contain heme b oxidoreductases that can convert chlorite to chloride and molecular oxygen (incorrectly denominated chlorite ‘dismutase’, Cld). Beside the water‐splitting manganese complex of photosystem II, this metalloenzyme is the second known enzyme that catalyses the formation of a covalent oxygen–oxygen bond. All cyanobacterial Clds have a truncated N‐terminus and are dimeric (i.e. clade 2) proteins. As model protein, Cld from Cyanothece sp. PCC7425 (CCld) was recombinantly produced in Escherichia coli and shown to efficiently degrade chlorite with an activity optimum at pH 5.0 [k_cat 1144 ± 23.8 s^?1, K_M 162 ± 10.0 μM, catalytic efficiency (7.1 ± 0.6) × 10⁶ M^?1 s^?1]. The resting ferric high‐spin axially symmetric heme enzyme has a standard reduction potential of the Fe(III)/Fe(II) couple of ?126 ± 1.9 mV at pH 7.0. Cyanide mediates the formation of a low‐spin complex with k_on = (1.6 ± 0.1) × 10⁵ M^?1 s^?1 and k_off = 1.4 ± 2.9 s^?1 (K_D ～ 8.6 μM). Both, thermal and chemical unfolding follows a non‐two‐state unfolding pathway with the first transition being related to the release of the prosthetic group. The obtained data are discussed with respect to known structure–function relationships of Clds. We ask for the physiological substrate and putative function of these O₂‐producing proteins in (nitrogen‐fixing) cyanobacteria.     

Acid-Catalyzed nucleophilic substitution and racemization of 3-methoxy-N-desmethyldiazepam enantiomers in methanol

pK_a1 values of 3-methoxy-N-desmethyldiazepam in acetonitrile and methanol containing various acid concentrations were determined by spectrophotometry to be 3.5 and 1.3, respectively. Temperature-dependent racemization of enantiomeric 3-methoxy-N-desmethyldiazepam in methanol containing 0.5 M H₂SO₄ was studied by circular dichroism spectropolorimetry and the racemization reactions were found to follow apparent first-order kinetics. Thermodynamic parameters of the racemization reaction were found to be: E_act = 18.8 kcal/mol, and at 25°C: ΔH^? = 18.3 kcal/mol, ΔS^? = ?14.8 entropy unit, and ΔG^? = 22.7 kcal/mol, respectively. The racemization had an isotope effect (k_H/k_D) of 1.6 at 42°C. Based on the results of this report and those of earlier reports by other investigators, a nucleophilically solvated C3 carbocation intermediate resulting from either a P (plus) or an M (minus) conformation is proposed to be an intermediate and responsible for the stereoselective nucleophilic substitution and the subsequent racemization of 3-methoxy-N-desmethyldiazepam enantiomers. © 1993 Wiley-Liss, Inc.     

The collapse of benthic macroalgal blooms in response to self‐shading

1. Our goal was to use physiological indicators [photosynthesis–irradiance (P–I) response, nutrient status], population level feedbacks (self‐shading) and ambient environmental conditions (dissolved nutrients, light, temperature) to improve our understanding of the seasonal and spatial population dynamics of Cladophora. 2. Cladophora grew in three distinct phases, rapid growth early in the season (May–July), a mid‐season population collapse (July–August) and autumn re‐growth. Across all sites and dates, mean net maximal photosynthesis [P_M (NET)] was 6.9 ± 3.9 mg O₂ g DM^?1 h^?1, and α was 0.055 ± 0.025 mg O₂ g DM^?1 μm photons^?1 m^?2. Mean values for critical irradiance (I_CR) and the half‐saturation light intensity (I_K), were 42.9 ± 32.1 and 189.3 ± 123.8 μm photons^?1 m^?2 s^?1 respectively. 3. At most sites growth was phosphorus‐limited. Values of α were significantly higher at a site influenced by a nutrient enriched river plume, where algal growth was phosphorus‐sufficient. 4. Photoinhibition was not apparent in any of our P–I experiments. Even if photoinhibition had been apparent during in vitro P–I experiments, population level photosynthetic rates in the field would be little affected because intense self‐shading restricts inhibiting irradiances to the upper few mm–cm of the algal canopy. 5. Our physiological (P–I response) experiments contradicted previous assertions that high ambient temperatures, or nutrient deficiency, were primary causes of mid‐summer sloughing. In our study, sloughing occurred simultaneously at nutrient enriched and nutrient deficient sites, at temperatures well below critical values found during in vitro experiments, and our indicator of physiological condition (P–I response) remained unchanged leading up to, or immediately after, the sloughing event. 6. Self‐shading can reduce the convexity of the P–I response within in vitro incubations, even when the amount of algal material is low. Our experiments used 0.08 g DM of algal material that formed clumps c. 1 cm thick. Under these conditions, we estimated negligible (<1%) effects on P_M, a 12% reduction in apparent values of α, and 14% and 17% increases in values of the α‐dependent terms I_CR and I_K, respectively. 7. Our results are consistent with the hypothesis that a population‐level negative feedback (self‐shading) is responsible for sloughing in dense macroalgal beds. Sloughing was probably inevitable once macroalgal bed density and thickness surpassed a critical threshold. Cells towards the base of the bed received insufficient light to maintain metabolic balance, began to decay and weaken, and became increasingly susceptible to physical detachment from shear stress.     

β‐Cell Function and Insulin Sensitivity in Adolescents From an OGTT

Given the increase in the incidence of insulin resistance, obesity, and type 2 diabetes in children and adolescents, it would be of paramount importance to assess quantitative indices of insulin secretion and action during a physiological perturbation, such as a meal or an oral glucose‐tolerance test (OGTT). A minimal model method is proposed to measure quantitative indices of insulin secretion and action in adolescents from an oral test. A 7 h, 21‐sample OGTT was performed in 11 adolescents. The C‐peptide minimal model was identified on C‐peptide and glucose data to quantify indices of β‐cell function: static φ_s and dynamic φ_d responsivity to glucose from which total responsivity φ was also measured. The glucose minimal model was identified on glucose and insulin data to estimate insulin sensitivity, S_I, which was compared to a reference measure, S_I^ref, provided by a tracer method. Disposition indices, which adjust insulin secretion for insulin action, were then calculated. Indices of β‐cell function were φ_s = 51.35 ± 8.89 × 10^?9min^?1, φ_d = 1,392 ± 258 × 10^?9, and φ = 82.09 ± 17.70 × 10^?9min^?1. Insulin sensitivity was S_I = 14.19 ± 2.73 × 10^?4, not significantly different from S_I^ref = 14.96 ± 3.04 × 10^?4 dl/kg·min per µU/ml, and well correlated: r = 0.98, P < 0.0001, thus indicating that S_I can be accurately measured from an oral test. Disposition indices were DI_s = 1,040 ± 201 × 10^?14 dl/kg/min² per pmol/l, DI_d = 33,178 ± 10,720 × 10^?14 dl/kg/min per pmol/l, DI = 1,844 ± 522 × 10^?14 dl/kg/min² per pmol/l. Virtually the same minimal model assessment was obtained with a reduced 3 h, 9‐sample protocol. OGTT interpreted with C‐peptide and glucose minimal model has the potential to provide novel insight regarding the regulation of glucose metabolism in adolescents, and to evaluate the effect of obesity and interventions such as diet and exercise.     

Calorimetric measurement of enthalpy change in the isothermal helix-coil transition of poly(L-ornithine) in aqueous solution.

The enthalpy change associated with the isothermal pH-induced uncharged coil-to-helix transition ΔH_h° in poly(L -ornithine) in 0.1 N KCl has been determnined calorimetrically to be ?1530 ± 210 and ?1270 ± 530 cal/mol at 10° and 25°C, respectively. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔH_h°, the observed calorimetric heat was corrected for the heat of breaking the sample cell, the heat of dilution of HCl, the heat of neutralization of the OH^? ion, and the heat of ionization of the δ-amino group in the random coil. The latter was obtained from similar calorimetric measurements on poly(D ,L -ornithine). Since it was discovered that poly(L -ornithine) undergoes chain cleavage at high pH, the calorimetric measurements were carried out under conditions where no degradation occurred. From the thermally induced uncharged helix–coil transition curve for poly(L -ornithine) at pH 11.68 in 0.1 N KCl in the 0°–40°C region, the transition temperature T_tr and the quantity (?θ_h/?T)_Ttr have been obtained. From these values, together with the measured values of ΔH_h°, the changes in the standard free energy ΔG_h° and entropy ΔG_h°, associated with the uncharged coil-to-helix transition at 10°C have been calculated to be ?33 cal/mol and ?5.3 cal/mol deg, respectively. The value of the Zimm–Bragg helix–coil stability constant σ has been calculated to be 1.4 × 10^?2 and the value of s calculated to be 1.06 at 10°C, and between 0.60 and 0.92 at 25°C.     

Hydrolytic properties of a thermostable α‐l‐arabinofuranosidase from Caldicellulosiruptor saccharolyticus

Aims: To characterize of a thermostable recombinant α‐l ‐arabinofuranosidase from Caldicellulosiruptor saccharolyticus for the hydrolysis of arabino‐oligosaccharides to l ‐arabinose. Methods and Results: A recombinant α‐l ‐arabinofuranosidase from C. saccharolyticus was purified by heat treatment and Hi‐Trap anion exchange chromatography with a specific activity of 28·2 U mg^?1. The native enzyme was a 58‐kDa octamer with a molecular mass of 460 kDa, as measured by gel filtration. The catalytic residues and consensus sequences of the glycoside hydrolase 51 family of α‐l ‐arabinofuranosidases were completely conserved in α‐l ‐arabinofuranosidase from C. saccharolyticus. The maximum enzyme activity was observed at pH 5·5 and 80°C with a half‐life of 49 h at 75°C. Among aryl‐glycoside substrates, the enzyme displayed activity only for p‐nitrophenyl‐α‐l ‐arabinofuranoside [maximum k_cat/K_m of 220 m(mol l^?1)^?1 s^?1] and p‐nitrophenyl‐α‐l ‐arabinopyranoside. This substrate specificity differs from those of other α‐l ‐arabinofuranosidases. In a 1 mmol l^?1 solution of each sugar, arabino‐oligosaccharides with 2–5 monomer units were completely hydrolysed to l ‐arabinose within 13 h in the presence of 30 U ml^?1 of enzyme at 75°C. Conclusions: The novel substrate specificity and hydrolytic properties for arabino‐oligosaccharides of α‐l ‐arabinofuranosidase from C. saccharolyticus demonstrate the potential in the commercial production of l ‐arabinose in concert with endoarabinanase and/or xylanase. Significance and Impact of the Study: The findings of this work contribute to the knowledge of hydrolytic properties for arabino‐oligosaccharides performed by thermostable α‐l ‐arabinofuranosidase.     

Energetics of Acidianus ambivalens growth in response to oxygen availability

All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔH_inc) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔG_inc) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy‐driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C‐mol biomass per mole sulfur consumed) and resulted in lower ΔG_inc and ΔH_inc. ΔG_inc in oxygen‐limited (OL) and oxygen‐ and CO₂‐limited (OCL) microaerophilic growth conditions resulted in averages of ?1.44 × 10³ kJ/C‐mol and ?7.56 × 10² kJ/C‐mol, respectively, and average ΔH_inc values of ?1.11 × 10⁵ kJ/C‐mol and ?4.43 × 10⁴ kJ/C‐mol, respectively. High‐oxygen experiments resulted in lower biomass yield values, an increase in ΔG_inc to ?1.71 × 10⁴ kJ/C‐mol, and more exothermic ΔH_inc values of ?4.71 × 10⁵ kJ/C‐mol. The observed inefficiency in high‐oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.     

Insights into In Vitro Binding of Parecoxib to Human Serum Albumin by Spectroscopic Methods

Herein, we report the effect of parecoxib on the structure and function of human serum albumin (HSA) by using fluorescence, circular dichroism (CD), Fourier transforms infrared (FTIR), three‐dimensional (3D) fluorescence spectroscopy, and molecular docking techniques. The Stern–Volmer quenching constants K_SV and the corresponding thermodynamic parameters ΔH, ΔG, and ΔS have been estimated by the fluorescence quenching method. The results indicated that parecoxib binds spontaneously with HSA through van der Waals forces and hydrogen bonds with binding constant of 3.45 × 10⁴ M^?1 at 298 K. It can be seen from far‐UV CD spectra that the α‐helical network of HSA is disrupted and its content decreases from 60.5% to 49.6% at drug:protein = 10:1. Protein tertiary structural alterations induced by parecoxib were also confirmed by FTIR and 3D fluorescence spectroscopy. The molecular docking study indicated that parecoxib is embedded into the hydrophobic pocket of HSA.     

Hypoxia tolerance of the mummichog: the role of access to the water surface

Low dissolved oxygen (DO) had a significant effect on specific growth rate (G_S), length increment (I_L) and haematocrit (Hct) of the mummichog Fundulus heteroclitus. Regardless of access to the water surface, F. heteroclitus maintained high growth rates (G_S and I_L) at DO concentrations as low as 3 mg O₂ l^?1. With access to the water surface, both G_S and I_L of F. heteroclitus decreased by c. 60% at 1·0 mg O₂ l^?1 compared to all higher DO treatments. When denied access to the water surface, a further decrease in G_S (c. 90%) and I_L (c. 75%) was observed at 1 mg O₂ l^?1. There was no effect of diel‐cycling DO (1–11 mg O₂ l^?1) with or without surface access on G_S, I_L or Hct of F. heteroclitus. Similar trends between G_S and faecal production across DO treatments suggest that decreased feeding contributed significantly to the observed decrease in growth rate. Haematocrit was significantly elevated at 1 mg O₂ l^?1 for fish with and without access to the water surface. Increased Hct, however, was not sufficient to maintain high G_S or I_L at severely low DO. When permitted to respire in the surface layer, however, F. heteroclitus was capable of maintaining moderate growth rates at DO concentrations of 1 mg O₂ l^?1 (c. 15% saturation). Although aquatic surface respiration (ASR) was not quantified in this study, F. heteroclitus routinely swam in contact with the water surface and performed ASR at DO concentrations ≤3 mg O₂ l^?1. No hypoxia‐related mortality was observed in any DO or surface access treatment for as long as 9 days. This study demonstrates that surface access, and thus potential for ASR, plays an important role in providing F. heteroclitus substantial independence of growth rate over a wide range of low DO conditions commonly encountered in shallow estuarine environments.