Functional roles of the N-terminal amino acid residues in the Mn(II)-L- malate binding and subunit interactions of pigeon liver malic enzyme

Pigeon liver malic enzyme has an N-terminal amino acid sequence of Met- Lys-Lys-Gly-Tyr-Glu-. In this work, various mutants of the enzyme with individual or combinational deletion (delta) or substitution at these amino acids were constructed and functionally expressed in Escherichia coli cells. A major protein band corresponding to an Mr of approximately 65000 was observed for all recombinant enzymes in sodium dodecyl sulfate polyacrylamide gel electrophoresis. However, when examining by polyacrylamide gel electrophoresis under native conditions, the recombinant enzymes were found to possess a tetrameric structure with Mr approximately 260000 or a mixture of tetramers and dimers with the exception of delta(K2K3G4) and delta(1-16) mutants, which existed exclusively as dimers at the protein concentration we employed. K3A and K3E also dissociated substantially. K(2,3)A was a tetramer but K(2,3)E essentially existed as dimers. All tetramers and dimers were enzymatically active in the gels. All mutants displayed a similar apparent Km value for NADP+. The apparent Km for L-malate and Mn(II), on the other hand, was increased by 4-27-fold for the delta(K2/K3) and the delta(1-16) mutants. The small binding affinity of delta(K2/K3) with Mn(II)-L-malate was specific. With additional deletion at positions 3 and/or 4, the delta(K2K3), delta(K2G4/K3G4) or delta(K2K3G4) mutants exhibited similar kinetic properties for the wild type. The lysine residues at the positions 2 or 3 seem to be crucial for the correct active site conformation. The results indicate that the N-terminus of malic enzyme is located at the Mn(II)-L-malate binding domain of the active center and is also near the subunit's interface. These results were interpreted with our asymmetric double-dimer model for the enzyme in which the N-terminus was involved in the head-to-tail monomer-monomer interactions but not the dimer-dimer interactions.      

Studies on enzymatic activity and conformational stability of muscle acylphosphatase mutated at conserved lysine residues

An oligonucleotide-directed mutagenesis study was carried out on the fiveacylphosphatase conserved lysine residues to assess their possibleparticipation in enzyme active site formation and their contribution to theenzyme conformational stability. The study was designed to eliminate theambiguity arising from the presence of a sulfate ion, an enzyme competitiveinhibitor, bound to lysine 32 and 68 in the crystal structure of theerythrocyte isoenzyme. Furthermore, previous kinetic studies suggested thepresence of residues with pKa=7.9 and 11, tentatively identified as twolysines. The kinetic parameters for the mutants under investigation are notsignificantly different from those of the wild-type enzyme, demonstratingthat none of the lysine residues are involved in catalysis or in substratebinding. In addition, thermal and urea denaturation experiments performedby circular dichroism indicate that the mutated lysine residues do not playa significant role in the enzyme structural stabilization, as thedestabilizing energy averages 1.40 kJ/mol. Such results are in agreementwith those obtained with other proteins indicating that lysine residuesmake little contribution to the stability of the native structure.     

Processing of N-terminal unnatural amino acids in recombinant human interferon-beta in Escherichia coli

Incorporation of unnatural amino acids into recombinant proteins represents a powerful tool for protein engineering and protein therapeutic development. While the processing of the N-terminal methionine (Met) residues in proteins is well studied, the processing of unnatural amino acids used for replacing the N-terminal Met remains largely unknown. Here we report the effects of the penultimate residue (the residue after the initiator Met) on the processing of two unnatural amino acids, L-azidohomoalanine (AHA) and L-homopropargylglycine (HPG), at the N terminus of recombinant human interferon-beta in E. coli. We have identified specific amino acids at the penultimate position that can be used to efficiently retain or remove N-terminal AHA or HPG. Retention of N-terminal AHA or HPG can be achieved by choosing amino acids with large side chains (such as Gln, Glu, and His) at the penultimate position, while Ala can be selected for the removal of N-terminal AHA or HPG. Incomplete processing of N-terminal AHA and HPG (in terms of both deformylation and cleavage) was observed with Gly or Ser at the penultimate position.     

The central enzymes of the aspartate family of amino acid biosynthesis

The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and microorganisms. The absence of this pathway in humans and animals makes the central enzymes potential targets for inhibition, with the aim of developing new herbicides and biocides, and also for enhancement, to improve the nutritional value of crops. Our current state of knowledge of these enzymes is reviewed, including recently determined structural information and newly constructed bifunctional fusion enzymes.     

Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris

A human lysozyme expression system by Pichia pastoris was constructedwith the expression vector of pPIC9, which contains the     

氨基酸分析在重组蛋白类生物制品质量控制中的应用

氨基酸分析是蛋白质一级结构分析的有力工具,氨基酸分析在重组蛋白类生物制品的质量控制中发挥着重要作用,其应用主要包括:氨基酸含量及组成分析、蛋白精确定量及消光系数计算,为重组蛋白的结构确证及功能研究提供依据。本文就氨基酸分析在重组蛋白类生物制品质量控制中的应用作一综述。     

Contribution of the C-terminal amino acid to the stability of Bacillus subtilis neutral protease

The role of the C-terminal Leu300 in maintaining thermal stabilityof the neutral protease of Bacillus subtilis was investigated.From model building studies based on the three dimensional structureof thermolysin, the neutral protease of B.thermoproteolyticus,it was conduded that this residue is located in a hydrophobicpocket composed of residues located in the C-terminal and themiddle domain. To test the hypothesis that Leu300, by contributingto a stabilizing interaction between these domains, is importantfor enzyme stability, several neutral protease mutants wereconstructed and characterized. The thermostability of the enzymewas lowered by deleting Leu300 or by replacing this residueby a smaller (Ala), a polar (Asn) or a sterically unfavourable(He) amino acid. Thermostabiity was increased upon replacingLeu300 by Phe. These results are in agreement with model-buildingstudies. The effects on thermostability observed after mutatingthe corresponding Val318 in the thermostable neutral proteaseof B.stearothermophilus were less pronounced.     

Synthesis and solution properties of a new pH-responsive polymer containing amino acid residues

The amine salt, N,N-diallyl-N-carboethoxymethylammonium chloride was cyclopolymerized in water using ammonium persulfate as an initiator to afford a cationic polyelectrolyte which on acidic hydrolysis of the pendant ester groups gave the corresponding cationic acid salt (CAS). The CAS was converted into an anionic polyelectrolyte (APE) and polybetaine (PB). The solution properties of the APE having two basic functionalities were investigated in detail by potentiometric and viscometric techniques. Basicity constants of the amine as well as the carboxylate groups in APE are ‘apparent’ and as such follow the modified Henderson-Hasselbalch equation; as the degree of protonation (α) of the whole macromolecule increases, the protonation of the amine nitrogens and carboxylate groups becomes increasingly more difficult and easier, respectively. While the APE, PB and CAS were found to be soluble in salt-free water, the corresponding PB and CAS of the SO₂ copolymers of the amine salt 1 were found to be insoluble in water.     

Phospholipids and component fatty acids of the pigeon liver

The phospholipids from the livers of adult pigeons were separated by thin layer chromatography and the component fatty acids analyzed by gas liquid chromatography. They consisted of 53.0% phosphatidylcholine, 26.3% phosphatidylethanolamine, 8.6% sphingomyelin, 6.3% cardiolipin and 4.8% lysophosphatidylcholine. Phosphatidylethanolamine and phosphatidylcholine were characterized by a high concentration of long-chain polyunsaturated fatty acids with the highest percentages in the phosphatidylethanolamine. Sphingomyelin contained up to 64.5% saturated acids. About 80% of the fatty acids present in the cardiolipin fraction consisted of linoleic acid. The liver phospholipids had the same composition in lactating as in nonlactating pigeons, but differed in many respects from those available in the crop-milk.     

Single amino acid substitutions can further increase the stability of a thermophilic L-lactate dehydrogenase

Lactate dehydrogenases are of considerable interest as stereospecificcatalysts in the chemical preparation of enantiomerically pure-hydroxyacid synthons. For such applications in synthetic organicchemistry it would be desirable to have enzymes which tolerateelevated temperatures for prolonged reaction times, to increaseproductivity and to extend then applicability to poor substrates.Here, two examples are reported of significant thermostabilizations,induced by sitedirected mutagenesis, of an already thermostableprotein, the L-lactate dehydrogenase (EC 1.1.1.27 [EC] , 35 kDa permonomer subunit) from Bacillus stearothermophilus. Thermal inactivationof this enzyme is accompanied by irreversible unfolding of thenative protein structure. The replacement of Argl71 by Tyr stabilizesthe enzyme against thermal inactivation and unfolding. Thisstabilizing effect appears to be based on improved interactionsbetween the subunits in the core of the active dimeric or tetramericforms of the enzyme. The thermal stability of L-lactate dehydrogenasevariants with an active site Arg residue, either in the 171(wild-type) or in the 102 position, is further increased bysulfate ions. The two stabilizing effects are additive, as foundfor the Argl71Tyr/ Gln1O2Arg double mutant, for which the stabilityof the protein in 100 mM sulfate solution reaches that of L-lactatedehydrogenases from extreme thermophiles. All mutant proteinsretain significant catalytic activity, both in the presenceand absence of stnhilfoing salts, and are viable catalysts inpreparative scale reactions.     

Synthesis and characterization of biodegradable and biocompatible amphiphilic block copolymers bearing pendant amino acid residues

Polylactide (PLA)-based biodegradable and biocompatible amphiphilic block copolymers bearing pendant amino acid residues were synthesized through a relatively easy and efficient way. The composition and structure of these copolymers were characterized by gel permeation chromatography (GPC) and ¹H nuclear magnetic resonance (¹H NMR) spectroscopy. The self-assembly behavior of the copolymers was investigated by fluorescence (FL), dynamic light scattering (DLS), and transmission electron microscope (TEM). It was shown that aggregates less than 100 nm in average size were formed by these copolymers, which changed from micelles to vesicles with the variation of the block length. In addition, the in vitro cytotoxicity of these copolymers was determined and compared with that of PEO-b-PLA in the presence of Bel-7402 cells. The result suggested that the block copolymers PAGE/cys-b-PLA exhibited better biocompatibility. Therefore, these PLA-based copolymers are expected to find promising applications in drug delivery or tissue engineering.     

Inhibition of mild steel corrosion in hydrochloric acid medium by polymeric inhibitors containing residues of essential amino acid methionine

Ethyl ester hydrochloride of amino acid l-methionine 1 was converted to cationic monomers N,N-diallyl methionine ethyl ester hydrochloride 2 and hydrochloride salt of N,N-diallylmethionine 3. Cationic monomers 2 and 3 underwent alternate copolymerization with SO₂ in dimethyl sulfoxide to give terpolymers 4 and 5, respectively, both having?≈?1:1 ratio of sulfide and sulfoxide motifs owing to O transfer from dimethyl sulfoxide to the S. The sulfide groups in 5 have been oxidized with H₂O₂ to give polymer sulfoxide 6. In the presence of a small concentration of 35.2 µM (~?11?±?1 ppm) of each of the polymers 4, 5 and 6, the inhibition efficiency against mild steel corrosion in 1.0 M HCl at 60 °C was determined to be 90.8, 98.7 and 93.0%, respectively. The inhibition efficiency obtained from gravimetric weight loss was corroborated by the findings of potentiodynamic polarization and electrochemical impedance spectroscopy methods. Adsorption of polymer compounds onto the mild steel surface followed a mixture of chemisorption and physisorption processes and obeyed Langmuir, Temkin and Freundlich adsorption isotherms. The X-ray photoelectron spectroscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy techniques further confirmed that the synthesized compounds formed a protective film onto the metal surface and prove it against further corrosion attack.     

Macromolecular recognition by cyclodextrins. Interaction of cyclodextrins with polymethacrylamides bearing hydrophobic amino acid residues

The interaction of cyclodextrins (CDs) with poly(N-methacryloyltryptophan) (pMTrp) and with poly(N-methacryloylphenylalanine) (pMPhe) was investigated as a simple model system of macromolecular recognition of proteins. The association constants (K) for the model compounds, sodium salts of tryptophan and phenylalanine, are not so different (i.e. 43 and 16 M⁻¹ for α-CD, 59 and 69 M⁻¹ for β-CD, and 12 and 3 M⁻¹ for γ-CD, respectively). On the other hand, there is a significant difference in the apparent K values for pMTrp and pMPhe (i.e. the K values for pMPhe are considerably smaller than ca. 10 M⁻¹, whereas those for pMTrp are 30, 83, and 11 M⁻¹ for α-, β-, and γ-CDs, respectively). These observations indicate that a subtle difference in polymer side chains can be critical in macromolecular recognition.     

Examination of Portland cement paste hydrated in the presence of malic acid

When malic acid (MA) solutions are added to ordinary Portland cement (OPC), rapid heat evolution takes place, but the hydration is retarded considerably at all the MA concentrations. To understand the mechanism of retardation, UV-visible and IR spectral studies were made and the results have revealed that some interaction occurs between MA and certain constituents of OPC. X-ray diffraction (XRD) and thermogravimetric (TG)/differential thermal analysis (DTA) studies have proved the formation of a new reaction product due to interaction between MA and some of the mineral phases of Portland cement. The retardation of the hydration of Portland cement may be attributed to the formation of this new compound.     

Engineered disulfide bonds in recombinant human interferon-{gamma}: the impact of the N-terminal helix A and the AB-loop on protein stability

Insertion sites for cysteines with optimal stereochemistry forthe formation of unstrained disulfide bridges were identifiedin recombinant human interferon- (rhu-IFN-) by computer modelling.We have engineered two different disulfide cross-linked mutants,containing a pair of symmetry-related disulfide bonds, whichstabilize the N-termini of both monomers of the homodimenc protein.Mutations E7C and S69C allow the formation of an intramonomerdisuffide bond between helices A and D. In contrast, the A17Cand H111C mutations lead to a covalent cross-link between bothmonomers. The AB-loop is linked to helix F. The fluorescenceproperties of native and disulfide cross-linked proteins werestudied as a function of guanidine hydrochloride concentration.Melting temperatures (T_m) were calculated from the decreasein CD ellipticity at 220 nm. The induction of the antiviraleffect was measured using A549 fibroblast cells infected withencephalomyocarditis virus. The ability to induce the expressionof the HLA-DR antigen in Colo 205 cells was determined by fluorescence-activatedcell scanning analysis. The stability of both mutants was stronglyenhanced against temperature- and cosolvent-induced unfolding.The T_m of mutant IFN- E7C/S69C was 15°C. All measured biologicalactivities of this mutant were equal to wild type. In the caseof the other mutant IFN- A17C/H111C, the T_m value was 25°C.This mutation abolishes nearly the entire biological activity(<1%) with no detectable changes of secondary structure inthe CD spectrum. Our results illustrate the importance of theN-terminal helix A and the AB-loop for the unfolding pathwayand thermodynamic stability of rhu-IFN-.     

Analysis and prediction of the location of catalytic residues in enzymes

The catalytic residues of an enzyme are defined as the aminoacids directly involved in chemical catalysis. They mainly actas a general acid–base, electrophilic or nucleophiliccatalyst or they polarize and stabilize the transition state.An analysis of the structural features of 36 catalytic residuesin 17 enzymes of known structure and with defined mechanismis reported. Residues that bind metal ions (Zn² and Cu²) areconsidered separately. The features examined are: residue type,location in secondary structure, separation between the residues,accessibility to solvent, intra-protein electrostatic interactions,mobility as evaluated from crystallographic temperature factors,polarity of the environment and the sequence conservation betweenhomologous enzymes of residues that were sequentially or spatiallyclose to the catalytic residue. In general the environment ofcatalytic residues is similar to that of polar side chains thathave low accessibility to solvent. Two algorithms have beendeveloped to identify probable catalytic residues. Scanningan alignment of homologous enzyme sequences for peaks of sequenceconservation identifies 13 out of the 16 catalytic residueswith 50 residues overpredicted. When the conservation of thespatially close residues is used instead, a different set of13 residues are identified with 47 residues overpredicted. Acombination of the two algorithms identifies 11 residues with36 residues overpredicted.     

Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme

To elucidate correlative relationships between structural changeand thermodynamic stability in proteins, a series of mutanthuman lysozymes modified at two buried positions (Ile56 andIle59) were examined. Their thermodynamic parameters of denaturationand crystal structures were studied by calorimetry and X-raycrystallography. The mutants at positions 56 and 59 exhibiteddifferent responses to a series of amino acid substitutions.The changes in stability due to substitutions showed a linearcorrelation with changes in hydrophobicity of substituted residues,having different slopes at each mutation site. However, thestability of each mutant was found to be represented by a uniqueequation involving physical properties calculated from mutantstructures. By fitting present and previous stability data formutant human lysozymes substituted at various positions to theequation, the magnitudes of the hydrophobicity of a carbon atomand the hydrophobicity of nitrogen and neutral oxygen atomswere found to be 0.178 and –0.013 kJ/mol.Ų, respectively.It was also found that the contribution of a hydrogen bond witha length of 3.0 Å to protein stability was 5.1 kJ/moland the entropy loss of newly introduction of a water moleculeswas 7.8 kJ/mol.     

Random exchanges of non-conserved amino acid residues among four parental termite cellulases by family shuffling improved thermostability

There have been two major problems preventing applications of termite cellulases; one was difficulty for their hetelologous overexpression, and another is their low thermostability. We previously achieved adaptation of termite cellulase genes to an overexpression system of Escherichia coli by family shuffling of four orthologous cDNAs (Biosci. Biotechnol. Biochem., 2005; 69: 1711-1720). Using the adapted mutant cDNAs as parental genes combined with native-form cDNAs, we performed further family shuffling and obtained mutant cDNAs, which gave enzymes with improved thermostability. The best-evolved clone (PA68) was improved by 10 degrees C in maximum stability (retaining 90% original activity for 30 min incubation) from the parental enzymes, and kept 54% of its original activity for 150 min at 50 degrees C, whereas the most thermostable enzyme amongst the parents (A18) retained 30% of its original activity. PA68 showed 889 (micromoles of reducing sugars/min/mg of protein) in V(max) and 560 (micromoles of reducing sugars/min/mg of protein) in the specific activity against carboxymethylcellulose, which corresponds to 9.8 and 13.1 times of those of one of the ancestral enzymes rRsEG. In summary, we improved thermostability of the termite cellulase and increased the V(max) value and specific activity by combining only cDNAs encoding enzymes adapted for normal temperatures.     

Decreasing the stability and changing the substrate specificity of the Bacillus stearothermophilus alcohol dehydrogenase by single amino acid replacements

The gene encoding the alcohol dehydrogenase (adh-hT) from the thermophilicbacterium Bacillus stearothermophilus LLD-R strain has been overexpressedin Escherichia coli and the corresponding recombinant protein purified tohomogeneity. Two putative structural determinants contributing to thehigher stability of ADH-hT had been identified by comparison with the lessthermostable ADH (ADH-T) from the less thermophilic B. stearothermophilusNCA 1503. In order to ascertain their role, mutations were designed toeliminate in ADH-hT a salt bridge at the N-terminus and a proline residuein the coenzyme binding domain replacing the amino acids located at thesame positions in ADH-T. Three mutants--Glu11Lys, Pro242Ala, andGlu11Lys/Pro242Ala-- were expressed at high level and the proteins purifiedand characterized. In general, the mutations had little effect on theactivity, indicating that they were not disruptive. The thermal resistancewas changed displaying quite additive effects.     

Activities of liver mitochondrial and peroxisomal fatty acid oxidation enzymes in rats fedtrans fat

The effect oftrans fat on the activities of liver mitochondrial and peroxisomal fatty acid oxidation enzymes was examined in various strains of rats. When Wistar and Sprague-Dawley rats were fed for 30 days diets containing either olive oil or partially hydrogenated corn oil as a source ofcis-ortrans-octadecenoate, respectively, the activities of various enzymes of mitochondrial and peroxisomal β-oxidation measured withcis- andtrans-9-octadecenoic acid as substratese showed little dietary fatdependent change. In Fischer 344 rats, feedingtrans fat for 15 mo increased only moderately various enzymes of β-oxidation except for carnitine acyltransferase. The rate of mitochondrial ketogenesis and the activity of carnitine acyltransferase measured withtrans-9-octadecenoic acid as a substrate were about half those with thecis-counterpart. Peroxisomes oxidizedtrans-9-octadecenoyl-CoA at a rate comparable to thecis-counterpart. It was concluded from this study and previous ones that the difference in the geometry of dietary fatty acid had only a marginal effect in modulating the hepatic fatty acid oxidation system, in spite of marked differences in the metabolic behavior ofcis-andtrans fatty acid in cell-free preparations and perfused liver.