A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment

Phosphoenolpyruvate carboxylase (PEPC) catalyzes the irreversible carboxylation of phosphoenolpyruvate (PEP) and plays a crucial role in fixing atmospheric CO(2) in C(4) and CAM plants. The enzyme is widespread in plants and bacteria and mostly regulated allosterically by both positive and negative effectors. Archaeal PEPCs (A-PEPCs) have unique characteristics in allosteric regulation and molecular mass, distinct from their bacterial and eukaryote homologues, and their amino acid sequences have become available only recently. In this paper, we generated a structure-based alignment of archaeal, bacterial and eukaryote PEPCs and built comparative models using a combination of fold recognition, sequence and structural analysis tools. Our comparative modeling analysis identified A-PEPC-specific strong interactions between the two loops involved in both allostery and catalysis, which explained why A-PEPC is not influenced by any allosteric activators. We also found that the side-chain located three residues before the C-terminus appears to play a key role in determining the sensitivity to allosteric inhibitors. In addition to these unique features, we revealed how archaeal, bacterial and eukaryote PEPCs would share a common catalytic mechanism and adopt a similar mode of tetramer formation, despite their divergent sequences. Our novel observations will help design more efficient molecules for ecological and industrial use.     

Engineering disulfide-linked single-chain Fv dimers [(sFv')2] with improved solution and targeting properties: anti-digoxin 26-10 (sFv')2 and anti-c-erbB-2 741F8 (sFv')2 made by protein folding and bonded through C-terminal cysteinyl peptides

Single-chain Fv fusions with C-terminal cysteinyl peptides (sFv')have been engineered using model sFv proteins based upon the26-10 anti-digoxin IgG and 741F8 anti-c-erbB-2 IgG monoclonalantibodies. As part of the 741F8 sFv construction process, thePCR-amplified 741F8 V_H gene was modified in an effort to correctpossible primer-induced errors. Genetic replacement of the N-terminalp-strandsequence of 741F8 VH with that from the FR1 of anti-c-erbB-2520C9 VH resulted in a dramatic improvement of sFv folding yields.Folding in urea-glutathione redox buffers produced active sFv'with a protected C-terminal sulfhydryl, presumably as the mixeddisulfide with glutathione. Disulfide-bonded (sFv')₂ homodimerswere made by disulfide interchange or oxidation after reductiveelimination of the blocking group. Both 26–10 (sFv')₂and 741F8 (sFv')₂ existed as stable dimers that were well behavedin solution, whereas 741F8 sFv and sFv' exhibited considerableself-association. The 741F8 sFv binds to the extracellular domain(ECD) of the c-erbB-2 oncogene protein, which is often overexpressedin breast cancer and other adenocarcinomas. The recombinantECD was prepared to facilitate the analysis of 741F8 bindingsite properties; the cloned ECD gene, modified to encode a C-terminalSer-Gly-His₆ peptide, was transfected into Chinese hamster ovarycells using a vector that also expressed dihydrofolate reductaseto facilitate methotrexate amplification. Optimized cell linesexpressed ECD-His₆ at high levels in a cell bioreactor; afterisolation by immobilized metal affinity chromatography, finalECD yields were as high as 47 mg/l. An animal tumor model complementedphysicochemical studies of 741F8 species and indicated increasedtumor localization of the targeted 741F8 (sFv')₂ over othermonovalent 741F8 species.     

负载型K2CO3/Al2O3二氧化碳吸收剂的碳酸化反应特性

The carbonation characteristics of K₂CO₃/Al₂O₃ supported sorbent for CO₂ capture was investigated with thermogravimetric apparatus（TGA）,X-ray diffraction（XRD）,scanning electron microscopy analysis（SEM）and N₂ adsorption.The results showed that the carbonation rate of K₂CO₃ before being loaded on Al₂O₃ was slow.However,the K₂CO₃/Al₂O₃ upported sorbent showed excellent carbonation performance.The difference in carbonation behavior between K₂CO₃ nd K₂CO₃/Al₂O₃ supported sorbent was analyzed from the microscopic view.The analytical reagent K₂CO₃ sample was of monoclinic crystal structure and could react quickly with H₂O in the experimental carbonation environment to produce K₂CO₃•1.5H₂O,which was unfavorable to carbonation reaction.When K₂CO₃was loaded on Al₂O₃,the surface area and porosity of the sorbent was improved greatly.So the carbonation properties of the K₂CO₃/Al₂O₃ supported sorbent was also improved.     

Cu/Zn/Al/Zr纳米纤维催化剂上的CO2加氢合成甲醇过程

A highly active Cu/Zn/Al/Zr fibrous catalyst was developed for methanol synthesis from CO₂ hydrogenation.Various factors that affect the activity of the catalyst,including the reaction temperature,pressure and space velocity,were investigated.The kinetic parameters in Graaf’s kinetic model for methanol synthesis were obtained.A quasistable economical process for CO₂ hydrogenation through CO circulation was simulated and higher methanol yield was obtained.     

Complexes in the Photocatalytic Reaction of CO(2) and H(2)O: Theoretical Studies

Complexes (H(2)O/CO(2), e-(H(2)O/CO(2)) and h(+)-(H(2)O/CO(2))) in the reaction system of CO(2) photoreduction with H(2)O were researched by B3LYP and MP2 methods along with natural bond orbital (NBO) analysis. Geometries of these complexes were optimized and frequencies analysis performed. H(2)O/CO(2) captured photo-induced electron and hole produced e-(H(2)O/CO(2)) and h(+)-(H(2)O/CO(2)), respectively. The results revealed that CO(2) and H(2)O molecules could be activated by the photo-induced electrons and holes, and each of these complexes possessed two isomers. Due to the effect of photo-induced electrons, the bond length of C=O and H-O were lengthened, while H-O bonds were shortened, influenced by holes. The infrared (IR) adsorption frequencies of these complexes were different from that of CO(2) and H(2)O, which might be attributed to the synergistic effect and which could not be captured experimentally.     

Site-directed mutagenesis and X-ray crystallography of two phospholipase A2 mutants: Y52F and Y73F

Tyr52 and Tyr73 are conserved amino acid residues throughoutall vertebrate phospholipases A₂. They are part of an extendedhydrogen bonding system that links the N-terminal -NH⁺₃ -groupto the catalytic residues His48 and Asp99. These tyrosines werereplaced by phenylalanines in a porcine pancreatic phospholipaseA₂ mutant, in which residues 62–66 had been deleted (62–66PLA₂).The mutations did not affect the catalytic properties of theenzyme, nor the folding kinetics. The stability against denaturatlonby guanidine hydrochloride was decreased, however. To analysehow the enzyme compensates for the loss of the tyrosine hydroxylgroup, the X-ray structures of the Y52F and AY73F mutants weredetermined. After crystallographic refinement the final crystallographicR-factors were 18.1% for the %Y52F mutant (data between 7 and2.3 Å resolution) and 19.1% for the Y73F mutant (databetween 7 and 2.4 Å resolution). No conformational changesoccurred in the mutants compared with the 62–66PLA₂, butan empty cavity formed at the site of the hydroxyl group ofthe former tyrosine. In both mutants the Asp99 side chain losesone of its hydrogen bonds and this might explain the observeddestabilization.     

O2/CO2气氛下煤燃烧SO2/NO析出特性

在水平管式炉上研究了O₂浓度、CO₂浓度、温度及石灰石添加等各参数对O₂/CO₂气氛下徐州烟煤和龙岩无烟煤燃烧过程中SO₂/NO排放特性的影响。结果发现,O₂/CO₂气氛下,烟煤和无烟煤燃烧SO₂/NO的析出规律与空气气氛下不同,同等O₂浓度下析出量比空气气氛下小。O₂/CO₂气氛下,随着O₂浓度的提高,烟煤和无烟煤SO₂/NO排放量均增大;随着CO₂浓度的升高, SO₂/NO排放量均减小。O₂/CO₂气氛下,石灰石添加对SO₂排放的抑制作用低于空气气氛下;石灰石添加对NO的排放有一定减排作用。对煤灰的元素分析显示O₂/CO₂燃烧对SO₂的抑制主要是由于煤灰的自固硫能力增强,而对NO的减排作用则是促进燃料N向其他含N气体的转换。     

Evidence for the involvement of tyrosine-69 in the control of stereospecificity of porcine pancreatic phospholipase A2

We have studied the role of Tyr-69 of porcine pancreatic phospholipaseA₂ in catalysis and substrate binding, using site-directed mutagenesis.A mutant was constructed containing Phe at position 69. Kineticcharacterization revealed that the Phe-69 mutant has retainedenzymatic activity on monomeric and micellar substrates, andthat the mutation has only minor effects on k_cat and K_m. Thisshows that Tyr-69 plays no role in the true catalytic eventsduring substrate hydrolysis. In contrast, the mutation has aprofound influence on the stereospecificity of the enzyme. Whereasthe wild-type phospholipase A₂ is only able to catalyse thedegradation of sn-3 phospholipids, the Phe-69 mutant hydrolysesboth the sn-3 isomers and, at a low (1–2%) rate, the sn-1isomers. Despite the fact that the stereospecificity of themutant phospholipase has been altered, Phe-69 phospholipasestill requires Ca²⁺ ions as a cofactor and also retains itsspecificity for the sn-2 ester bond. Our data suggest that inporcine pancreatic phospholipase A₂ the hydroxyl group of Tyr-69serves to fix and orient the phosphate group of phospholipidmonomers by hydrogen bonding. Because no such interaction canoccur between the Phe-69 side-chain and the phosphate moietyof the substrate monomer, the mutant enzyme loses part of itsstereospecificity but not its positional specificity.     

Molecular dynamics simulations of phospholipases A2

An extensive molecular dynamics study of phospholipases A₂ frompancreatic bovine and Crotalus atrox venom has shown that thewell-conserved homologous core of the phospholipases A₂, includingthe so called catalytic network, is very stable during the courseof the calculations. The fluctuations which occur are locatedin segments which have significantly different three-dimensionalconformations in the two phospholipases A₂ studied, suggestingthat a particularly stable core conformation gives rise to alarge homologous family of similar three-dimensional structure.The calcium ion, which exhibits a crucial structural role inthe monomeric phospholipases A₂, appears not to be requiredto stabilize the C.atrox dimer. Moreover, the behaviour of thedimeric structure during the dynamics raises the question ofa possible dissociation of the two subunits into functionalmonomers.     

Engineering linear F(ab')2 fragments for efficient production in Escherichia coli and enhanced antiproliferative activity

We developed a novel bivalent antibody fragment, the linear(L-) F(ab')₂, comprising tandem repeats of a heavy chain fragmentV_H–C_H1–V_H–C_H1 cosecreted with a light chain.Functional humanized L-F(ab')₂ directed against p185^HER2 wassecreted from Escherichia coli at high titer (100 mg/l) andpurified to homogeneity. The L-F(ab')₂ binds two equivalentsof antigen with an apparent affinity (K_d = 0.46 nM) that iswithin 3-fold of the corresponding thioether-linked F(ab')₂fragment The N-terminal site binds antigen with an affinity(K_d = 1.2 nM) that is 4-fold greater than that for the C-terminalsite, as shown by the comparison of L-F(ab')₂ variants containinga single functional binding site. L-F(ab')₂ has greater antiproliferativeactivity than the thioether-linked F(ab')₂ against the p185^HER2-overexpressingtumor cell line BT474. Linear and thioether-linked F(ab')₂ havevery similar pharmacokinetic properties in normal mice, andtheir serum permanence times are respectively 7- and 8-foldlonger than the corresponding Fab fragment L-F(ab')₂ offersa facile route to bivalent antibody fragments that are potentiallysuitable for clinical applications, and that may have improvedbiological activity compared with thioether-linked F(ab')₂ fragments.     

Isotope effect of H2/D2 and H2O/D2O for the PROX reaction of CO on the FeOx/Pt/TiO2 catalyst

The oxidation reaction of CO with O₂ on the FeOx/Pt/TiO₂ catalyst is markedly enhanced by H₂ and/or H₂O, but no such enhancement occurs on the Pt/TiO₂ catalyst. Isotope effects were studied by H₂/D₂ and H₂O/D₂O on the FeOx/Pt/TiO₂ catalyst, and almost the same magnitude of isotope effect of ca. 1.4 was observed for the enhancement of the CO conversion by H₂/D₂ as well as by H₂O/D₂O at 60 °C. This result suggests that the oxidation of CO with O₂ via such intermediates as formate or bicarbonate in the presence of H₂O, in which H₂O or D₂O acts as a molecular catalyst to promote the oxidation of CO as described below.      

铜铁尾矿制酸烧渣制备纳米Fe/SiO2核壳复合粒子的微波吸收性能

以铜铁尾矿制酸烧渣为原料,经熟化、酸浸、还原和净化等步骤制备亚铁离子;在乙醇-水液相体系中,以NaBH₄作为还原剂,反应生成纳米Fe粒子;最后通过正硅酸四已酯（TEOS）水解包覆制得纳米Fe/SiO₂核壳复合粒子。产物分别采用XRD、TEM、IR等手段进行表征。进一步地,使用矢量网络分析仪在2.0 ~ 18.0 GHz波段内来研究样品的吸波性能。结果表明,IR光谱上在1389 cm^-1和878 cm^-1分别出现对应于四配位Si—O键和Si—O—Fe键的特征吸收峰,说明在Fe粒子表面包覆有SiO₂。通过测试计算得知,当吸波样品厚度为4.5 mm时,其微波吸收性能在17.2 GHz处达到最小值-39.0 dB。由此可见,以铜铁尾矿制酸烧渣为原料,可制得吸波性能优良的纳米Fe/SiO₂核壳复合粒子微波吸收材料。     

Floral CO2 Reveals Flower Profitability to Moths

The hawkmoth Manduca sexta (Lepidoptera: Sphingidae), an experimentally favorable Lepidopteran that is highly sensitive to carbon dioxide (CO2), feeds on the nectar of a range of flowering plants, such as Datura wrightii (Solanaceae). Newly opened Datura flowers give off dramatically elevated levels of CO2 and offer ample nectar. Thus, floral CO2 emission could indicate food-source profitability. This study documents that foraging Manduca moths prefer surrogate flowers that emit high levels of CO2, characteristic of newly opened Datura flowers. We show for the first time that CO2 may play an important role in the foraging behavior of nectar-feeding insects.     

固体碱K_2CO_3/Al_2O_3催化酯交换法合成乙二醇甲醚乙酸酯

以固体碱K2CO3/Al2O3为催化剂,催化乙酸乙酯和乙二醇甲醚酯交换合成了乙二醇甲醚乙酸酯。考察了反应物摩尔比,催化剂用量,反应时间,催化剂重复使用等因素对反应的影响,结果表明:当n(乙酸乙酯)∶n(乙二醇甲醚)=4∶1,K2CO3/Al2O3用量为总反应物质量的1.0%,反应4.5h时,乙二醇甲醚的转化率为98.8%,选择性为100%;催化剂重复使用5次后,乙二醇甲醚的转化率仅下降3.7%。     

Influence of size and polarity of residue 31 in porcine pancreatic phospholipase A2 on catalytic properties

Residue 31 of porcine pancreatic phospholipase A₂ (PLA₂) islocated at the entrance to the active site. To study the roleof residue 31 in PLA₂, six mutant enzymes were produced by site-directedmutagenesis, replacing Leu by either Trp, Arg, Ala, Thr, Seror Gly. Direct binding studies indicated a three to six timesgreater affinity of the Trp31 PLA₂ for both monomeric and micellarsubstrate analogs, relative to the wild-type enzyme. The otherfive mutants possess an unchanged affinity for monomers of theproduct analog n-decylphosphocholine and for micelles of thediacyl substrate analog rac-l,2-dioctanoylamino-dideoxy-glycero-3-phosphocholine.The affinities for micelles of the monoacyl product analog n-hexadecylphosphocholinewere decreased 9–20 times for these five mutants. Kineticstudies with monomeric substrates showed that the mutants haveV_max values which range between 15 and 70% relative to the wild-typeenzyme. The V_max values for micelles of the zwitterionic substratel,2-dioctanoyl-sn-glycero-3-phosphocholine were lowered 3–50times. The K_m values for the monomeric substrate and the k_mvalues for the micellar substrate were hardly affected in thecase of five of the six mutants, but were considerably decreasedwhen Trp was present at position 31. The results of these investigationspoint to a versatile role for the residue at position 31: involvementin the binding and orientating of monomeric substrate (analogs),involvement in the binding of the enzyme to micellar substrateanalogs and possibly involvement in shielding the active sitefrom excess water.     

Significant enhancement of the oxidation of CO by H2 and/or H2O on a FeO x /Pt/TiO2 catalyst

Oxidation of CO on the FeO _x /Pt/TiO₂ catalyst is markedly enhanced by H₂ and/or H₂O at 60 °C, but no such enhancement is observed on the Pt/TiO₂ catalyst, but shift reaction (CO + H₂O → H₂ + CO₂) does not occur on the FeO _x /Pt/TiO₂ catalyst at 60 °C. DRIFT-IR spectroscopy reveals that the fraction of bridge bonded CO increases while that of linearly bonded CO decreases on the FeO _x loaded Pt/TiO₂ catalyst. The in-situ DRIFT IR spectra proved that the bridged CO is more reactive than the linearly bonded CO with respect to O₂, and the reaction of the bridge-bonded CO with O₂ as well as of the linearly bonded CO is markedly enhanced by adding H₂ to a flow of CO + O₂. From these results, we deduced that the promoting effect of H₂ and/or H₂O is responsible for the preferential oxidation (PROX) reaction of CO on the FeO _x /Pt/TiO₂ catalyst, and a following new mechanism via the hydroxyl carbonyl or bicarbonate intermediate is proposed for the oxidation of CO in the presence of H₂O.      

Influenza virus M2 protein: a molecular modelling study of the ion channel

The influenza A M₂ protein forms cation-selective ion channelswhich are blocked by the anti-influenza drug amantadine. A molecularmodel of the M₂ channel is presented in which a bundle of fourparallel M₂ transbilayer helices surrounds a central ion-permeablepore. Analysis of helix amphipathicity was used to aid determinationof the orientation of the helices about their long axes. Thehelices are tilted such that the N-terminal mouth of the poreis wider than the C-terminal mouth. The channel is lined byresidues V27, S31 and I42. Residues D24 and D44 are locatedat opposite mouths of the pore, which is narrowest in the vicinityof I42. Energy profiles for interaction of the channel withNa⁺, amantadine-H⁺ and cyclopentylamine-H⁺ are evaluated. Theinteraction profile for Na⁺ exhibits three minima, one at eachmouth of the pore, and one in the region of residue S31. Theamantadine-H⁺ profile exhibits a minimum close to S31 and abarrier near residue I42. This provides a molecular model foramantadine-H⁺ block of M₂ channels. The profile for cyclopentylamine-H⁺does not exhibit such a barrier. It is predicted that cyclopentyl-amine-H⁺will not act as an M₂ channel blocker.     

Incorporation of an unnatural amino acid in the active site of porcine pancreatic phospholipase A2. Substitution of histidine by l,2,4-triazole-3-alanine yields an enzyme with high activity at acidic pH

The effect of the substitution of the active site histidine48 by the unnatural 1,2,4-triazole-3-alanine (TAA) amino acidanalogue in porcine pancreas phospholipase A₂ (PLA₂) was studied.TAA was introduced biosynthetically using a his-auxotrophicEscherichia coli strain. To study solely the effect of the substitutionof the active site histidine, two nonessential histidines (i.e.His17 and His 115) were replaced by asparagines, resulting ina fully active mutant enzyme (His-PLA₂). In this His-PLA₂ thesingle histidine at position 48 was substituted by TAA withan incorporation efficiency of about 90%, giving a mixture ofHis-PLA₂ and TAA-PLA₂. Based on the charge difference at acidicpH, both forms could be separated by FPLC, allowing for thepurification of TAA-PLA₂ free from His-PLA₂. At pH 6, TAA-PLA₂has a fivefold reduced activity compared with His-PLA₂. Thisreduced activity paralells a reduced rate of covalent modificationwith p-nitrophenacyl bromide of TAA-PLA₂ compared with His-PLA₂.Competitive inhibition gave comparable IC₅₀ values for WT-PLA₂,His-PLA₂ and TAA-PLA₂. These results indicate that the reductionin activity is not caused by a different affinity for the substrate,but more likely results from a reduced k_cat value in TAA-PLA₂.The enzymatic activities for native and mutant PLA₂s were measuredat different pH values. For WT-PLA₂ and His-PLA₂ the activityis optimal at pH 6 and is strongly deminished at acidic pH,with no observable activity at pH 3. In contrast, TAA-PLA₂ isas active at pH 3 as at pH 6. Most likely, the decrease in activityobserved for WT-PLA₂ and His-PLA₂ is caused by the protonationof the active site His48, which is the general base involvedin the activation of the nucleophilic water molecule. In TAA-PLA₂,however, the active site residue TAA48 is unprotonated at bothpH 3 and 6 as a result of the low pK_a of TAA compared with histidine.     

Adaptability of restrained molecular dynamics for tertiary structure prediction: application to Crotalus atrox venom phospholipase A2

In order to assess the adaptability and/or applicability ofthe restrained molecular dynamics (RMD) simulation for buildinga possible tertiary structure of a protein from the X-ray crystalstructure of a family reference protein, the tertiary structureprediction of Crotalus atrox venom phospholipase A₂ (PLA₂) wasattempted based on the X-ray crystal structure of bovine pancreaticPLA₂. For the formation of secondary and tertiary structuresfrom the fully extended starting structure, the RMD simulationwith interatomic distance restraints and torsion angle restraints,which were derived from homologous amino acid sequence regionsin the reference protein, was carried out until the molecularsystem was fully equilibrated. The predicted tertiary structureof C.atrox venom PLA₂ was compared with its X-ray crystal structure,and furthermore the utility of this method was discussed byreference to the similar tertiary structure prediction of ß-trypsinfrom the X-ray crystal structure of an elastase.     

Kinetic modeling of storage and reduction with different reducing agents (CO, H2, and C2 H4) on a Pt–Ba/-Al2O3 catalyst in the presence of CO2 and H2O

In this paper a global reaction kinetic model is used to understand and describe the NO_x storage/reduction process in the presence of CO₂ and H₂O. Experiments have been performed in a packed bed reactor with a Pt–Ba/γ-Al₂O₃ powder catalyst (1 wt% Pt and 30 wt% Ba) with different lean/rich cycle timings at different temperatures (200, 250, and ) and using different reductants (H₂, CO, and C₂H₄). Model simulations and experimental results are compared. H₂O inhibits the NO oxidation capability of the catalyst and no NO₂ formation is observed. The rate of NO storage increases with temperature. The reduction of stored NO with H₂ is complete for all investigated temperatures. At temperatures above , the water gas shift (WGS) reaction takes place and H₂ acts as reductant instead of CO. At , CO and C₂H₄ are not able to completely regenerate the catalyst. At the higher temperatures, C₂H₄ is capable of reducing all the stored NO, although C₂H₄ poisons the Pt sites by carbon decomposition at . The model adequately describes the NO breakthrough profile during 100 min lean exposure as well as the subsequent release and reduction of the stored NO. Further, the model is capable of simulating transient reactor experiments with 240 s lean and 60 s rich cycle timings.