A comparative study of the adsorption of water and methanol in zeolite BEA: a molecular simulation study

Grand canonical Monte Carlo simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica BEA zeolite and HBEA zeolites with different Si/Al ratios over a wide range of temperatures and loadings. These zeolites have oval-shaped channels with one side longer than the other. Water sorption into the hydrophobic BEA zeolite had a sharp transition with its sorption going from zero to near full capacity over a very small pressure range. Methanol sorption was much more gradual with respect to pressure. With the addition of hydrophilic sites for the HBEA zeolites by decreasing the Si/Al ratio, adsorption at lower pressures increased significantly for water and methanol. At higher loadings, water and methanol adsorption were found to behave in fundamentally different ways. Water structures in the zeolite channels formed hydrogen-bonded chains while maximising contact with the surfaces on the longer edges of the zeolite channels. Methanol molecules, in contrast, formed very few hydrogen bonds between themselves, with their hydroxyl groups primarily binding with surface of the shorter edge of the zeolite channels and their methyl groups located near the middle of the zeolite channels. The addition of hydrophilic groups in the HBEA zeolites strongly influenced positions of the methanol hydroxyl groups at high loadings, but did not have a significant effect on water structure.     

Solubility of cyclomaltooligosaccharides (cyclodextrins) in H2O and D2O: a comparative study

Cyclomaltooligosaccharides (cyclodextrins, CDs) are cyclic oligomers having six, seven, or eight units of alpha-D-glucose, named as cyclomaltohexaose (alpha-CD), cyclomaltoheptaose (beta-CD) and cyclomaltooctaose (gamma-CD), respectively. The molecule of CD has a cavity in which the interior is hydrophobic relative to its outer surface. The solubility of cyclodextrins in water is unusual, as an irregular trend is observed in the series of the cyclic oligomers of glucose. beta-CD is at least nine times less soluble than the others CDs. This intriguing behavior has been investigated, and some interesting explanations in terms of the effect caused by CD on the water lattice structure have been proposed. In this work a comparative study on the solubility of alpha, beta, and gamma-cyclodextrins was carried out in H2O and D2O and reveals a much lower solubility of the three CDs in D2O. The solid-phase structure of the CDs in equilibrium with the solution is quite similar with both solvents. The results are discussed in terms of the CD molecular structure and the differences in the hydrogen bonds formed between H2O and D2O.     

Refolding of lactate dehydrogenase by zeolite beta

We used zeolite beta as an adsorbing matrix to refold recombinant lactate dehydrogenase (LDH) protein collected as an insoluble aggregate from a bacterial expression system. The adsorption isotherm revealed that 1 g of zeolite adsorbed 200 mg of denatured LDH solubilized with a buffer containing 6 M of guanidine hydrochloride. The pH of the buffer had little effect on the adsorption, but this property was abolished by preincubation of the zeolite with polyethylene glycol (PEG) in a weight ratio of 1:10. These data suggest that the adsorption of LDH depends on the hydrophobicity of the zeolite surface, and that the adsorption of PEG to zeolite is sufficient to release LDH from its surface. LDH was thus released by refolding buffer containing PEG and arginine, and soluble LDH was obtained in its active enzymatic form. The addition of arginine dramatically increased the yield of LDH in a dose‐dependent manner. The overall refolding efficiency was optimized to 35%. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Interaction of fusion peptides from HIV gp41 with membranes: a time-resolved membrane binding, lipid mixing, and structural study

The interaction of the so-called fusion peptide of the human immunodeficiency virus gp41 envelope glycoprotein with the target cell membrane is believed to trigger the fusion process which allows the entry of the virus into the cell. Many studies on the interaction of the fusion peptide with biological membranes have been carried out using synthetic peptides and model membranes. Due to the variety of experimental systems and sequences used, some controversy exists, concerning mainly the type of structure which triggers membrane destabilization and fusion (alpha helix or beta structure). With the aim of contributing to shed some light on the subject we have undertaken a series of experiments on the interaction of the three most representative fusion sequences with model membranes under the same experimental conditions. The results show that the fusion peptides, which adopt an unordered structure when dissolved in DMSO, form a mixture of aggregated beta and helical + unordered structures in aqueous buffer. Model membranes are shown to enhance the formation of aggregated beta structures. The nature of the membrane binding event, the kinetics of the binding and lipid mixing processes, and the kinetics of the structural changes depend on whether both ends of the fusion sequence or just one bears a positive charge. Analysis of the kinetic data shows that lipid mixing depends on the transformation of unordered + helical structures into aggregated beta structures upon binding to the membrane.     

Determination of the secondary structure and molecular topology of interleukin-1 beta by use of two- and three-dimensional heteronuclear 15N-1H NMR spectroscopy

A study of the regular secondary structure elements of recombinant human interleukin-1 beta has been carried out using NMR spectroscopy. Using a randomly 15N labeled sample, a number of heteronuclear three- and two-dimensional NMR experiments have been performed, which have enabled a complete analysis of short-, medium-, and long-range NOEs between protons of the polypeptide backbone, based on the sequence-specific resonance assignments that have been reported previously [Driscoll, P. C., Clore, G. M., Marion, D., Wingfield, P. T., & Gronenborn, A. M. (1990) Biochemistry 29, 3542-3556]. In addition, accurate measurements of a large number of 3JHN alpha coupling constants have been carried out by two-dimensional heteronuclear multiple-quantum-coherence-J spectroscopy. Amide NH solvent exchange rates have been measured by following the time dependence of the 15N-1H correlation spectrum of interleukin-1 beta on dissolving the protein in D2O solution. Analysis of these data indicate that the structure of interleukin-1 beta consists of 12 extended beta-strands aligned in a single extended network of antiparallel beta-sheet structure that in part folds into a skewed six-stranded beta-barrel. In the overall structure the beta-strands are connected by tight turns, short loops, and long loops in a manner that displays approximate pseudo-three-fold symmetry. The secondary structure analysis is discussed in the light of the unrefined X-ray structure of interleukin-1 beta at 3-A resolution [Priestle, J. P., Sch?r, H.-P., & Grütter, M. G. (1988) EMBO J. 7, 339-343], as well as biological activity data. Discernible differences between the two studies are highlighted. Finally, we have discovered conformational heterogeneity in the structure of interleukin-1 beta, which is characterized by an exchange rate that is slow on the NMR chemical shift time scale.     

Investigation of the electronic and dynamic properties of sodium and caesium exchanged zeolite by MO and MD simulations

For the pyrochemical reprocessing of spent metallic fuels in molten salt baths it is of importance to investigate the electronic and dynamic properties of the negative elements like Cs in aluminosilicates framework. The molecular orbital simulation has been performed on three types of clusters and 4A-zeolite frameworks with exchangeable alkali-ions containing as significant fission products in order to estimate the geometry optimization, the vibrational frequency factors and the electric densities, etc. These quantum chemical results enable us to conclude that the most stable structure is consistent with the X-ray results. Moreover, the obtained infrared spectrum was reproduced by the experimental results. Furthermore, the molecular dynamics simulation for Na-A and Cs-A zeolites has been carried out at 673 K in order to investigate the dynamics of Na⁺ and Cs⁺ions in Na-A and Cs-A zeolite frameworks. These results revealed that Na I ion in β-cage was more stable than the other Na ions in Na-A zeolite and Cs I ion in α-cage was maintained stability in Cs-A zeolite in consideration of the self-diffusion coefficients.     

The crystal state binding of dithionite to deoxy-hemoglobin.

The crystal state binding of sodium dithionite to deoxyhemoglobin is reported. Dithionite has been used extensively to deoxygenate hemoglobin and myoglobin and there has been considerable interest among users of dithionite about its effect on protein structure and binding site(s). We have determined that dithionite binds to deoxygenated hemoglobin crystals at the interface of two molecules in the crystal lattice. Specific residues involved in hydrogen bonds or salt interactions with dithionite include His116 and His117 of the beta 2 subunit and Lys16 of the alpha 1 subunit of the adjacent hemoglobin molecule. No binding was observed at the symmetry related His116 and 117 beta 1 residues. We have shown that dithionite does not affect the native hemoglobin structure or the binding of several allosteric inhibitors to hemoglobin and can be used to mount T state crystals in the air.     

Structural, kinetic and cytotoxicity aspects of 12-28 beta-amyloid protein fragment: a reappraisal.

A chemical, structural and biological study on the beta-amyloid peptide beta12-28 is reported which was carried out in order to assess the feasibility using this peptide fragment as a model of the natural beta-amyloid protein. The aggregation properties of beta12-28 have been investigated by pulse field-gradient NMR spectroscopy, Fourier transform infrared spectroscopy and transmission electron microscopy. The results obtained suggest that beta12-28 behaviour is comparable to that of the natural beta-amyloid protein although kinetically slower. Translational diffusion coefficients obtained by NMR on an aged beta12-28 solution suggest that the soluble peptide fraction is composed of oligomeric intermediates adopting an extended ellipsoidal assembly rather than a spherical one. The beta12-28 peptide proved to be cytotoxic in PC12 cell cultures as monitored by the MTT assay, although a lack of reproducibility was observed in the dose-response experiments.     

Kinetics and modelling of an alcoholysis reaction catalyzed by cutinase immobilized on NaY zeolite

Fusarium solani pisi recombinant cutinase was immobilized by adsorption on NaY zeolite. The kinetics of the alcoholysis reaction of butyl acetate with hexanol in isooctane catalyzed by cutinase immobilized on NaY zeolite, was studied. The reaction kinetics is suggested to follow a Ping-Pong bi–bi mechanism in which competitive inhibition by excess of alcohols has been identified. No evidence of any significant external diffusional limitation has been detected. The time validation of the model was successfully achieved simultaneously for 15 experimental product evolutions in a batch stirred tank reactor (BSTR) for different initial reactant concentrations.     

Lateral energy transfer model for adjacent light-harvesting antennae rods of C-phycocyanins

Modeling of excitation transfer pathways have been carried out for the structure of Spirulina platensis C-phycocyanin. Calculations by F?rster mechanism using the crystal structure coordinates determined in our laboratory indicate ultra-fast lateral energy transfer rates between pairs of chromophores attached to two adjacent hexamer disks. The pairwise transfer times of the order of a few pico-seconds correspond to resonance transitions between peripheral beta155 chromophores. A quantitative lateral energy transfer model for C-phycocyanin light-harvesting antenna rods that is suggestive to its native structural organization emerges from this study.     

Active enzyme sedimentation, sedimentation velocity, and sedimentation equilibrium studies of succinyl-CoA synthetases of porcine heart and Escherichia coli

Succinyl-CoA synthetases from Escherichia coli and porcine heart muscle have been viewed as prototypes of two classes of the enzyme. The bacterial enzyme has been reported to be an alpha 2 beta 2 tetramer, with many suggestions in the literature for cooperative interactions between active sites that may contribute to its catalytic efficacy. In contrast, gel filtration experiments of others have indicated that the heart enzyme is a simple alpha beta dimer, with no evidence of dimerization or interaction between like sites. All previous estimates of molecular size of these enzymes have been carried out at concentrations that are much higher than those that are used during activity measurements. The present study was carried out to confirm the differences in the quaternary structures of these two species of succinyl-CoA synthetase and to extend our knowledge of these structures to very low concentrations to enable correlation of their subunit structures with their catalytic properties. Conventional sedimentation velocity centrifugation with both enzymes indicates behavior typical of noninteracting globular proteins with no evidence of size heterogeneity. The sedimentation coefficients at infinite dilution (s20,w) have been determined to be 7.04 S and 4.55 S for the E. coli and porcine heart enzymes, respectively. Sedimentation velocity measurements have been extended to very low enzyme concentrations (typical of those used in activity measurements) by active enzyme centrifugation experiments, in which we have determined the rate of sedimentation of a zone of active enzyme through a chromogenic substrate solution.(ABSTRACT TRUNCATED AT 250 WORDS)     

Discovery of novel fatty acid synthase (FAS) inhibitors based on the structure of ketoaceyl synthase (KS) domain

Development of fatty acid synthase (FAS) inhibitors has increasingly attracted much attention in recent years due to their potential therapeutic use in obesity and cancers. In this investigation, pharmacophore modeling based on the first crystal structure of human KS domain of FAS was carried out. The established pharmacophore model was taken as a 3D query for retrieving potent FAS inhibitors from the chemical database Specs. Docking study was further carried out to refine the obtained hit compounds. Finally, a total of 28 compounds were selected based on the ranking order and visual examination, which were first evaluated by a cell line-based assay. Seven compounds that have good inhibition activity against two FAS overexpressing cancer cell lines were further evaluated by an enzyme-based assay. One compound with a new chemical scaffold was found to have low micromolar inhibition potency against FAS, which has been subjected to further chemical structural modification.     

Energy of stabilization of the right-handed beta alpha beta crossover in proteins

An explanation in terms of conformational energies is provided for the observed nearly exclusive preference of the beta alpha beta structure for forming a right-handed, rather than a left-handed, crossover connection. Conformational energy computations have been carried out on a model beta alpha beta structure, consisting of two six-residue Val beta-strands and of a 12-residue Ala alpha-helix, connected by two flexible four-residue Ala links to the strands. The energy of the most favorable right-handed crossover is 15.51 kcal/mol lower than that of the corresponding left-handed cross-over. The right-handed crossover is a strain-free structure. Its energy of stabilization arises largely from the interactions of the two beta-strands with one another and with the alpha-helix. On the other hand, the left-handed crossover is either disrupted after energy minimization or it remains conformationally strained, as indicated by an energetically unfavorable left twisting of the beta-sheet and by the presence of high-energy local residue conformations. In the energetically most favorable right-handed crossover, the right twisting of the beta-sheet and its manner of interacting with the alpha-helix are identical with those computed earlier for isolated beta-sheets and for packed alpha/beta structures. This result supports a proposed principle that it is possible to account for the main features of frequently occurring structural arrangements in globular proteins in terms of the properties of their component structural elements.     

Hydroprocessing of sunflower oil-gas oil blends over sulfided Ni-Mo-Al-zeolite beta composites

Mixtures of sunflower oil and a straight run gas oil in the diesel fuel range were hydroprocessed over sulfided NiO(3%)-MoO3(12%)-γ-Al2O3 incorporating 0, 15 or 30 wt.% zeolite beta (BEA). The studies were carried out at 320-350 °C; 30-60 bars, and weight hourly space velocities (WHSV), 1-4 h(-1). Catalyst containing 30% BEA achieved nearly 100 % conversion of the vegetable oil into hydrocarbons at 330 °C, 60 bars and a WHSV of 2 h(-1) compared to 95.5% by the Ni-Mo-γ-alumina catalyst without BEA. Hydroprocessing with blends containing oleic acid revealed that the catalysts were able to transform the acid into hydrocarbons. An analysis of the ratios of the n-C18 and n-C17 paraffins formed from the vegetable oil at different process conditions revealed that the catalyst containing 15% BEA was most active for hydrodeoxygenation. The gas oil-hydrodesulfurization activity of the Ni-Mo-Al2O3 was enhanced by the addition of BEA by more than 10%.     

Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics

A long-standing problem of molecular biology is the prediction of globular protein tertiary structure from the primary sequence. In the context of a new, 24-nearest-neighbor lattice model of proteins that includes both alpha and beta-carbon atoms, the requirements for folding to a unique four-member beta-barrel, four-helix bundles and a model alpha/beta-bundle have been explored. A number of distinct situations are examined, but the common requirements for the formation of a unique native conformation are tertiary interactions plus the presence of relatively small (but not irrelevant) intrinsic turn preferences that select out the native conformer from a manifold of compact states. When side-chains are explicitly included, there are many conformations having the same or a slightly greater number of side-chain contacts as in the native conformation, and it is the local intrinsic turn preferences that produce the conformational selectivity on collapse. The local preference for helix or beta-sheet secondary structure may be at odds with the secondary structure ultimately found in the native conformation. The requisite intrinsic turn populations are about 0.3% for beta-proteins, 2% for mixed alpha/beta-proteins and 6% for helix bundles. In addition, an idealized model of an allosteric conformational transition has been examined. Folding occurs predominantly by a sequential on-site assembly mechanism with folding initiating either at a turn or from an isolated helix or beta-strand (where appropriate). For helical and beta-protein models, similar folding pathways were obtained in diamond lattice simulations, using an entirely different set of local Monte Carlo moves. This argues strongly that the results are universal; that is, they are independent of lattice, protein model or the particular realization of Monte Carlo dynamics. Overall, these simulations demonstrate that the folding of all known protein motifs can be achieved in the context of a single class of lattice models that includes realistic backbone structures and idealized side-chains.     

Common reeds (Phragmites australis) as sustainable energy source: experimental and modelling analysis of torrefaction and pyrolysis processes

The aim of this study is to apply advanced analytical techniques and kinetic modelling to common reeds (Phragmites australis) to characterize its pyrolysis and torrefaction as possible environmental friendly and sustainable pathways of fuel upgrading. Simultaneous thermogravimetric and differential scanning calorimetry analysis have been carried out on common reeds. The evolved gases during the decomposition process have been analysed by a coupled infrared gas analyser and gas chromatograph/mass spectrometer. Different reed origins (China and Italy) and plant parts (stem and leaves) have been compared. The results have been used to calibrate a torrefaction kinetic model. The model has also been tested simulating a reed torrefaction run occurring in a bench‐scale apparatus, supplementing the chemical analysis with a thermal simulation of the reactor carried out through a finite elements approach. The results show that the proposed modelling approach allows the prediction of the reaction products with a satisfying degree of accuracy. Besides its phytodepuration potential, P. australis has proven to be an interesting natural biomass resource for thermochemical conversion processes and energy production both for its suitability and availability.     

Modelling and refinement of the crystal structure of nucleoprotamine from Gibbula divaricata

The molecular structure of nucleoprotamine from Gibbula divaricata and its packing in oriented fibers has been modelled both to fit the X-ray diffraction pattern and to avoid steric compression. The representative model consists of 51 poly (dinucleotide) B-DNA helices with 51 poly(hexapeptide) chains associated with the major grooves. The prevailing peptide conformation is beta. The four arginine residues present are hydrogen-bonded to DNA phosphates while neutral peptides protrude into the minor grooves of neighboring nucleoprotamine molecules which are packed 2.61 nm apart in a screw-disordered, quasi-hexagonal lattice. This model reconciles a number of earlier, apparently conflicting experimental results and explains the remarkable stability of nucleoprotamines.     

Theoretical Studies of the Electrostatic Effect on Carbocations Adsorbed over Zeolitic Sites

Theoretical studies, at MNDO level, of carbocations adsorbed over a zeolite active site were carried out, taking into account the effect of electrostatic fields. Clusters 1 and 2 were placed between two electrostatic charges of opposite sign. The distance from each charge to the center of the oxygen atom bearing the proton or alkyl group was varied in order to find the minimum in energy. The ionicity, expressed by the decrease in bond order, slightly increased with the inclusion of the charges. A more pronounced effect was observed for a positive charge of +2. The energy of the system decreased with the introduction of electrostatic charges. This fact may be partly explained by the electrostatic interaction between the opposed charges and also to an observed increase in the Si–-O–-Al bond angle, decreasing the steric repulsions between the substituents and the acid site. The bond orders remained high, indicating a predominant covalent character for the adsorption of the carbocations. The calculations are in agreement with experimental data of exchange of polyvalent cations, which pointed to an increase in the acid strength of the zeolite, due to decrease in the electron density in the aluminum atom. This revised version was published online in June 2006 with corrections to the Cover Date.     

负载金属离子的5A 沸石的体外抗菌实验

目的:探讨负载金属离子的5A沸石的体外抗菌作用。方法:选用金黄色葡萄球菌、铜绿假单孢菌、白色念珠菌,利用倍比稀释法对5A沸石组、磺胺嘧啶银组及载不同浓度Ag+、Zn2+5A沸石共15组进行了体外抗菌试验研究,确定最佳抗菌效果离子负载方案。结果:三种细菌的MIC,双金属离子负载在抗菌上具有协同载Ag+5A沸石分别达到了125μg/ml~500μg/ml、31.25μg/ml~500μg/ml、250μg/ml~500μg/ml;附载Zn2+5A沸石分别达到了12.5mg/ml~25mg/ml、6.25mg/ml~50mg/ml、25mg/ml;负载双离子5A沸石分别为250μg/ml~500μg/ml、62.5μg/ml~500μg/ml、500μg/ml。结论:5A沸石负载金属离子后均具有抗菌作用,且抗菌作用与附载金属离子的量正相关;负载相同质量Ag+的5A沸石较附载Zn2+者具有更强的抗菌作用;双金属离子负载在抗菌上具有协同作用;2%Ag++8%Zn2+与2%Ag++10%Zn2+及4%载银组与阳性对照组无显著性差异。     

Probing multiple effects on 15N, 13C alpha, 13C beta,and 13C' chemical shifts in peptides using density functional theory

We have used density functional calculations on model peptides to study conformational effects on (15)N, (13)C alpha, (13)C beta, and (13)C' chemical shifts, associated with hydrogen bonding, backbone conformation, and side-chain orientation. The results show a significant dependence on the backbone torsion angles of the nearest three residues. Contributions to (15)N chemical shifts from hydrogen bonding (up to 8 ppm), backbone conformation (up to 13 ppm), side-chain orientation and neighborhood residue effects (up to 22 ppm) are significant, and a unified theory will be required to account for their behavior in proteins. In contrast to this, the dependence on sequence and hydrogen bonding is much less for (13)C alpha and (13)C beta chemical shifts (<0.5 ppm), and moderate for carbonyl carbon shifts (<2 ppm). The effects of side-chain orientation are mainly limited to the residue itself for both nitrogen and carbon, but the chi(1) effect is also significant for the nitrogen shift of the following residue and for the (13)C' shift of the preceding residue. The calculated results are used, in conjunction with an additive model of chemical shift contributions, to create an algorithm for prediction of (15)N and (13)C shifts in proteins from their structure; this includes a model to extrapolate results to regions of torsion angle space that have not been explicitly studied by density functional theory (DFT) calculations. Crystal structures of 20 proteins with measured shifts have been used to test the prediction scheme. Root mean square deviations between calculated and experimental shifts 2.71, 1.22, 1.31, and 1.28 ppm for N, C alpha, C beta, and C', respectively. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement.