Expression of a functional non-ribosomal peptide synthetase module in Escherichia coli by coexpression with a phosphopantetheinyl transferase

Background: Non-ribosomal peptide synthetases (NRPSs) found in bacteria abd fungi are multifunctional enzymes that catalyze the synthesis of a variety of biologically important peptides. These enzymes are composed of modular units, each responsible for the activation of an amino acid to an aminoacyl adenylate and for the subsequent formation of an aminoacyl thioester with the sulfhydryl group of a 4′-phosphopantetheine moiety. Attempts to express these modules in Escherichia coli have resulted in recombinant proteins deficient in 4′-phosphopantetheine. The recent identification of a family of phosphopantetheinyl transferases (P-pant transferases) associated with NRPS have led us to investigate whether coexpression of NRPS modules with P-pant transferases in E. coli would lead to the incorporation of 4′-phosphopantetheine.Results: A truncated module of gramicidin S synthetase, PheAT(His₆), was expressed as a His₆ fusion protein in E. coli with and without Gsp, the P-pant transferase associated with gramicidin S synthetase. Although PheAT(His₆) expressed alone in E. coli catalyzed Phe-AMP formation from Phe and ATP, < 1% was converted to the Phe thioester. In contrast, >80% of the PheAT(His₆) that was coexpressed with Gsp could form the Phe thioester in the presence of Phe and ATP.Conclusions: Our finding indicates the presence of an almost equimolar amount of 4′-phosphopantetheine covalently bound to the NRPS module PheAT(His₆), and that the functional expression of NRPS modules in E. coli is possible, provided that they are coexpressed with an appropriate P-pant transferase.     

Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation

Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H₃ (His₃), H₄ (His₄), H₂DH (His₃Asp with two His and one Asp in the same plane) and H₃D (His₃Asp with three His in the same plane) by using the scaffold of the de novo protein GRα₃D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good Cu^II-bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.     

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.     

Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K₁₀ + 3H]³⁺ and the reagent cluster [5R_5Na – Na]^–). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

A fluorous tag-bound fluorescence derivatization reagent, F-trap pyrene, for reagent peak-free HPLC analysis of aliphatic amines

We have developed a novel pre-column fluorescence derivatization reagent for amines, F-trap pyrene. This reagent comprises a fluorescent pyrene moiety, an amine-reactive Marshall linker, and a fluorophilic perfluoroalkyl group known as fluorous tag. When the reagent reacts with aliphatic amines and amino acids to give fluorescent derivatives, the fluorous tag in the reagent is eliminated simultaneously. Therefore, excess unreacted reagents in the derivatization reaction solution still have the fluorous tag and could be removed by fluorous solid-phase extraction selectively before high-performance liquid chromatography (HPLC) analysis. By using this reagent, 13 kinds of aliphatic amine (C₂–C₁₆) derivatives can be separated within 40 min by reversed-phase HPLC with gradient elution. In this chromatogram, unreacted reagents peak at around 28 min, greatly decrease after fluorous solid-phase extraction, and do not interfere with the quantification of each amine. The detection limits (S/N = 3) for examined aliphatic amines are 3.6–25 fmol per 20 μL injection. We have also applied this reagent successfully to the amino acid analysis.

Highly Selective Lysine Acylation in Proteins Using a Lys-His Tag Sequence

Chemical modification of proteins has numerous applications, but it has been challenging to achieve the required high degree of selectivity on lysine amino groups. Recently, we described the highly selective acylation of proteins with an N-terminal Gly-His₆ segment. This tag promoted acylation of the N-terminal N^α-amine resulting in stable conjugates. Herein, we report the peptide sequences His_n-Lys-His_m, which we term Lys-His tags. In combination with simple acylating agents, they facilitate the acylation of the designated Lys N^ϵ-amine under mild conditions and with high selectivity over native Lys residues. We show that the Lys-His tags, which are 7 to 10 amino acids in length and still act as conventional His tags, can be inserted in proteins at the C-terminus or in loops, thus providing high flexibility regarding the site of modification. Finally, the selective and efficient acylation of the therapeutic antibody Rituximab, pure or mixed with other proteins, demonstrates the scope of the Lys-His tag acylation method.     

Luciferase-streptavidin fusion proteins: Preparation and properties

We constructed plasmids encoding genes of fusion proteins of a thermostable mutant of Luciola mingrelica firefly luciferase (Luc) and streptavidin (SA) with the polyhistidine sequence (His₆) at the N- or C-terminus of the protein: SA-Luc-His₆, His₆-SA-Luc, Luc-SA-His₆. Fusion proteins were produced and purified; their composition, luciferase activity, thermal stability, bioluminescence spectra, and biotin-binding capacity were investigated. Streptavidin introduction does not affect the bioluminescence spectra, but it decreases the thermal stability twofold at 47°C. It was shown by size-exclusion chromatography that, depending on the plasmid structure, the fusion proteins were expressed as dimers, tetramers, and larger oligomers, which differ in luciferase activity and biotin-binding capacity. The His₆-SA-Luc fusion protein demonstrated the most optimal properties.     

Easy‐to‐Attach/Detach Solubilizing‐Tag‐Aided Chemical Synthesis of an Aggregative Capsid Protein

A solubilizing Trt‐K₁₀ tag was developed for the effective chemical preparation of peptides/proteins with low solubility. The Trt‐K₁₀ tag comprises a hydrophilic oligo‐Lys sequence and a trityl anchor, and can be selectively introduced to a side chain thiol of Cys of deprotected peptides/proteins with a trityl alcohol‐type introducing reagent Trt(OH)‐K₁₀ under acidic conditions. Significantly, the ligation product in the reaction mixture of a thiol‐additive‐free native chemical ligation can be modified directly in a one‐pot manner to facilitate the isolation of the product by high‐performance liquid chromatography. Finally, the Trt‐K₁₀ tag can be readily removed with a standard trifluoroacetic acid cocktail. Using this easy‐to‐attach/detach tag‐aided method, a hepatitis B virus capsid protein that is usually difficult to handle was synthesized successfully.     

标签谷胱甘肽S-转移酶的二价亲和标记试剂的制备与应用

设计合成融合表达标签谷胱甘肽S-转移酶(GST)的二价亲和标记试剂,用于功能化磁珠后位点选择性固定化标签GST,为磁分离筛选配体混合物库提供固定化融合靶蛋白的候选方案。 为减少疏水配体在标签GST活性位点的结合,需同时占据标签GST双活性中心内疏水结合位点并发生共价修饰的二价亲和标记试剂。以双苯环为疏水定位基、溴乙酰基为巯基修饰基团、羧基为连接官能团得单价标记试剂,以二乙基三胺为连接臂将单价标记试剂与连接臂两端伯胺连接得标签GST的对称二价亲和标记试剂,再以线性三胺连接臂中间的氨基与羧基磁珠偶联得功能化磁珠。 表征目标化合物对标签GST的标记动力学、结合比;功能化磁珠对标签GST的不可逆固定化动力学和固载容量,及将磁珠表面二价亲和标记试剂转变成还原型谷胱甘肽(GSH)加合物后对标签GST可逆固定化的效果;以碱性磷酸酶及疏水荧光配体为模型考察磁珠固定化标签GST后的非特异结合。 目标化合物对标签GST半抑制浓度为(22±0.2) μmol/L,其与GSH的饱和加合物半抑制浓度为(0.41±0.06) μmol/L,二者与标签GST二聚体结合比接近1：1。 功能化磁珠对标签GST不可逆及可逆固定化的容量均接近25 mg/g磁珠。 偶联GST的磁珠对蛋白非特异吸附很弱,再进一步用单价亲和标记试剂和GSH加合物封闭固定化标签GST剩余的活性位点后对疏水小分子也无显著结合。 结果表明,所设计二价亲和标记试剂功能化磁珠适合用于标签GST及其融合表达蛋白的位点选择性固定化。     

Novel polyelectrolyte complexes based on diazo-resins

Polyelectrolyte complexes containing diazonium groups (PEC-N₂) with a high ionic crosslinking rate were prepared as a precipitate by mixing the diazo-resin with polyanion solutions. The photochemical decomposition of the complexes from different polyanions was studied. It was shown that PEC-N₂ exhibit high photosensitive properties. Under irradiation of UV light, the complexes which can be dissolved in ternary mixtures such as H₂O-DMF-LiCl,H₂O-DMF-NaSCN or H₂O-DMF-ZnCl₂ (DMF: N,N-dimethylformamide) become indissoluble since the crosslinking structure of the complexes changes from ionic to covalent.     

An Artificial Hemoprotein with Inducible Peroxidase- and Monooxygenase-Like Activities

A novel inducible artificial metalloenzyme obtained by covalent attachment of a manganese(III)-tetraphenylporphyrin (MnTPP) to the artificial bidomain repeat protein, (A3A3′)Y26C, is reported. The protein is part of the αRep family. The biohybrid was fully characterized by MALDI-ToF mass spectrometry, circular dichroism and UV/Vis spectroscopies. The peroxidase and monooxygenase activities were evaluated on the original and modified scaffolds including those that have a) an additional imidazole, b) a specific αRep bA3-2 that is known to induce the opening of the (A3A3′) interdomain region and c) a derivative of the αRep bA3-2 inducer extended with a His₆-Tag (His₆-bA3-2). Catalytic profiles are highly dependent on the presence of co-catalysts with the best activity obtained with His₆-bA3-2. The entire mechanism was rationalized by an integrative molecular modeling study that includes protein–ligand docking and large-scale molecular dynamics. This constitutes the first example of an entirely artificial metalloenzyme with inducible peroxidase and monooxygenase activities, reminiscent of allosteric regulation of natural enzymatic pathways.     

Improved Resolution of Hydrophobic Penicillin-binding Proteins and Their Covalently Linked Complexes on a Modified C18 Reversed Phase Column

ABSTRACT

Hydrophobic proteins have proven to be difficult to separate chromatographically. The use of a C18 reversed phase column with embedded polar groups showed improved separation and recovery of the hydrophobic, membrane associated, penicillin-binding proteins of Bacillus subtilis and their covalently linked complexes. The covalently linked complexes were generated by a time course reaction of the non-covalently associated complexes in the intact cell with the paired group specific reagent, cyanogen (C₂N₂).     

Charge density studies on [(NO)Fe(S2C6H4)2][PPN] and [(NO)3Fe(S2C6H4)3] complexes

Charge density studies of chemical bonds for two iron complexes, [(NO)Fe(S,S-C₆H₄)₂] [PPN] (1), where PPN = N(Pph₃)₂ and Fe₃(NO)₃(S,S-C₆H₄)₃ (2) are investigated in terms of the topological properties at bond critical points based on the ‘atoms in molecule’ theory. The one electron reduction form (1R) of complex 1 and the one electron oxidation form (2O) of complex 2 are also included for comparison. The X-ray absorption spectroscopy of Fe K- and L_III,II-edges, as well as the N/S K-edge are applied to verify the illustration in the variation of the electronic structures. Based on the ρ_c, ?²ρ_c, and H_b values among the compound studied, Fe-S/N can be regarded as polarized covalent bond, and Fe-N bonds show stronger covalent character than that of the Fe–S bond, which is believed to be a highly polarized covalent bond.     

Insertion of an unnatural amino acid into the protein structure: preparation and properties of 3-fluorotyrosine-containing organophosphate hydrolase

Five Tyr residues present in the native organophosphate hydrolase (OPH) containing a hexahistidine tag at the N-terminus of the protein molecule (His₆-OPH) were replaced by fluorine-containing analogs using a biosynthetic approach. The modified enzyme had an extended pH-optimum of action shifted to acidic pH and an enhanced thermal stability in the alkaline pH region. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 357–361, February, 2006.     

SLAP: Small Labeling Pair for Single‐Molecule Super‐Resolution Imaging

Protein labeling with synthetic fluorescent probes is a key technology in chemical biology and biomedical research. A sensitive and efficient modular labeling approach (SLAP) was developed on the basis of a synthetic small‐molecule recognition unit (Ni‐trisNTA) and the genetically encoded minimal protein His_6‐10‐tag. High‐density protein tracing by SLAP was demonstrated. This technique allows super‐resolution fluorescence imaging and fulfills the necessary sampling criteria for single‐molecule localization‐based imaging techniques. It avoids masking by large probes, for example, antibodies, and supplies sensitive, precise, and robust size analysis of protein clusters (nanodomains).     

Copper(I) complexes with 1-(2-carboxyphenyl)-5-heterylhydrazidinyl-6-celluloses as reversible redox indicators

A number of reagent test papers were designed on the basis of redox indicators: copper(I) complexes with sheet polydentate 1-(2-carboxyphenyl)-5-heterylhydrazidinyl-6-celluloses (I?CIV) (heteryl = 6-methoxy-4-methylpyrimidin-2-yl, 4,6-dimethylpyrimidin-2-yl, benzoxazol-2-yl, and benzothiazol-2-yl). Complexes I?CIV were transformed under the action of H₂O₂ into copper(II) complexes with 1-(2-carboxyphenyl)-5-heterylformazanyl-6-celluloses (V?CVIII), respectively. When treated with Na₂S, complexes V?CVIII were reversibly reduced to the starting copper(I) complexes I?CIV. The reactions were accompanied by bathochromic shifts from the central region of the visible spectrum to the higher wavelengths. Complex I was used to develop visual and reflectometric test methods for checking the peroxide content of pharmaceuticals and cosmetics at a level of 0.01% and above.     

Chiral recognition of protected amino acids by means of fluorescent binary complex pyrene/heptakis-(6-amino)-(6-deoxy)-β-cyclodextrin

The ability of the binary complex pyrene (Py)/heptakis-(6-amino)-(6-deoxy)-β-cyclodextrin (am-β-CD) to act as a chiral selector was tested at two pH values (8.0 and 9.0). Phenylalanine (Phe), methionine (Met) and histidine (His) were used as chiral model molecules. The stability of ternary complexes Py/am-β-CD/amino acid was determined by means of spectrofluorimetric measurements. The data collected showed an increase in stability going from the binary to ternary complex and above all the possibility to use the binary complex as a chiral selector. Finally, data collected at two pH values showed that the binary complex is a better chiral selector when charged rather than in its neutral form.     

Design and synthesis of a highly efficient labelling reagent for incorporation of tetrafluorinated aromatic azide into proteins

Chemical labelling can significantly extend the structures and functions of proteins for advanced applications. Herein, a highly efficient bench-stable reagent diazo-azide was designed and synthesized for the incorporation of tetrafluorinated aromatic azides into proteins via the diazonium coupling. The diazo-azide-labelled proteins could be further functionalized via the nonhydrolysis Staudinger reaction to achieve fluorescence labelling, PEGylation and biotinylation. The whole protein labelling processes were catalysis-free and could be finished within several hours under the mild conditions. To this end, we have prepared thickened viral nanoparticles with controllable diameters.     

Super‐Chelators for Advanced Protein Labeling in Living Cells

Live‐cell labeling, super‐resolution microscopy, single‐molecule applications, protein localization, or chemically induced assembly are emerging approaches, which require specific and very small interaction pairs. The minimal disturbance of protein function is essential to derive unbiased insights into cellular processes. Herein, we define a new class of hexavalent N‐nitrilotriacetic acid (hexaNTA) chelators, displaying the highest affinity and stability of all NTA‐based small interaction pairs described so far. Coupled to bright organic fluorophores with fine‐tuned photophysical properties, the super‐chelator probes were delivered into human cells by chemically gated nanopores. These super‐chelators permit kinetic profiling, multiplexed labeling of His₆‐ and His₁₂‐tagged proteins as well as single‐molecule‐based super‐resolution imaging.