Sequence diversity in the lasso peptide framework: discovery of functional microcin J25 variants with multiple amino acid substitutions

Microcin J25 (MccJ25) is a ribosomally synthesized antimicrobial peptide that has an unusual threaded lasso structure in which the C-terminal "tail" of the peptide is fed through a macrocyclic "ring" formed by the N-terminal residues. Production of MccJ25 in Escherichia coli is dependent upon a four-gene cluster encoding the structural gene mcjA, two maturation enzymes mcjB and mcjC, and an immunity factor, mcjD, in the form of an MccJ25 export pump. Here we have developed a system for orthogonal control of the expression of mcjA and mcjD, thus permitting independent control of MccJ25 production and export/immunity in E. coli. We used this system to screen saturation mutagenesis libraries targeted to either the ring or tail portions of MccJ25 and discovered nearly 100 new MccJ25 variants that retain antimicrobial function. While multiple amino acid substitutions in the tail portion of the peptide are well-tolerated, mutagenesis of the ring portion of the peptide is detrimental to the antimicrobial function of MccJ25. We demonstrated that the decreased function of the ring variants is due to the inability of these variants to be transported to the cytoplasm of susceptible strains. Additionally, we found several MccJ25 variants from the tail library with improved efficacy toward the MccJ25-sensitive strains E. coli and Salmonella enterica serovar Newport with the best variants exhibiting a nearly 5-fold increase in potency. The results described here provide further evidence that diverse amino acid sequences can be tolerated by the rigid lasso peptide fold.     

Investigation of cytolysin variants by peptide mapping: enhanced protein characterization using complementary ionization and mass spectrometric techniques

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have been used in conjunction with time-of-flight (TOF) and quadrupole ion trap (IT) mass spectrometry, respectively, to analyze various cytolysin proteins isolated from the sea anemone Stichodactyla helianthus and digested by the protease trypsin. By employing different ionization methods, the subsequent changes in ionization selectivity for the peptides in the digested protein samples resulted in ion abundance variation reflected in the mass spectra. Upon investigation of this variation generated by the two ionization processes, it has been shown in this study that enhanced protein coverage (e.g., >95% for cytolysin III) can be achieved. Additionally, capillary and microbore reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ESI mass spectrometry (MS) as well as flow injection analysis by nanoflow ESI-MS afforded the necessary limit of detection (LOD) for detailed structural information of the cytolysin proteins by tandem mass spectrometry (MS/MS) methods. It can be concluded that cytolysins II and III correspond to sticholysins I and II, that "cytolysin I" is a mixture of modified forms of cytolysins II and III, and that "cytolysin IV" is an incompletely processed precursor of cytolysin III.     

Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis

A new sample preparation method for MALDI based on the use of a mixture of the two commonly used matrices, DHB and CHCA, is described. The matrix mixture preparation results in increased sequence coverage and spot-to-spot reproducibility for peptide mass mapping compared to the use of the single matrix components. This results in more reliable protein identification in proteomics studies and facilitates automated data acquisition. This method shows better tolerance towards salts and impurities, eliminating the need for pre-purification of the samples. It has also been found to be advantageous for the analysis of intact proteins, and especially for glycoproteins. The mixture allows the presence of rather high concentrations of urea in the sample solutions.     

Observation of heterogeneous gene products by FT-ICR MS

The ability of FT-ICR MS to resolve isotopic variants of intact proteins for each of the charge states formed by electrospray ionization offers a sensitive, rapid method for detecting "low mass" heterogeneity, where this is defined as the presence of structural variants differing in mass by 2 Da or less. Such heterogeneity may reflect biological or chemical modifications of structure or may result from the coexpression of related proteins from a multi-gene family. In the analytical approach described here, comparisons are made between observed isotopic distributions and those expected for predicted protein sequences. Close agreement is demonstrated for a homogeneous model protein, and the utility of the method has been evaluated in the study of mouse major urinary proteins (MUPs), a group of closely related sequences. Divergence of the experimental isotopic distribution from distributions predicted for known MUP sequences can be explained, in quantitative terms, by the coexpression of closely related sequences. This approach provides a facile method for the assessment of protein homogeneity and for the detection of structural variants, without recourse to proteolytic digestion and analysis of the resulting products.     

Indirect ultrasonication for protein quantification and peptide mass mapping through mass spectrometry-based techniques

We report in this work a fast protocol for protein quantification and for peptide mass mapping that rely on ¹⁸O isotopic labeling through the decoupling procedure. It is demonstrated that the purity and source of trypsin do not compromise the labeling degree and efficiency of the decoupled labeling reaction, and that the pH of the labeling reaction is a critical factor to obtain a significant ¹⁸O double labeling. We also show that the same calibration curve can be used for MALDI protein quantification during several days maintaining a reasonable accuracy, thus simplifying the handling of the quantification process. In addition we demonstrate that ¹⁸O isotopic labeling through the decoupling procedure can be successfully used to elaborate peptide mass maps. BSA was successfully quantified using the same calibration curve in different days and plasma from a freshwater fish, Cyprinus carpio, was used to elaborate the peptide mass maps.     

Determination of the amino acid sequence of cystine-containing peptides by tandem mass spectrometry.

A method has been developed for the determination of the amino-acid sequence of a cyclic peptide containing cystine. It is based on the reduction of the peptide in a reductive matrix prior to ionization by fast-atom bombardment. The amino-acid sequence of the resulting linear peptide is then determined by tandem mass spectrometry from the spectrum produced by the collision-induced decomposition of the [M + H]+ ion of the peptide.     

Fast on-column protein digestion with subsequent peptide mapping using tandem mass spectrometry with information dependent acquisition

A platform for rapid on-line protein digestion of protein mixtures for direct infusion to a mass spectrometer is presented. A mixture of protein A, staphylococcal enterotoxin B and cytochrome c was used as a model mixture injected on a gel filtration column and a trypsin reactor which were connected in series to a micro liquid chromatography (microLC) system. The peptides in the column eluate were analyzed with ESI tandem mass spectrometry, utilizing information dependent acquisition (IDA). In one step, the proteins in the mixture (microM concentrations) were concomitantly desalted, separated, digested and identified with an overall analysis time of less than 40 min. Protein sequence coverage of 78-95% for the involved substances was achieved.     

微波辅助萃取-GC/MS联用分析竹子中氨基酸

建立了微波辅助萃取-GC/MS联用测定竹子中谷氨酸、天冬氨酸和苯丙氨酸等10种氨基酸的分析方法, 优化了微波辅助萃取条件, 方法的线性范围在0.100～100 μg/mL之间, 检出限在0.0098～0.36 μg/mL之间, RSD为4.1%～9.7%, 回收率在84.3%～118%之间. 分析了4种不同产地、竹龄竹子的竹叶、竹枝和竹沥中氨基酸含量. 结果表明, 不同竹种、产地及竹龄的竹子中氨基酸总量有较大差异;相同竹种其竹沥中氨基酸含量显著高于竹叶及竹枝中氨基酸含量.     

电喷雾电离源结合傅立叶变换离子回旋共振质谱分析地下水中可溶性有机质分子组成

应用电喷雾电离源结合傅立叶变换离子回旋共振质谱(ESI FT-ICR MS)对地下水进行分析,基于高精确度的分子量检测结果,鉴定出O_x,N_1O_x和N_2O_x3大类,共计27小类含杂原子的化合物。杂原子化合物中O_x类化合物占绝大多数,而含N化合物则以结合大量氧原子的形式广泛存在。结合各类杂原子化合物的等效双键数(DBE)及碳数分布,发现O_x类化合物中存在大量的羧酸结构,推测含氮化合物可能来自于O_x类化合物的衍生反应。实验结果拓宽了对地下水中可溶性有机质的认识,为进一步确定其中杂原子化合物的结构类型奠定了基础。     

Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra

We report an automated method for determining charge states from high-resolution mass spectra. Fourier transforms of isotope packets from high-resolution mass spectra are compared to Fourier transforms of modeled isotopic peak packets for a range of charge states. The charge state for the experimental ion packet is determined by the model isotope packet that yields the best match in the comparison of the Fourier transforms. This strategy is demonstrated for determining peptide ion charge states from "zoom scan" data from a linear quadrupole ion trap mass spectrometer, enabling the subsequent automated identification of singly- through quadruply-charged peptide ions, while reducing the numbers of conflicting identifications from ambiguous charge state assignments. We also apply this technique to determine the charges of intact protein ions from LC-FTICR data, demonstrating that it is more sensitive under these experimental conditions than two existing algorithms. The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution.     

Characterization of deamidated peptide variants by micro-preparative capillary electrophoresis and mass spectrometry

Capillary electrophoresis (CE) was compared with reversed-phase liquid chromatography for its ability to separate native and deamidated peptides. CE is shown to provide superior resolution of these peptides due to its charge-based separation mechanism. Fraction collection performed using a standard CE instrument equipped with a 96-well plate permits subsequent characterization by nanospray mass spectrometric (MS) analysis. Additional in-depth analysis by MS/MS is able to provide the location of the deamidation site based on y-ion mass shifts of 1 Da.     

Enzyme modification by MPEG with an amino acid or peptide as spacer arms

A method for the modification of enzymes by MPEG carrying an amino acid or peptide as a spacer arm is described and tested with aliphatic or aromatic side chains amino acids. The procedure involves MPEG activation by p-nitrophenylchloroformate for the amino acid or peptide coupling that is in turn activated for the protein binding. The advantage of the method resides in the possibility to introduce proper reporter groups between the polymer and the protein as norleucine for a direct evaluation of the bound polymer chains, tryptophan for structural studies of the polymer-protein adduct, and radioactive amino acid for pharmacokinetic investigations. The method was positively tested with arginase, ribonuclease, and superoxide dismutase as enzymes of therapeutic value.     

Combination of MALDI-TOF mass spectrometry with immobilized enzyme microreactor for peptide mapping

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been combined with immobilized enzyme microreactor for the rapid, sensitive, and accurate tryptic mapping of protein and polypeptides. The technique utilizes the trypsin microreactor by immobilized enzyme on the glycidyl methacrylate (GMA)-modified cellulose membrane. The membrane micro-reactor was used for the tryptic mapping of cytochrome C and the results were compared with those obtained by using free trypsin. A significant increase in the overall sensitivity of the process was observed using the membrane microreactor, as well as the elimination of background signals due to the autolysis of the trypsin. Further, membrane microreactor digestions were found to be rapid and convenient.     

Protein quantification by selective isolation and fragmentation of isotopic pairs using FT-ICR MS

Isolation of tryptic peptide ions, along with their differentially labeled analogs derived from an artificial QconCAT protein, is performed using multiple correlated harmonic excitation fields in an FT-ICR cell. Simultaneous fragmentation of the isolated unlabeled and labeled peptide pairs using IRMPD yields specific y-series fragment ions useful for quantification. The mass increment attributed to stable isotope labeling at the C-terminus is maintained in the C-terminal fragment ions, providing multiple measurements of labeled/unlabeled intensity ratios during highly selective detection. The utility of this approach has been demonstrated in the absolute quantification of components of an unfractionated chicken muscle protein mixture.     

Determination of phytochelatins by capillary zone electrophoresis with electrospray tandem mass spectrometry detection (CZE-ES MS/MS)

The coupling of capillary zone electrophoresis with electrospray mass spectrometry was optimized for the direct determination of phytochelatins (PCs) in extracts obtained from cells and plants that had been exposed to metal stress. Gluthathione and phytochelatins belonging to the different families (gamma Glu-Cys)nGly (n-PC), (gamma Glu-Cys)nSer, (gamma Glu-Cys)n beta Ala and (gamma Glu-Cys)n were separated in an uncoated capillary at pH 4 using a 5 mM ammonium acetate buffer, and detected by electrospray (ES) MS in the full scan mode (300-1100 u). The use of on-line tandem MS detection in the product ion scan mode of putative protonated molecules of PCs allowed the unambiguous confirmation of the identity of the compounds detected by ES MS. The operational conditions were optimized and the figures of merit were evaluated using n-PC2, n-PC3 and n-PC4 standards purified from a mixture obtained after the reaction of glutathione in the presence of Cd2+ and the enzyme PC-synthase. The method was applied to the characterization of bioinduced ligands in cell cultures of soybeans (Glycine max) and in rice (Oryza sativa) roots without the need for a preliminary sample cleanup by size-exclusion and/or reversed phase chromatography.