Biochemical characterization of peptidyl carrier protein (PCP), the thiolation domain of multifunctional peptide synthetases

Background: A structurally diverse group of bioactive peptides is synthesized by peptide synthetases which act as templates for a growing peptide chain, attached to the enzyme via a thloester bond. The protein templates are composed of distinctive substrate-activating modules, whose order dictates the primary structure of the corresponding peptide product. Each module contains defined domains that catalyze adenylation, thioester and peptide bond formation, as well as substrate modifications. To show that a putative thiolation domain (PCP) is involved in covalent binding and transfer of amino aryl residues during non-ribosomal peptide synthesis, we have cloned and biochemically characterized that region of tyrocidine synthetase 1, TycA.Results: The 327-bp gene fragment encoding PCP was cloned using its homology to the genes for the acyl carrier proteins of fatty acid and polyketide biosynthesis. The protein was expressed as a His₆, fusion protein, and purified in a single step by affinity chromatography. Incorporation of β-[³H]alanine, a precursor of coenzyme A, demonstrated the modification of PCP with the cofactor 4′-phosphopantetheine. When an adenylation domain is present to supply the amino adenylate moiety, PCP can be acylated in vitro.Conclusions: PCP can bind covalently to the cofactor phosphopantetheine and can subsequently be acylated, strongly supporting the multiple carrier model of non-ribosomal peptide synthesis. The adenylation and thiolation domains can each act as independent multifunctional enzymes, further confirming the modular structure of peptide synthees, and can also perform sequential steps in trans, as do multienzyme complexes.     

Exploring the substrate specificity of OxyB, a phenol coupling P450 enzyme involved in vancomycin biosynthesis

OxyB is a cytochrome P450 enzyme that catalyzes the first oxidative phenol coupling reaction during vancomycin biosynthesis. The preferred substrate is a linear peptide linked as a C-terminal thioester to a peptide carrier protein (PCP) domain of the glycopeptide antibiotic non-ribosomal peptide synthetase. Previous studies have shown that OxyB can efficiently oxidize a model hexapeptide-PCP conjugate (R-Leu(1)-R-Tyr(2)-S-Asn(3)-R-Hpg(4)-R-Hpg(5)-S-Tyr(6)-S-PCP) (Hpg = 4-hydroxyphenylglycine) into a macrocyclic product by phenolic coupling of the aromatic rings in residues-4 and -6. In this work, the substrate specificity of OxyB has been explored using a series of N-terminally truncated peptides related in sequence to this model hexapeptide-PCP conjugate. Deletion of one or three residues from the N-terminus afforded a penta- (Ac-Tyr-Asn-Hpg-Hpg-Tyr-S-PCP) and a tri- (Ac-Hpg-Hpg-Tyr-S-PCP) peptide that were also efficiently transformed into the corresponding macrocyclic cross-linked product by OxyB. The tripeptide, representing the core of the macrocycle in vancomycin created by OxyB, is thus sufficient, as a thioester with the PCP domain, for phenol coupling to occur. The related tetrapeptide-PCP thioester was not cyclized by OxyB, neither was a related model hexapeptide containing tryptophan in place of tyrosine-6, nor were tripeptides (related to the natural product K-13) with the sequence Ac-Tyr-Tyr-Tyr-S-PCP cross-linked by OxyB.     

Study of ITO Glass Electrode Modified with Iron Oxide Nanoparticles and Nafion for Glucose Biosensor Application

In this study, we report the fabrication of the indium tin oxide (ITO) glass electrode modified with iron oxide nanoparticles (IONPs) and nafion for glucose biosensor applications. The IONPs was synthesized using the precipitation method and functionalized with citric acid (CA) to provide hydrophilic surface and functional group for glucose oxidase (GOx) enzyme immobilization. The structural and morphological studies of CA-IONPs were characterized using X-ray diffractometer (XRD) and transmission electron microscope (TEM). The size of the IONPs measured from TEM image was ∼17 nm. The bioelectrode designated as Nafion/GOx/CA-IONPs/ITO was developed by drop casting of the CA-IONPs, GOx and nafion on the ITO glass. The Nafion/GOx/CA-IONPs/ITO bioelectrode showed good electrochemical performance for glucose detection. The functionalized CA-IONPs acted as the catalyst and help to improve the electron transfer rate between GOx and ITO electrode. In addition, thin nafion film was coated on the electrode to prevent interference and improve chemical stability. The Nafion/GOx/CA-IONPs/ITO bioelectrode showed high sensitivity of 70.1 μAmM^-1cm^-2 for the linear range of 1.0-8.0 mM glucose concentrations.     

Isolation and characterization of an antibacterial peptide fraction from the pepsin hydrolysate of half-fin anchovy (Setipinna taty)

Enzymatic proteolysis of food proteins is considered a promising method to generate antibacterial peptides. The objective of the present study was to isolate and characterize peptide fraction from the pepsin hydrolysate of half-fin anchovy (Setipinna taty) with antibacterial activity against Escherichia coli. The most active peptide fraction HAHp2-3-I was isolated by a series of chromatographic methods, including Sephadex G-25 chromatography, reverse high-performance liquid chromatography (RP-HPLC) and Source 5RPC ST. Peptides identification of HAHp2-3-I was carried out using UPLC-LTQ-Orbitrap mass spectrometer. HAHp2-3-I contained five cationic peptides (MLTTPPHAKYVLQW, SHAATKAPPKNGNY, PTAGVANALQHA, QLGTHSAQPVPF and VNVDERWRKL) and three anionic peptides (LATVSVGAVELCY, NPEFLASGDHLDNLQ and PEVVYECLHW). Prediction of peptide secondary structure indicated that these anionic peptides should have extended strand and random coil structures, whereas cationic peptides PTAGVANALQHA and VNVDERWRKL could form alpha helixes. In addition, results of scanning electron microscopy (SEM) revealed that treatment by HAHp2-3-I could cause the morphological changes of E. coli and destruction of the cell integrity via irreversible membrane damage. The results could provide information for investigating the antibacterial model of antibacterial peptides derived from fish protein hydrolysates.     

Dipeptide formation on engineered hybrid peptide synthetases

BACKGROUND: Nonribosomal peptide synthetases (NRPSs) are modular 'megaenzymes' that catalyze the assembly of a large number of bioactive peptides using the multiple carrier thiotemplate mechanism. The modules comprise specific domains that act as distinct units to catalyze specific reactions associated with substrate activation, modification and condensation. Such an arrangement of biosynthetic templates has evoked interest in engineering novel NRPSs. RESULTS: We describe the design and construction of a set of dimodular hybrid NRPSs. By introducing domain fusions between adenylation and thiolation (PCP) domains we designed synthetic templates for dipeptide formation. The predicted dipeptides, as defined by the specificity and arrangement of the adenylation domains of the constructed templates, were synthesized in vitro. The effect of the intramolecular fusion was investigated by determining kinetic parameters for substrate adenylation and thiolation. The rate of dipeptide formation on the artificial NRPSs is similar to that of natural templates. CONCLUSIONS: Several new aspects concerning the tolerance of NRPSs to domain swaps can be deduced. By choosing the fusion site in the border region of adenylation and PCP domains we showed that the PCP domain exhibits no general substrate selectivity. There was no suggestion that selectivity of the condensation reaction was biased towards the donor amino acid, whereas at the acceptor position there was a size-determined selection. In addition, we demonstrated that a native elongation module can be converted to an initiation module for peptide-bond formation. These results represent the first example of rational de novo synthesis of small peptides on engineered NRPSs.     

Identification and characterization of a type II peptidyl carrier protein from the bleomycin producer Streptomyces verticillus ATCC 15003.

BACKGROUND: Nonribosomal peptide synthetases (NRPSs) catalyze the assembly of a structurally diverse group of peptides by the multiple-carrier thiotemplate mechanism. All NRPSs known to date are exclusively type I modular enzymes that consist of domains, such as adenylation (A), peptidyl carrier protein (PCP) and condensation (C) domains, for individual enzyme activities. Although several A and PCP domains have been demonstrated to function independently, aminoacylation in trans has been successful only between PCPs and their cognate A domains. RESULTS: We have identified within the bleomycin-biosynthesis gene cluster from Streptomyces verticillus ATCC15003 the blmI gene that encodes a discrete PCP protein. We overexpressed the blmI gene in Escherichia coli, purified the BlmI protein, and demonstrated that apo-BlmI can be efficiently modified into holo-BlmI either in vivo or in vitro by PCP-specific 4'-phosphopantetheine transferases (PPTases). Unlike the PCP domains in type I NRPSs, BlmI lacks its cognate A domain and can be aminoacylated by Val-A, an A domain from a completely unrelated type I NRPS. CONCLUSIONS: BlmI represents the first characterized type II PCP. The BlmI type II PCP, like the PCP domains of type I NRPSs, can be 4'-phospho-pantetheinylated by PCP-specific PPTases but is biochemically distinct in that it can be aminoacylated by an A domain from a completely unrelated type I NRPS. Our results provide for the first time the genetic and biochemical evidence to support the existence of a type II NRPS, which might be useful in the combinatorial manipulation of NRPS proteins to generate novel peptides.     

Phase behavior and the partitioning of caveolin-1 scaffolding domain peptides in model lipid bilayers

The membrane binding and model lipid raft interaction of synthetic peptides derived from the caveolin scaffolding domain (CSD) of the protein caveolin-1 have been investigated. CSD peptides bind preferentially to liquid-disordered domains in model lipid bilayers composed of cholesterol and an equimolar ratio of dioleoylphosphatidylcholine (DOPC) and brain sphingomyelin. Three caveolin-1 peptides were studied: the scaffolding domain (residues 83-101), a water-insoluble construct containing residues 89-101, and a water-soluble construct containing residues 89-101. Confocal and fluorescence microscopy investigation shows that the caveolin-1 peptides bind to the more fluid cholesterol-poor phase. The binding of the water-soluble peptide to lipid bilayers was measured using fluorescence correlation spectroscopy (FCS). We measured molar partition coefficients of 10(4) M(-1) between the soluble peptide and phase-separated lipid bilayers and 10(3) M(-1) between the soluble peptide and bilayers with a single liquid phase. Partial phase diagrams for our phase-separating lipid mixture with added caveolin-1 peptides were measured using fluorescence microscopy. The water-soluble peptide did not change the phase morphology or the miscibility transition in giant unilamellar vesicles (GUVs); however, the water-insoluble and full-length CSD peptides lowered the liquid-liquid melting temperature.     

基于柔性衬底的ZnO葡萄糖酶电极制备及特性

通过水热法在长有ZnO籽晶层的柔性聚酰亚胺(PI)衬底上生长了整齐的ZnO纳米棒,ZnO纳米棒的晶体结构和表面形貌通过X射线衍射(XRD)、扫描电子显微镜(SEM)等进行表征.通过静电吸附方式,将葡萄糖氧化酶(GOx)固定在其表面.分别对GOx及修饰前后的ZnO纳米棒进行了紫外-可见光谱表征,发现修饰后存在ZnO的吸收峰和GOx的特征吸收峰,表明GOx固定在ZnO表面.通过对修饰样品进行傅里叶变换红外(FTIR)光谱测试发现了与GOx相关的吸收峰,这进一步表明GOx仍保持生物活性.最后在循环伏安曲线的测试中,这种在柔性衬底上制备的生物酶电极表现出非常灵敏的电流响应,为制备柔性葡萄糖生物传感器奠定了实验基础.     

Biological Glucose Metabolism Regulated Peptide Self‐Assembly as a Simple Visual Biosensor for Glucose Detection

A glucose oxidase (GOx)‐mediated glucose metabolism was in vitro mimicked and employed to regulate the self‐assembly of peptide‐based building blocks. In this new stimuli‐responsive self‐assembly system, two peptide‐based building blocks, respectively, having aspartic acid (gelator 1 ) and lysine (gelator 2 ) residues were designed and prepared. When adding glucose and GOx to the aqueous solution of gelator 1 or the self‐assembled fibrillar hydrogel of gelator 2 to construct glucose metabolism system, the metabolic product (gluconic acid) can trigger the protonation of the peptide molecules and induce the phase transitions of gelators 1 (sol‐gel) and 2 (gel‐sol). Because this glucose metabolism regulated peptide self‐assembly is built on the oxidation of glucose, it can be used as a simple visual biosensor for glucose detection.     

Ultrahigh-throughput screening system for directed glucose oxidase evolution in yeast cells

A compartmentalized tyramide labeling system (CoaTi) employing flow cytometry for sorting of yeast cells was developed as ultrahigh-throughput screening for Glucose oxidase (GOx) from Aspergillus niger. CoaTi combines in vitro compartmentalization technology with the CARD reporter system which uses fluorescein tyramide labels for detection of peroxidase activity. Physical connection between cells and fluorescein tyramide radicals was achieved by compartmentalization of yeast cells inside microdroplets of single water-in-oil emulsions. After reaction cells were recovered from single emulsions and sorted by flow cytometry, an error prone PCR mutant library of Glucose oxidase (GOx) containing 10(7) cells and ~10(5) of different GOx variants was screened. Mutagenic conditions of GOx mutant library were selected to generate <1 % of active GOx population in order to explore influence of high mutation frequency on GOx activity. GOx variant Mut12 that contains 5 mutations (N2Y, K13E, T30V, I94V, K152R) showed a 1.2 times decreased K(m) (22.0 vs 18.1 mM) and a 2.7 fold increased k(cat) (150 s(-1) vs 54.8 s(-1)) compared to wt GOx. Compared to the employed parent B11 GOx (16 mM, 80 s(-1)) it has a slightly increased K(m) and 1.8 times increased k(cat).     

Synthesis of peptide alkylthioesters using the intramolecular N,S-acyl shift properties of bis(2-sulfanylethyl)amido peptides

The design of novel methods giving access to peptide alkylthioesters, the key building blocks for protein synthesis using Native Chemical Ligation, is an important area of research. Bis(2-sulfanylethyl)amido peptides (SEA peptides) 1 equilibrate in aqueous solution with S-2-(2-mercaptoethylamino)ethyl thioester peptides 2 through an N,S-acyl shift mechanism. HPLC was used to study the rate of equilibration for different C-terminal amino acids and the position of equilibrium as a function of pH. We show also that thioester form 2 can participate efficiently in a thiol-thioester exchange reaction with 5% aqueous 3-mercaptopropionic acid. The highest reaction rate was obtained at pH 4. These experimental conditions are significantly less acidic than those reported in the past for related systems. The method was validated with the synthesis of a 24-mer peptide thioester. Consequently, SEA peptides 1 constitute a powerful platform for access to native chemical ligation methodologies.     

利用多中心合成方法同步合成含N-取代甘氨酸的类肽化合物

N-取代甘氨酸聚合体是一类新的聚合体化合物, 同多肽相比, N-取代甘氨酸聚合体具有抗酶解稳定性, 同时使用市售的伯胺作为构建单元(building block)大大地扩展了天然多肽分子结构的多样性, 本文报道了利用多中心多肽合成方法合成了九个含N-取代甘氨酸聚合体多肽杂合休, 由于此类聚合体具有抗酶的能力, 因此可用于蛋白酶抑制剂的研究。     

Enhancement of the protein loading density by a pre-cleaning process of a gold substrate: confocal laser scanning microscopic study.

The immobilization of glucose oxidase (GOx), using self assembled monolayers (SAMs) on gold surfaces, was investigated by grazing angle FT-IR spectroscopy, surface plasmon resonance (SPR) spectroscopy, and atomic force microscopy (AFM) in conjunction with confocal laser scanning microscopy (CLSM). To find an optimum condition for the maximum GOx loading density on gold surfaces, different cleaning protocols were examined. The loading density of GOx on surfaces was investigated by AFM and CLSM. In particular, CLSM was more effective for identifying the GOx density than AFM, since its scanning speed is much faster and it covers a larger area. Based on CLSM images of the GOx immobilized on the surfaces, it was concluded that the pre-cleaning process of gold substrates using different solvents, such as acetone, ethanol and 2-propanol, is very important for enhancing the GOx loading density. This result enables us to investigate an effective fabrication process in fabricating biosensors.     

Electrochemical Behaviors of Glucose Oxidase Based on Biocatalytic Deposition of Gold Nanoparticles

Coupling nanotechnology with biocatalysis, a highly sensitive glucose biosensor for the study of electrochemical behaviors of glucose oxidase (GOx) was proposed by using monkshoodvine root–bark like carbon (MLC) as the platform for the biocatalytic deposition of AuNPs. The biosensor showed a linear range from 0.25 to 130 μM with a detection limit of 0.1 μM (S/N = 3) towards glucose and sensitivity of 3010 μA/mM. K value was calculated to be 67.4 μM. Furthermore, the proposed AuNPs/GOx–MLC modified pyrolytic graphite electrode (AuNPs/GOx–MLC/PGE) achieved direct electron transfer of GOx. Γ* was calculated to be 2.79 × 10^?11 mol/cm² and k_s was 1.79 s^?1. It also showed a remarkable electrocatalysis towards glucose.     

Design and synthesis of peptides that bind alpha-bungarotoxin with high affinity

BACKGROUND: Alpha-bungarotoxin (alpha-BTX) is a highly toxic snake venom alpha-neurotoxin that binds to acetylcholine receptor (AChR) at the neuromuscular junction, and is a potent inhibitor of this receptor. We describe the design and synthesis of peptides that bind alpha-BTX with high affinity, and inhibit its interaction with AChR with an IC(50) of 2 nM. The design of these peptides was based on a lead peptide with an IC(50) of 3x10(-7) M, previously identified by us [M. Balass et al., Proc. Natl. Acad. Sci. USA 94 (1997) 6054] using a phage-display peptide library. RESULTS: Employing nuclear magnetic resonance-derived structural information [T. Scherf et al., Proc. Natl. Acad. Sci. USA 94 (1997) 6059] of the complex of alpha-BTX with the lead peptide, as well as structure-function analysis of the ligand-binding site of AChR, a systematic residue replacement of the lead peptide, one position at a time, yielded 45 different 13-mer peptides. Of these, two peptides exhibited a one order of magnitude increase in inhibitory potency in comparison to the lead peptide. The design of additional peptides, with two or three replacements, resulted in peptides that exhibited a further increase in inhibitory potency (IC(50) values of 2 nM), that is more than two orders of magnitude better than that of the original lead peptide, and better than that of any known peptide derived from AChR sequence. The high affinity peptides had a protective effect on mice against alpha-BTX lethality. CONCLUSIONS: Synthetic peptides with high affinity to alpha-BTX may be used as potential lead compounds for developing effective antidotes against alpha-BTX poisoning. Moreover, the procedure employed in this study may serve as a general approach for the design and synthesis of peptides that interact with high affinity with any desired biological target.     

Application of thiolated gold nanoparticles for the enhancement of glucose oxidase activity

Glucose oxidase (GOx) has been covalently immobilized onto chemically synthesized thiolated gold nanoparticles (5-8 nm) via N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS). The lower value of the Michaelis-Menton constant obtained for the immobilized (3.74 mM) GOx compared with that for the free (5.85 mM) GOx suggests significant enhancement in the activity of GOx attached to thiolated gold nanoparticles. The covalently immobilized GOx thiolated nanoparticles exhibit a response time of 30 s, a shelf life of more than 6 months, and improved tolerance to both pH and temperature.     

Electrochemical Activity Studies of Glucose Oxidase (GOx)‐Based and Pyranose Oxidase (POx)‐Based Electrodes in Mesoporous Carbon: Toward Biosensor and Biofuel Cell Applications

A simple study using a fixed amount of mesoporous carbon (MSU‐F‐C) was performed for the comparison of pyranose oxidase (POx) and glucose oxidase (GOx) in their electrochemical performance under biosensor and biofuel cell operating modes. Even though the ratio of POx to GOx in the glucose oxidation activity per unit weight of MSU‐F‐C was 0.35, the ratios of POx to GOx in sensitivity and power density were reversed to be 6.2 and 1.4, respectively. POx with broad substrate specificity and an option of large scale production using recombinant E. coli has a great potential for various electrochemical applications, including biofuel cells.     

Mass-based classification (MBC) of peptides: Highly accurate precursor ion mass values can be used to directly recognize peptide phosphorylation

Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1,000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than +/-0.1 ppm. At a peptide mass of 1,500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution table of theoretical peptides. A mass distribution table of nonphosphorylated and monophosphorylated peptides with a bin width of 0.1 mu was made available via the open web site www.peptidecomposer.com.     

Structure-Function Analysis of the Emulsifying and Interfacial Properties of Apomyoglobin and Derived Peptides

Apomyoglobin was chosen as a model to study the emulsifying properties of proteins. It was cleaved into three peptides using cyanogen bromide and these peptides were purified and tested for emulsifying and interfacial properties. Two of the peptides had improved emulsifying activity compared to the whole protein. The peptide (residues 1-55) with the highest emulsifying activity and whole apomyoglobin were studied further. The amount of protein or peptide adsorbed at the oil-water interface of an emulsion was measured and the surface area occupied per molecule was calculated. For apomyoglobin, at maximal surface coverage each molecule occupied a surface area of approximately 8 nm2. This is consistent with a packed monolayer, based on the approximate dimensions of apomyoglobin. For peptide (1-55), at maximal surface coverage each molecule occupied a surface area of approximately 3 nm2. This is consistent with the area that the two amphipathic alpha-helices which are potentially present in this molecule would cover, if they were aligned along the oil-water interface. The different structural characteristics of these molecules responsible for their emulsifying properties are discussed. Copyright 1999 Academic Press.     

Adsorption behavior of glucose oxidase on a dipalmitoylphosphatic acid monolayer and the characteristics of the mixed monolayer at air/liquid interfaces

A dipalmitoylphosphatic acid (DPPA) monolayer at the air/liquid interface is used as a binding layer to incorporate glucose oxidase (GOx) from the subphase. The effects of the adsorption time of GOx on the behavior of the mixed DPPA/GOx monolayer and the relevant structure of the mixed LB film were studied using the characteristics of the pressure-area (pi-A) isotherm, Brewster angle microscopy (BAM), and atomic force microscopy (AFM). The experimental results show that two equilibrium states of GOx adsorption exist in the presence of a DPPA monolayer. The first equilibrium stage occurs at tens of minutes after spreading of DPPA, and a surface pressure of ca. 7.5 mN/m is obtained. The second equilibrium stage approaches slowly, and a higher equilibrium surface pressure (ca. 16 mN/m) was obtained at ca. 8 h after the first stage. The BAM and AFM images show that, after the second equilibrium stage is reached, a more condensed phase and rough morphology are obtained on the mixed DPPA/GOx monolayer, indicating a higher amount of GOx incorporated into the mixed film. For the first equilibrium stage of GOx adsorption, DPPA molecules can still pack regularly and closely under compression, suggesting that GOx molecules are mainly located beneath the DPPA monolayer at the compressed state. A more uniform phase was detected on a film prepared after the first equilibrium stage was reached. The present result indicates that distinct structures and properties of mixed DPPA/GOx films can be prepared from the various stages of GOx adsorption.