Solid-phase C-terminal sequencing of peptides

Summary C-terminal amino acid sequence analysis seemed to be established procedure, as the counterpart of Edman's N-terminal sequencing method. However, poor recovery of the C-terminal amino acids in the reaction in homogeneous solution suggested further improvement of the method. In the present study, N-terminal amino acid was fixed covalently to the controlled pore glass (CPG) beads and the C-terminal amino acid was activated (by treating with acetic anhydride), coupled with thiocyanate to form thiohydantoin (TH) ring at the C-terminus. Then, the C-terminal amino acid was split off as the corresponding TH derivative, and analyzed by HPLC. Hydrolysis of the TH derivative was achieved at 60°C in the presence of 2 M HC1 for 2 h. Solid phase fixed peptide was washed simply with acetone, and dried for the next cycle of the reaction. So far obtained results in the heterogeneous mixture are not satisfactory in terms of the recovery of the C-terminal TH, and improvement of the recovery and further steps are under progress.     

Configuration and racemization determination of cysteine residues in peptides by chiral derivatization and HPLC: application to oxytocin peptides.

An improved RP-HPLC method was developed for the determination of the configuration and stereochemical purity of cysteine residues in peptides. The method consists of oxidation of cysteine and cystine residues to cysteic acid, followed by hydrolysis and pre-column chiral derivatization with Val-Marfey's reagent.     

大豆肽体外抗氧化活性研究

研究大豆肽的体外抗氧化的作用。采用邻二氮菲-Fe^2＋检测大豆肽对羟自由基（·OH）的清除作用,邻苯三酚检测大豆肽对超氧阴离子（·O2^-）的清除作用,用硫代巴比妥酸法测定小鼠肝匀浆丙二醛（MDA）的含量,用比色法测定小鼠红细胞溶血度,来研究大豆肽的抗氧化效果。结果表明：大豆肽可以清除·OH和·O2^-,抑制·OH所致的丙二醛的产生,减少H2O2所致的红细胞溶血,在2～15g／L内均具有明显的量效关系。表明大豆肽在体外具有明显的抗氧化效果。     

基于生物质谱的胶原蛋白定量检测方法

本研究旨在建立一种基于特征多肽的胶原定量检测方法,通过序列比对的方法筛选胶原蛋白特征多肽,利用胰蛋白酶将牛Ⅰ型胶原蛋白标准品进行酶解,采用液质联用技术(HPLC-MS)对特征多肽进行检测,建立特征多肽丰度与胶原蛋白浓度对应关系并用于实际样品分析。结果表明,牛Ⅰ型胶原蛋白中检测出6种特征多肽,其中多肽GEAGPSGPAGPTGAR由于其丰度高且二级质谱稳定适合作为定量检测的特征多肽,多肽信号强度与蛋白浓度(0.1-3.0 mg/m L)呈良好线性关系。将所建方法用于实际样品分析,牛跟腱胶原蛋白含量为90.2%,胶原海绵中胶原蛋白含量为93.4%,检测结果与基于氨基酸组成分析的结果一致。该研究表明基于HPLC-MS的特征多肽分析方法进行胶原蛋白定量检测具有可行性,该方法在含胶原蛋白医疗器械等生物制品质量控制方面具有应用前景。     

Alkylation of cysteine-containing peptides to mimic palmitoylation.

Numerous proteins that are involved in cell signaling and viral replication require post-translational modification by palmitoylation to function properly. The molecular details by which this palmitoyl modification affects protein function remain poorly understood. To facilitate in vitro biochemical and structural studies of the role of palmitoylation on protein function, a method was developed for alkylating peptides with saturated C16 groups at cysteine residues and demonstrated using peptides derived from the palmitoylated region of Sindbis virus E2 glycoprotein. The synthetic approach takes advantage of disulfide chemistry to specifically modify only the cysteine residues within peptides and covalently links C16 groups via disulfide bridges using a new thioalkylating reagent, hexyldexyldithiopyridine. The chemistry presented here takes place in solution under mild conditions without the need for protection of the peptide functional groups. A method for purifying these modified peptides is also described. This protocol can be of general use to investigators studying the role of palmitoylation in biological systems.     

MALD-MS in the quantitative analysis of peptides and proteins

A modified method of isotope dilution was applied to the quantitative determination of peptides and proteins by MALDI MS at subpicomolar level. The essence of the method consists in the quantitative analysis of the enzymic hydrolysis products rather than the starting compounds. This allows the measurements to be performed at a higher resolution and makes the method independent of the molecular mass of oligopeptides and proteins examined. Fragments obtained by hydrolysis of the same oligopeptide or protein in a known concentration by the same enzyme and labeled with the stable 18O isotope are used as internal standards. The label is introduced by carrying out the hydrolysis in H(2)18O, and the oligopeptide concentration is calculated from the isotope distribution between the labeled and unlabeled hydrolysis products in the mass spectrum. This method was tested in the determination of concentrations of the angiotensinogen (1-14) fragment (oligopeptide), extracellular RNAase from Bacillus amyloliquefaciens (protein) and its protein inhibitor, barstar M. Usefulness of this method in kinetic studies was also demonstrated.     

Recombinant protein purification using complementary peptides as affinity tags

Affinity tags have become highly popular tools for purifying recombinant proteins from crude extracts by affinity chromatography. Besides, short peptides are excellent ligands for affinity chromatography, as they are not likely to cause an immune response in case of leakage into the product, they are more stable than antibodies to elution and cleaning conditions and they usually have very acceptable selectivity. Hydropathically complementary peptides designed de novo show enough selectivity to be used successfully as peptide ligands for protein purification from crude extracts. Recognition specificity and selectivity in the interaction between the complementary peptide pair His-Leu-Leu-Phe-Pro-Ile-Ile-Ile-Ala-Ala-Ser-Leu and Lys-Asn-Tyr-Pro-Lys-Lys-Lys-Met-Glu-Lys-Arg-Phe have been demonstrated by other authors. In this work, we designed a recombinant protein purification method using a peptide affinity tag that binds to a peptide-binding partner immobilized on a chromatographic matrix. The enhanced green fluorescent protein expressed (EGFP) in Escherichia coli was used as the model. The peptide Gly-Gly-Gly-His-Leu-Leu-Phe-Pro-Ile-Ile-Ile-Ala-Ala-Ser-Leu was synthesized by solid phase using the Fmoc chemistry and immobilized in NHS-Sepharose (PC-Sepharose). Gly residues were added as a spacer arm at the N terminus. The EGFP was expressed either with the fusion tag Lys-Asn-Tyr-Pro-Lys-Lys-Lys-Met-Glu-Lys-Arg-Phe on the C terminus (EGFP-CPTag) or without any fusion tag. After cell disruption, the extract was directly applied to the PC-Sepharose column equilibrated with 20mM sodium phosphate buffer, pH 7.0. The adsorbed EGFP-CPTag was then eluted with 1M Tris. The yield was 98% and the purification factor 4.6. By contrast, EGFP without tag pass through without interacting with the PC-Sepharose column. The method designed can be applied for the purification of other recombinant proteins.     

Disulfide interchange reactions between cystamine and cystine peptides

A method is presented for carrying out interchange reactions on a small scale between cystamine and low molecular weight cystine peptides. The products of the reaction were separated from unchanged peptides and from excess cystamine by high-voltage electrophoresis on paper. The opening of intrachain disulfide bonds required substantially higher concentrations of cystamine than did the reaction of interchain bonds. The interchange reaction can be used to separate cysteine peptides on an analytical or a preparative scale from other components of enzymic digests of proteins. A cys-gly bond in one interchange product was hydrolyzed by trypsin, but a cys-leu bond in another interchanged peptide was insensitive to trypsin.     

Interaction of antimicrobial peptides with lipopolysaccharides

We study the interaction of antimicrobial peptides with lipopolysaccharide (LPS) bilayers to understand how antimicrobial peptides interact with the LPS monolayer on the outer membrane of Gram-negative bacteria. LPS in water spontaneously forms a multilamellar structure composed of symmetric bilayers. We performed X-ray lamellar diffraction and wide-angle in-plane scattering to study the physical characteristics of LPS multilayers. The multilayer alignment of LPS is comparable to phospholipids. Thus, it is suitable for the application of oriented circular dichroism (OCD) to study the state of peptides in LPS bilayers. At high hydration levels, the chain melting temperature in multilamella detected by X-ray diffraction is the same as that of LPS aqueous dispersions, as measured by calorimetry. LPS has a strong CD, but with a careful subtraction of the lipid background, the OCD of peptides in LPS is measurable. The method was tested successfully with melittin. It was then applied to two representative antimicrobial peptides, magainin and protegrin. At peptide concentrations comparable to the physiological conditions, both peptides penetrate transmembrane in LPS bilayers. The results imply that antimicrobial peptides readily penetrate the LPS monolayer of the outer membrane.     

Separation of peptides dissolved in a sodium dodecyl sulfate solution by reversed-phase liquid chromatography: removal of sodium dodecyl sulfate from peptides using an ion-exchange precolumn

Separation of peptides by reversed-phase liquid chromatography is significantly affected by sodium dodecyl sulfate (SDS) in the sample solution. The strongly acidic group of SDS binds to the reversed-phase column where it serves as an ion exchanger and retards the elution of peptides. By using a DEAE precolumn connected in series to a reversed-phase column, the interference of SDS in the separation of peptides by reversed-phase chromatography can be significantly diminished. This simple method is applicable to the separation of peptide mixtures obtained by digestion of proteins extracted from SDS-polyacrylamide gels. Peptide production with some proteases in the presence of SDS was examined using the present method. Lysylendopeptidase was suitable for digestion in the presence of SDS, but V8 protease was not.     

Metal-binding properties of phytochelatin-related peptides

Phytochelatins (PCs, (gamma Glu-Cys)(n)-Gly, n=2-11) are produced by higher plants, algae and some fungi in order to detoxify Cd(2+) by sequestration to form Cd-PCs complexes. In order to investigate what chemical structures of PCs are responsible for their metal-binding ability, various cysteine-rich peptides ((X-Cys)(7)-Gly, X=Glu, Asp, Lys, Gly, Ser and Gln) were chemically synthesized. Water-solubility, metal-binding property, and detoxification effect toward Cd(2+) were analyzed and compared with those of (gamma EC)(7)G. (SC)(7)G and (QC)(7)G were insoluble at pH below 10, and (GC)(7)G was not soluble at any pH between 1 and 12, indicating that charged side chains were at least required for the molecules to be solubilized in aqueous solution. By spectroscopic analyses using DTNB method and UV method, we found that (EC)(7)G and (DC)(7)G had almost equivalent abilities of Cd(2+)-binding as PC ((gamma EC)(7)G), indicating that the distance between each thiol group was not a major factor for the binding to Cd(2+). (beta DC)(7)G and (KC)(7)G interacted to Cd(2+) with fourth coordination as in the case of other soluble PC-related peptides. However, compared to (gamma EC)(7)G, (beta DC)(7)G displayed a slightly weaker binding to Cd(2+), and (KC)(7)G showed a drastic decrease in binding ability. The affinities of PC-related peptides toward Cd(2+) were evaluated as below; (gamma EC)(7)G=(EC)(7)G=(DC)(7)G>(beta DC)(7)G>(KC)(7)G=weak binding. The results of Cd(2+)-detoxification assays were consistent with the affinity between Cd(2+) and the peptides. We concluded that the structure consisting of thiol and carboxyl groups were essential for the formation of a tight Cd-peptides complex such as Cd-PCs.     

Selective acylation of primary amines in peptides and proteins

N-hydroxysuccinimide (NHS) esters are derivatizing agents that target primary amine groups. However, even a small molar excess of NHS may lead to acylation of hydroxyl-containing amino acids as a side reaction. We report a straightforward method for the selective removal of ester-linked acyl groups after NHS ester-mediated acylation of peptides and proteins. It is based on incubation in a boiling water bath and does not require a change in pH or the addition of chemicals. It is therefore particularly suited for proteomics samples that are often small in volume and contain low amounts of peptides. The method was optimized and evaluated with two peptides and one protein that were acetylated at a high excess of NHS-acetate. While the large molar excess resulted in complete acylation of all primary amines, hydroxyl-containing amino acids were shown to react as well. By incubating the peptide or protein solutions in a boiling water bath, acetyl-ester bonds were hydrolyzed, whereas acetyl-amide bonds remained stable. The reaction was also performed in 6 M guanidine-HCl, which prevented protein precipitation. In conclusion, the present method allows the selective acylation of primary amines by NHS esters and constitutes a valuable alternative to the treatment with hydroxylamine under alkaline conditions.     

Supramolecular assembly using helical peptides

We investigated supramolecular assemblies of various hydrophobic helical peptides. The assemblies were formed at the air/water interface or in aqueous medium. The hexadecapeptide, Boc-(Ala-Aib)₈-OMe (BA16M), was reported to take α-helical structure by X-ray analysis. Several derivatives were prepared, which have the repeating sequence of Ala-Aib, Lys(Z)-Aib or Leu-Aib, or have the terminal chemically modified. CD spectra of the peptides indicated helical conformation in ethanol solution. The surface pressure-area isotherms of the peptide monolayers showed an inflection at the surface area corresponding to the cross section along the helix axis, and the monolayers were collapsed by further compression. All the helical peptides oriented their helix axis parallel to the air/water interface on the basis of the results of transmission IR spectra and RAS of the monolayers transferred onto substrates.A small mound was observed in the isotherm of BA16M and other derivatives, which was ascribed to the phase transition from the liquid state to the solid state. One mol% of FITC-labeled peptide was mixed into the monolayers to visualize the phase separation of the solid and liquid states at the surface pressure of the coexisting region. Various shapes of the dark domain were observed at the top of the mound in the isotherms by fluorescence microscopy. The helical peptides formed two-dimensional crystals at the air/water interface when they were compressed to the solid state.An amino-terminated helical peptide, HA16B, was suspended in an aqueous medium by a sonication method and transparent dispersion was obtained. The dynamic light scattering measurement of the dispersion revealed the particle size of 75 nm with a narrow size distribution. The molecular assembly of the helical peptide in water was called “Peptosome”, because it takes a vesicular structure.     

Solid-phase synthesis of peptides containing arginine with an unprotected guanidine group

A new variant of the solid phase synthesis of arginine-containing peptides was proposed. The conditions for the attachment to the Wang polymer of N alpha-Fmoc-arginine containing a protonated guanidine group were found. We demonstrated that this attachment is accompanied by neither racemization nor the attachment of the second Arg residue. Side reactions involving the guanidine group of arginine were studied, and methods for their prevention were proposed. The comparison of the carbodiimide method with a 1-hydroxybenzotriazole additive and a modified method with the use of Kastro's reagent for the introduction of N alpha-Fmoc-Arg residue with the unprotected guanidine group into the growing peptide chain demonstrated the advantages of the second method. Bradykinin and a peptide corresponding to the 584-591 sequence of the transmembrane gp41 from HIV-1 were synthesized by the method proposed here.     

The Chemical Shift Index method applied to resin-bound peptides.

The Chemical Shift Index (CSI) method proposed by Wishart et al. [Biochemistry (1992) 31, 1647-1651] to evaluate the secondary structure of peptides in aqueous solution uses as its reference the chemical shift values of each of the 20 natural amino acids (X) in a typical nonstructured sequence GGXAGG (17-20). In order to apply the CSI method to protected resin-bound peptides, we established a new database of chemical shift values for the same GGXAGG sequences in their protected form and anchored to a polystyrene resin swollen in DMF-d7. The predictive value of this new reference set in the CSI protocol was tested on different resin-bound peptides that were previously characterized by a full NOE analysis.     

Prediction of lipoprotein signal peptides in Gram-negative bacteria

A method to predict lipoprotein signal peptides in Gram-negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII-cleaved proteins), SPaseI-cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI-cleaved, cytoplasmic, and transmembrane proteins. The results obtained were significantly better than those of previously developed methods. Even though Gram-positive lipoprotein signal peptides differ from Gram-negatives, the HMM was able to identify 92.9% of the lipoproteins included in a Gram-positive test set. A genome search was carried out for 12 Gram-negative genomes and one Gram-positive genome. The results for Escherichia coli K12 were compared with new experimental data, and the predictions by the HMM agree well with the experimentally verified lipoproteins. A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/.     

Gas-phase hydrolysis of proteins and peptides

A simplified gas-phase hydrolysis procedure for proteins and peptides is described. The apparatus consists of a glass vacuum desiccator, a ceramic plate, and a Teflon ring. The method was shown to give reproducible compositions for hydrolysis of human serum albumin and microanalysis of α-melanocyte stimulating hormone including the quantitation of as little as one residue of tryptophan. It minimizes sample handling and allows for the simultaneous hydrolysis of a large number of samples.     

Computational identification of self-inhibitory peptides from envelope proteins

Fusion process is known to be the initial step of viral infection and hence targeting the entry process is a promising strategy to design antiviral therapy. The self-inhibitory peptides derived from the enveloped (E) proteins function to inhibit the protein-protein interactions in the membrane fusion step mediated by the viral E protein. Thus, they have the potential to be developed into effective antiviral therapy. Herein, we have developed a Monte Carlo-based computational method with the aim to identify and optimize potential peptide hits from the E proteins. The stability of the peptides, which indicates their potential to bind in situ to the E proteins, was evaluated by two different scoring functions, dipolar distance-scaled, finite, ideal-gas reference state and residue-specific all-atom probability discriminatory function. The method was applied to α-helical Class I HIV-1 gp41, β-sheet Class II Dengue virus (DENV) type 2 E proteins, as well as Class III Herpes Simplex virus-1 (HSV-1) glycoprotein, a E protein with a mixture of α-helix and β-sheet structural fold. The peptide hits identified are in line with the druggable regions where the self-inhibitory peptide inhibitors for the three classes of viral fusion proteins were derived. Several novel peptides were identified from either the hydrophobic regions or the functionally important regions on Class II DENV-2 E protein and Class III HSV-1 gB. They have potential to disrupt the protein-protein interaction in the fusion process and may serve as starting points for the development of novel inhibitors for viral E proteins.     

Conformation characteristics of gamma-glutamyl-containing peptides

Conformational analysis, by the method of atom-atomic potentials, has been carried out for five tripeptides containing gamma-glutamyl bonds and having general formula Glu(gamma)-X-Gly. The spatial structures have been determined and the changes arising on varying the second residue have been analyzed. A comparison of possible conformations and biological activity in respect to a number of enzymes allows to conceive what structural features of these compounds are important for the substrate specificity of the enzymes. In particular, the active site topography has been surmised for glutathione synthetase (EC 6.3.2.3) and gamma-glutamyltranspeptidase (EC 2.3.2.2). The glutathione thiol group has been found to be exposed in all possible conformations that explains its accessibility for various reagents.     

Cyclic peptides revisited

A multistep computational scheme was used to deduce possible conformations for a cyclic antagonist analog of somatostatin that has been reported by Coy and coworkers. An algebraic algorithm was used to find dihedral angles that give cyclic structures, the energy was computed for these structures, the lower-energy structures were classified into conformational families, the energy was minimized for the lowest-energy member of each family, and finally, the structures from energy minimization were reclassified. Analysis revealed seven distinct conformational families that contain reverse turns. The families differ in the position of the turns in the primary sequence; frame-shifted turns are observed at each possible position.