Contribution of hydrophobic interactions to protein stability

Our goal was to gain a better understanding of the contribution of hydrophobic interactions to protein stability. We measured the change in conformational stability, Δ(ΔG), for hydrophobic mutants of four proteins: villin headpiece subdomain (VHP) with 36 residues, a surface protein from Borrelia burgdorferi (VlsE) with 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa and T1. We compared our results with those of previous studies and reached the following conclusions: (1) Hydrophobic interactions contribute less to the stability of a small protein, VHP (0.6 ± 0.3 kcal/mol per -CH₂- group), than to the stability of a large protein, VlsE (1.6 ± 0.3 kcal/mol per -CH₂- group). (2) Hydrophobic interactions make the major contribution to the stability of VHP (40 kcal/mol) and the major contributors are (in kilocalories per mole) Phe18 (3.9), Met13 (3.1), Phe7 (2.9), Phe11 (2.7), and Leu21 (2.7). (3) Based on the Δ(ΔG) values for 148 hydrophobic mutants in 13 proteins, burying a -CH₂- group on folding contributes, on average, 1.1 ± 0.5 kcal/mol to protein stability. (4) The experimental Δ(ΔG) values for aliphatic side chains (Ala, Val, Ile, and Leu) are in good agreement with their ΔG_tr values from water to cyclohexane. (5) For 22 proteins with 36 to 534 residues, hydrophobic interactions contribute 60 ± 4% and hydrogen bonds contribute 40 ± 4% to protein stability. (6) Conformational entropy contributes about 2.4 kcal/mol per residue to protein instability. The globular conformation of proteins is stabilized predominantly by hydrophobic interactions.     

Hydrophobic hydration processes thermal and chemical denaturation of proteins

The hydrophobic hydration processes have been analysed under the light of a mixture model of water that is assumed to be composed by clusters (W₅)_I, clusters (W₄)_II and free water molecules W_III. The hydrophobic hydration processes can be subdivided into two Classes A and B. In the processes of Class A, the transformation A(− ξ_wW_I → ξ_wW_II + ξ_wW_III + cavity) takes place, with expulsion from the bulk of ξ_w water molecules W_III, whereas in the processes of Class B the opposite transformation B(− ξ_wW_III − ξ_wW_II → ξ_wW_I − cavity) takes place, with condensation into the bulk of ξ_w water molecules W_III. The thermal equivalent dilution (TED) principle is exploited to determine the number ξ_w. The denaturation (unfolding) process belongs to Class A whereas folding (or renaturation) belongs to Class B. The enthalpy ΔH_den and entropy ΔS_den functions can be disaggregated in thermal and motive components, ΔH_den = ΔH_therm + ΔH_mot, and ΔS_den = ΔS_therm + ΔS_mot, respectively. The terms ΔH_therm and ΔS_therm are related to phase change of water molecules W_III, and give no contribution to free energy (ΔG_therm = 0). The motive functions refer to the process of cavity formation (Class A) or cavity reduction (Class B), respectively and are the only contributors to free energy ΔG_mot. The folded native protein is thermodynamically favoured (ΔG_fold ≡ ΔG_mot < 0) because of the outstanding contribution of the positive entropy term for cavity reduction, ΔS_red ? 0. The native protein can be brought to a stable denatured state (ΔG_den ≡ ΔG_mot < 0) by coupled reactions. Processes of protonation coupled to denaturation have been identified. In thermal denaturation by calorimetry, however, is the heat gradually supplied to the system that yields a change of phase of water W_III, with creation of cavity and negative entropy production, ΔS_for ? 0. The negative entropy change reduces and at last neutralises the positive entropy of folding. In molecular terms, this means the gradual disruption by cavity formation of the entropy-driven hydrophobic bonds that had been keeping the chains folded in the native protein. The action of the chemical denaturants is similar to that of heat, by modulating the equilibrium between W_I, W_II, and W_III toward cavity formation and negative entropy production. The salting-in effect produced by denaturants has been recognised as a hydrophobic hydration process belonging to Class A with cavity formation, whereas the salting-out effect produced by stabilisers belongs to Class B with cavity reduction.Some algorithms of denaturation thermodynamics are presented in the Appendices.     

An unusual thermostable aspartic protease from the latex of Ficus racemosa (L.)

The most extensively studied ficins have been isolated from the latex of Ficus glabrata and Ficus carica. However the proteases (ficins) from other species are less known. The purification and characterization of a protease from the latex of Ficus racemosa is reported. The enzyme purified to homogeneity is a single polypeptide chain of molecular weight of 44,500 ± 500 Da as determined by MALDI-TOF. The enzyme exhibited a broad spectrum of pH optima between pH 4.5-6.5 and showed maximum activity at 60 ± 0.5 °C. The enzyme activity was completely inhibited by pepstatin-A indicating that the purified enzyme is an aspartic protease. Far-UV circular dichroic spectra revealed that the purified enzyme contains predominantly β-structures. The purified protease is thermostable. The apparent T_m, (mid point of thermal inactivation) was found to be 70 ± 0.5 °C. Thermal inactivation was found to follow first order kinetics at pH 5.5. Activation energy (E_a) was found to be 44.0 ± 0.3 kcal mol⁻¹. The activation enthalpy (ΔH^∗), free energy change (ΔG^∗) and entropy (ΔS^∗) were estimated to be 43 ± 4 kcal mol⁻¹, −26 ± 3 kcal mol⁻¹ and 204 ± 10 cal mol⁻¹ K⁻¹, respectively. Its enzymatic specificity studied using oxidized B chain of insulin indicates that the protease preferably hydrolyzed peptide bonds C-terminal to glutamate, leucine and phenylalanine (at P₁ position). The broad specificity, pH optima and elevated thermal stability indicate the protease is distinct from other known ficins and would find applications in many sectors for its unique properties.     

Particle reworking and solute transport by the sediment-living polychaetes Marenzelleria neglecta and Hediste diversicolor

This experimental study quantified and compared particle-mixing and solute transport by the polychaetes Marenzelleria neglecta (2 g ww, 3200 ind. m^− 2) and Hediste diversicolor (2 g ww, 800 ind. m^− 2) in Baltic Sea sediments. Particle tracers (luminophores) were added to the sediment surface and their vertical distribution in the sediment was measured after 10 d. The rate of particle mixing was quantified using a gallery-diffusion model calculating the biodiffusion coefficient D_b and the non-local transport parameter r. Bioirrigation was measured by adding an inert solute tracer (bromide) to the overlying water 1, 1.5 and 2 d before the end of the experiment, and quantified by calculating the net bromide flux and fitting the bromide profiles to a 1D diffusion model providing an apparent biodiffusion coefficient D_a. The two polychaete worms displayed similar particle-mixing and solute transport efficiencies (based on total biomass) despite different modes of bioturbation. However, H. diversicolor was a more efficient particle-reworker and M. neglecta a more efficient bioirrigator, on an individual level. H. diversicolor buried a higher percentage (13%) of luminophores below the top 0.5 cm surface layer than M. neglecta (6%). D_b did not differ between the two species (2.4 × 10^− 3 cm² d^− 1) indicating a similar rate of diffusive mixing of the top sediment, however, the non-local transport parameter r was 2.5 y^− 1 for H. diversicolor and zero for M. neglecta, suggesting no significant particle-transport below the biodiffusive layer by M. neglecta. The average individual net bromide fluxes obtained were ca. 0.01 mL min^− 1 for H. diversicolor and 0.003 mL min^− 1 for M. neglecta, corresponding to an area-specific rate of ca. 12 L m^− 2 d^− 1 at the used densities. D_a did not differ between the two polychaetes, suggesting a higher individual solute exchange efficiency of M. neglecta considering the much higher ventilation rates reported for H. diversicolor than for Marenzelleria sp. The ongoing colonization of Baltic Sea sediments by M. neglecta at high densities may thus lead to an enhanced soluble release of both nutrients and contaminants. These results add information to the understanding of the potential effects of the invasion of M. neglecta on sediment biogeochemistry when competing with and/or replacing native species.     

Physiological,morphological and anatomical trait variations between winter and summer leaves of Cistus species

Morphological, anatomical and physiological summer and winter leaf traits of Cistus incanus subsp. incanus, C. salvifolius and C. monspeliensis growing at the Botanical garden of Rome were analyzed. With regard to differences between summer and winter leaves of the considered species, leaf thickness (L) was 21% higher in summer than in winter leaves (mean of the considered species) and this increase was mostly the result of the increased palisade parenchyma thickness over the spongy parenchyma one (24 and 16% higher in summer than in winter leaves, respectively). Leaf mass area (LMA) and leaf tissue density (LTD) were 38% and 17% higher in summer than in winter leaves, respectively (mean of the considered species). The photosynthetic rate (P_N), stomatal conductance (g_s) and chlorophyll content (Chl) of summer leaves were 54%, 17% and 14% lower, respectively, than in winter leaves. C. monspeliensis summer leaves had the highest LMA, LTD, adaxial cuticle thickness (14.6 ± 1.8 mg cm⁻², 1091 ± 94 mg cm⁻³, and 5.8 ± 1.7 μm, respectively) and the lowest mesophyll intercellular spaces (f_ias 38 ± 3%). Moreover, C. monspeliensis had the highest P_N in summer (2.6 ± 0.1 μmol m⁻² s⁻¹) and C. incanus the highest P_N and WUE (84% and 59% higher than the other species) in the favorable period, associated to a higher f_ias (42 ± 2%). C. salvifolius had the highest P_N (54% higher than the other species) in winter. The plasticity index could allow a better interpretation of the habitat preference of the considered species. The physiological plasticity (PI_p = 0.39, mean value of the considered species) was higher than the morphological (PI_m = 0.22, mean value) and anatomical (PI_a = 0.13, mean value) plasticity. Moreover, among the considered species, C. salvifolius and C. incanus are characterized by a larger PI_a (0.14, mean value) which seems to be correlated with their wider ecological distribution and the more favorable conditions of the environments where they naturally occur. The highest PI_m (0.29) of C. monspeliensis indicates that it can play a high adaptive role in highly stressed environments, like fire degraded Mediterranean areas in which it occurs.     

Community metabolism and buffering capacity of nitrogen in a ruppia cirrhosa meadow

Fluxes of oxygen, inorganic nitrogen (DIN) and denitrification (isotope pairing) were measured from January 1997 to February 1998 via intact cores incubation in a shallow brackish area within the eutrophic Valli di Comacchio (northern Adriatic coast, Italy). Rates were measured in the light and in the dark in sediments colonized by the rooted macrophyte Ruppia cirrhosa and in adjacent sediments with benthic microalgae. Ruppia biomass (25-414 g DW m^− 2) exhibited a seasonal evolution whilst that of microphytobenthos (12-66 mg chl a m^− 2) was more erratic. Net (NP) and gross (GP) primary productivity was 1.15 and 6.89 mol C m^− 2y^− 1 for bare and 25.4 and 51.7 mol C m^− 2y^− 1 for Ruppia vegetated sediments. Nitrogen pools in Ruppia standing stock varied from 43.6 to 631.4 (annual average 201.2) mmol N m^− 2; the macrophyte N content was correlated with DIN concentration in the water column. Estimated N pool in microphytobenthos was one order of magnitude lower (from 2.4 to 14.5 mmol N m^− 2, annual average 7.2). Theoretical DIN assimilation calculated from NP was 127.8 and 1112.6 mmol N m^− 2y^− 1 whilst that calculated from GP was 765 and 2282 mmol N m^− 2y^− 1 for microphytobenthos and Ruppia respectively. Measured annual fluxes of DIN were 974.6 and − 577 mmol N m^− 2y^− 1 in bare and Ruppia vegetated sediments meaning that the two sites were a source and sink for DIN and that from 25 to 50% of Ruppia annual DIN requirements came from the water column. During the period of this study total denitrification was lower in the macrophyte colonized (92.3 mmol N m^− 2y^− 1) compared to bare sediments (163.3 mmol N m^− 2y^− 1) as a probable consequence of higher competition between denitrifiers and phanerogams. At both sites the ratio between denitrification of water column nitrate (D_W) and denitrification coupled to nitrification (D_N) was >1.6 due to little oxygen penetration in reducing sediments (< 1.2 mm) and scarce nitrification activity. D_W (0-35 µmol N m^− 2h^− 1) was significantly correlated with water column NO₃⁻  (2-16 µM). Theoretical DIN assimilation to denitrification ratio varied from 12.0 to 24.8 for Ruppia vegetated and from 0.8 to 4.7 for unvegetated sediments.At Valle Smarlacca, Ruppia may influence nitrogen cycling by incorporating large DIN pools in biomass which is scattered in surrounding areas and fuels intense bacterial activity. With increasing anthropogenic nutrient input and insignificant organic matter export in the open sea the already severe eutrophic conditions are enhanced and may accelerate the decline of the macrophyte meadow.     

Ice nucleation and supercooling behavior of polymer aqueous solutions

We determined the homogeneous nucleation temperature depression, ΔT_f,hom, the equilibrium melting point depression, ΔT_m, and the value λ, which can be obtained from the linear relationship ΔT_f,hom = λΔT_m, for aqueous solutions of PEG (200-20,000 g mol⁻¹), PVP (10,000, 35,000, 40,000 g mol⁻¹), and dextran (10,000 g mol⁻¹) in the concentration range 0-40 wt% using the emulsion method. The molecular weight dependence of T_f,hom, T_m, and λ in PEG aqueous solutions was found to change in the vicinity of Mw 600-1540 at all concentrations. In addition, it was confirmed that for all of the polymers studied, there was a good linear relationship between λ and the logarithmic value of the self-diffusion coefficient D₀ of the solute molecule. These results indicate that the parameters that describe non-equilibrium freezing, such as T_f,hom and λ, are dependent on solution properties such as viscosity and self-diffusion of solute molecules.     

1,10-Phenanthroline-5,6-dione complexes of middle transition elements: Mono- and dinuclear derivatives

The synthesis and the characterization of several mono- and dinuclear middle transition metal derivatives of 1,10-phenanthroline-5,6-dione, 1, are presented. The reaction of 1 with CrCl₂(THF)₂ gives CrCl₂(O,O′-C₁₂H₆N₂O₂)(THF)₂, 2, while the halides of iron(II), cobalt(II) and nickel(II) afford adducts of general formula MX₂(N,N′-C₁₂H₆N₂O₂), M = Fe, 4, Co, 5, X = Cl; M = Ni, 6, X = Br. DFT calculations on CrCl₂(L)(THF)₂ with L = O,O′-C₁₂H₆N₂O₂ or O,O′-C₁₄H₈O₂ allowed a direct comparison of the coordination properties of 9,10-phenanthrenequinone and 1,10-phenanthroline-5,6-dione to be made. Dinuclear compounds of general formula CrCl₂(THF)₂(O,O′-C₁₂H₆N₂O₂-N,N′)MX_nL_m, M = Zr, 7, X = Cl, n = 4, m = 0; M = Cr, 8, X = Cl, n = 2, L = THF, m = 2; M = Fe, 9, Co, 10, X = Cl, n = 2, m = 0; M = Ni, 11, X = Br, n = 2, m = 0, are prepared from 2 and the corresponding metal halide, while VCp₂(O,O′-C₁₂H₆N₂O₂-N,N′)FeCl₂, 12, is synthesized by reacting 4 with VCp₂. The electronic properties of the different complexes are investigated by magnetic moment measurements and EPR spectroscopy.     

Thermodynamic and structural analysis of homodimeric proteins: Model of β-lactoglobulin

The energetics of protein homo-oligomerization was analyzed in detail with the application of a general thermodynamic model. We have studied the thermodynamic aspects of protein-protein interaction employing β-lactoglobulin A from bovine milk at pH = 6.7 where the protein is mainly in its dimeric form. We performed differential calorimetric scans at different total protein concentration and the resulting thermograms were analyzed with the thermodynamic model for oligomeric proteins previously developed. The thermodynamic model employed, allowed the prediction of the sign of the enthalpy of dimerization, the analysis of complex calorimetric profiles without transitions baselines subtraction and the obtainment of the thermodynamic parameters from the unfolding and the association processes and the compared with association parameters obtained with Isothermal Titration Calorimetry performed at different temperatures. The dissociation and unfolding reactions were also monitored by Fourier-transform infrared spectroscopy and the results indicated that the dimer of β-lactoglobulin (N₂) reversibly dissociates into monomeric units (N) which are structurally distinguishable by changes in their infrared absorbance spectra upon heating. Hence, it is proposed that β-lactoglobulin follows the conformational path induced by temperature:N₂ ? 2N ? 2D. The general model was validated with these results indicating that it can be employed in the study of the thermodynamics of other homo-oligomeric protein systems.     

Differential xanthophyll cycling and photochemical activity in symbiotic dinoflagellates in multiple locations of three species of Caribbean coral

Changes in in situ xanthophyll activity were compared in symbiotic dinoflagellates within the reef-building corals, Montastraea faveolata, Montastraea annularis, and Acropora cervicornis over a daily light cycle from morning until dusk on a shallow (4 m) patch reef. Examination of algae collected from the tops and sides of M. faveolata and M. annularis revealed typical inter-conversion of diadinoxanthin and diatoxanthin, with the greatest abundance of diatoxanthin noted by the mid-morning to afternoon, correlating to daily reduction in the effective quantum yield of photosystem II (ΔF / F_m′) for the respective colony location. A. cervicornis had the highest proportion of diatoxanthin relative to the total xanthophyll pool, yet it also displayed the least amount of total daily xanthophyll cycling which did not correlate well with patterns of change in ΔF / F_m′. For intraspecific comparisons, no significant difference in daily xanthophyll activity was noted between the different locations in each coral species, while differences in ΔF / F_m′ were detected. In some cases temporal trends in nonphotochemical quenching (NPQ) of chlorophyll fluorescence did not match patterns in xanthophyll activity when peak xanthophyll cycling tended to lag behind the immediate light intensity measured in the mid-morning at some colony locations. Genetic characterization of symbionts using polymerase chain reaction-denaturing gradient electrophoresis of the rDNA internal transcribed spacer 2 region (ITS2) revealed that M. faveolata and M. annularis hosted the type B1 symbiont at all locations, while the type A3 symbiont was noted throughout A. cervicornis. Results indicate that while xanthophyll cycling appears to be largely a ubiquitous phenomenon in symbiotic dinoflagellates, the degree of cycling can be quite different between coral species at the same depth and that other biochemical pathways for daily photoprotection may predominate some host-symbiont combinations.     

Design of novel iron compounds as potential therapeutic agents against tuberculosis

In the search for new therapeutic tools against tuberculosis two novel iron complexes, [Fe(L-H)₃], with 3-aminoquinoxaline-2-carbonitrile N¹,N⁴-dioxide derivatives (L) as ligands, were synthesized, characterized by a combination of techniques, and in vitro evaluated. Results were compared with those previously reported for two analogous iron complexes of other ligands of the same family of quinoxaline derivatives. In addition, the complexes were studied by cyclic voltammetry and EPR spectroscopy. Cyclic voltammograms of the iron compounds showed several cathodic processes which were attributed to the reduction of the metal center (Fe(III)/Fe(II)) and the coordinated ligand. EPR signals were characteristic of magnetically isolated high-spin Fe(III) in a rhombic environment and arise from transitions between m_S = ± 1/2 (g_eff ~ 9) or m_S = ± 3/2 (g_eff ~ 4.3) states. Mössbauer experiments showed hyperfine parameters that are typical of high-spin Fe(III) ions in a not too distorted environment. The novel complexes showed in vitro growth inhibitory activity on Mycobacterium tuberculosis H₃₇Rv (ATCC 27294), together with very low unspecific cytotoxicity on eukaryotic cells (cultured murine cell line J774). Both complexes showed higher inhibitory effects on M. tuberculosis than the “second-line” therapeutic drugs.     

Chemical implantation of Group 4 cations on silica via cyclopentadienyl- and N,N-dialkylcarbamato derivatives

Chemical implantation of Group 4 cations [Ti(III), Ti(IV), Zr(IV), Hf(IV)] has been carried out under mild conditions by the reaction of polycyclopentadienyl- (MCp_n; M = Ti, n = 3, 4; M = Zr, Hf, n = 4), mixed cyclopentadienyl/N,N-dialkylcarbamato (ML_x(O₂CNEt₂)_y; M = Ti, L = Cp, C₅Me₅ (Cp*), x = 2, y = 1; M = Hf, L = Cp, x = 1, y = 3), and N,N-dialkylcarbamato (M(O₂CNR₂)_n, M = Ti, n = 3, R = ⁱPr; M = Ti, Hf, n = 4, R = Et; M = Zr, n = 4, R = ⁱPr) derivatives, with the silanol groups of amorphous silica. Cyclopentadiene/pentamethylcyclopentadiene and/or carbon dioxide and the secondary amine are released in the process. The amount of implanted cations depends on the metal and on the ligands, the pentamethylcyclopentadienyl complex being less reactive than the unsubstituted congener. The starting complexes and the final products have been characterized by EPR or by ¹³C CP-MAS NMR spectroscopy.     

Simultaneous true, gated, and coupled electron-transfer reactions and energetics of protein rearrangement

Cytochromes c₆ and f react by three et mechanisms under similar conditions. We report temperature and viscosity effects on the protein docking and kinetics of ³Zncyt c₆ + cyt f(III) → Zncyt c₆⁺ + cyt f(II). At 0.5-40.0 °C, this reaction occurs within the persistent (associated) diprotein complex with the rate constant k^pr and within the transient (collision) complex with the rate constant k^tr. The viscosity independence of k^pr, the donor-acceptor coupling H_ab = (0.5 ± 0.1) cm⁻¹, and reorganizational energy λ = (2.14 ± 0.02) eV indicate true et within the persistent complex. The viscosity dependence of k^tr and a break at 30 °C in the Eyring plot for k^tr reveal mechanisms within the transient complex that are reversibly switched by temperature change. Kramers protein friction parameters differ much for the reactions below (σ = 0.3 ± 0.1, δ = 0.85 ± 0.07) and above (σ = 4.0 ± 0.9, δ = 0.40 ± 0.06) 30 °C. The transient complex(es) undergo(es) coupled et below ca. 30 °C and gated et above ca. 30 °C. Brownian dynamics simulations reveal two broad, dynamic ensembles of configurations “bridged” by few intermediate configurations through which the interconversion presumably occurs.     

Influence of ammonium sulphate feeding time on fed-batch Arthrospira (Spirulina) platensis cultivation and biomass composition with and without pH control

Previous work demonstrated that a mixture of NH₄Cl and KNO₃ as nitrogen source was beneficial to fed-batch Arthrospira (Spirulina) platensis cultivation, in terms of either lower costs or higher cell concentration. On the basis of those results, this study focused on the use of a cheaper nitrogen source mixture, namely (NH₄)₂SO₄ plus NaNO₃, varying the ammonium feeding time (T = 7-15 days), either controlling the pH by CO₂ addition or not. A. platensis was cultivated in mini-tanks at 30 °C, 156 μmol photons m⁻² s⁻¹, and starting cell concentration of 400 mg L⁻¹, on a modified Schlösser medium. T = 13 days under pH control were selected as optimum conditions, ensuring the best results in terms of biomass production (maximum cell concentration of 2911 mg L⁻¹, cell productivity of 179 mg L⁻¹ d⁻¹ and specific growth rate of 0.77 d⁻¹) and satisfactory protein and lipid contents (around 30% each).     

Evaporative water loss and energy metabolic in two small mammals,voles (Eothenomys miletus) and mice (Apodemus chevrieri), in Hengduan mountains region

Evaporative water loss (EWL) and energy metabolism were measured at different temperatures in Eothenomys miletus and Apodemus chevrieri in dry air. The thermal neutral zone (TNZ) of E. miletus was 22.5–30 °C and that of A. chevrieri was 20–27.5 °C. Mean body temperatures of the two species were 35.75±0.5 and 36.54±0.61 °C. Basal metabolic rates (BMR) were 1.92±0.17 and 2.7±0.5 ml O₂/g h, respectively. Average minimum thermal conductance (C_m) were 0.23±0.08 and 0.25±0.06 ml O₂/g h °C. EWL in E. miletus and A. chevrieri increased with the increase in temperature; the maximal EWL at 35 °C was 4.78±0.6 mg H₂O/g h in E. miletus, and 5.92±0.43 mg H₂O/g h in A. chevrieri. Percentage of evaporative heat loss to total heat production (EHL/HP) increased with the increase in temperature; the maximal EHL/HP was 22.45% at 30 °C in E. miletus, and in A. chevrieri it was 19.96% at 27.5 °C. The results may reflect features of small rodents in the Hengduan mountains region: both E. miletus and A. chevrieri have high levels of BMR and high levels of total thermal conductance, compared with the predicted values based on their body masses, while their body temperatures are relatively low. EWL plays an important role in temperature regulation.     

A convenient synthesis of phosphine-functionalized N-heterocyclic carbene ligand precursors, structural characterization of their palladium complexes and catalytic application in Suzuki coupling reaction

A series of imidazolium chlorides as ligand precursors, L · HCl (L = (1-R)-(3-diphenylphosphanylethyl)-imidazol-2-ylidene; R = aryl, benzyl, naphthylmethyl), for the phosphine-functionalized N-heterocyclic carbene (NHC), L, were prepared by a convenient synthetic procedure of reacting 1,2-dichloroethane with appropriate N-substituted imidazoles to give (β-chloroethyl)imidazolium chlorides, which were subsequently reacted with HPPh₂ producing L · HCl in good yield. Palladium complexes of L, PdLCl₂ (4), were prepared by a one pot reaction of PdCl₂, sodium acetate, and L · HCl in DMSO. Complexes 4b (R = naphthylmethyl) and 4e (R = m-methoxybenzyl) were characterized by X-ray crystallography. Catalytic studies have shown that the palladium complexes are efficient in Suzuki coupling reactions of aryl bromides with phenylboronic acid.     

Purification and characterization of YxeI, a penicillin acylase from Bacillus subtilis

The paper reports the purification and characterization of the first penicillin acylase from Bacillus subtilis. YxeI, the protein annotated as hypothetical, coded by the gene yxeI in the open reading frame between iol and hut operons in B. subtilis was cloned and expressed in Eshcherichia coli, purified and characterized. The purified protein showed measurable penicillin acylase activity with penicillin V. The enzyme was a homotetramer of 148 kDa. The apparent K_m of the enzyme for penicillin V and the synthetic substrate 2-nitro-5-(phenoxyacetamido)-benzoic acid was 40 mM and 0.63 mM, respectively, and the association constants were 8.93 × 10² M⁻¹ and 2.51 × 10⁵ M⁻¹, respectively. It was inhibited by cephalosporins and conjugated bile salts, substrates of the closely related bile acid hydrolases. It had good sequence homology with other penicillin V acylases and conjugated bile acid hydrolases, members of the Ntn hydrolase family. The N-terminal nucleophile was a cysteine which is revealed by a simple removal of N-formyl-methionine. The activity of the protein was affected by high temperature, acidic pH and the presence of the denaturant guanidine hydrochloride.     

Aminocarboxylate complexes of vanadium(III): Electronic structure investigation by high-frequency and -field electron paramagnetic resonance spectroscopy

Aminocarboxylate complexes of vanadium(III) are of interest as models for biologically and medicinally relevant forms of this interesting and somewhat neglected ion. The V(III) ion is paramagnetic, but not readily suited to conventional EPR, due to its integer-spin ground state (S = 1) and associated large zero-field splitting (zfs). High-frequency and -field EPR (HFEPR), however, has the ability to study such systems effectively. Three complexes, all previously structurally characterized: Na[V(trdta)] · 3H₂O, Na[V(edta)(H₂O)] · 3H₂O, and [V(nta)(H₂O)₃] · 4H₂O (where trdta stands for trimethylenediamine-N,N,N′,N′-tetraacetate and nta stands for nitrilotriacetate) were studied by HFEPR. All the investigated complexes produced HFEPR responses both in the solid state, and in aqueous solution, but those of [V(nta)(H₂O)₃] · 4H₂O were poorly interpretable. Analysis of multi-frequency HFEPR spectra yielded a set of spin Hamiltonian parameters (including axial and rhombic zfs parameters: D and E, respectively) for these first two complexes as solids: Na[V(trdta)] · 3H₂O: D = 5.60 cm⁻¹, E = 0.85 cm⁻¹, g = 1.95; Na[V(edta)(H₂O)] · 3H₂O: D = 1.4 cm⁻¹, E = 0.14 cm⁻¹, g = 1.97. Spectra in frozen solution yielded similar parameters and showed multiple species in the case of the trdta complex, which are the consequence of the flexibility of this ligand. The EPR spectra obtained in frozen aqueous solution are the first, to our knowledge, of V(III) in solution in general and show the applicability of HFEPR to these systems. In combination with very insightful previous studies of the electronic absorption of these complexes which provided ligand-field parameters, it has been possible to describe the electronic structure of V(III) in [V(trdta)]⁻ and [V(edta)(H₂O)]⁻; the quality of data for [V(nta)(H₂O)₃] does not permit analysis. Qualitatively, six-coordinate V(III) complexes with O,N donor atoms show no electronic absorption band in the NIR region, and exhibit relatively large magnitude zfs (D ? 5 cm⁻¹), while analogous seven-coordinate complexes do have a NIR absorption band and show relatively small magnitude zfs (D < 2 cm⁻¹).     

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.