Characterization of peptides by liquid chromatography/electrospray ionization mass spectrometry using silver nitrate as a post-column complexant

Two model peptides, des-Arg1-bradykinin (DAB) and bradykinin (B), were cationized by Ag+ after their separation by reversed-phase liquid chromatography (RPLC) prior to mass spectrometry (MS). Silver nitrate solution was used as a post-column reagent. The RPLC and MS experimental conditions were optimized using flow injection in order to obtain sufficiently abundant silver adducts to permit MS/MS experiments. The use of water-methanol with 0.1% formic acid as mobile phase allowed a good chromatographic separation of the two peptides with a polymeric stationary phase and sufficiently abundant silver-containing adducts, [M + Ag + H]2+ and [M + 2Ag]2+. The gas-phase dissociation of [DAB + Ag + H]2+ and [DAB + 2Ag]2+ led to interpretable mass spectra during the on-line cationization experiment. Most of the ions obtained by dissociating [DAB + Ag + H]2+ and [DAB + 2Ag]2+ species are silver-containing ions but the ions produced depend on the parent. The ions coming from the dissociation of the doubly charged silver adducts [DAB + Ag + H]2+ or [DAB + 2Ag]2+ are of interest compared with those coming from the singly charged silver species or doubly charged protonated species. The fragmentation of the doubly charged silver adducts provides ions over the entire mass range. Although the presence of several prolines in des-Arg1-bradykinin prevents the formation of some expected ions, the observation of triplets [an-H + Ag]+, [bn-H + Ag]+ and [bn + OH + Ag]+ produced by the dissociation of on-line Ag(+)-cationized peptides could contribute to greater success of automatic sequencing of peptides.     

五氯化磷辅助下氨基酸的自组装成肽反应研究

L-α-氨基酸和D-α-氨基酸可与五氯化磷直接发生磷酰化反应，随后自组装成多肽，但β-氨基酸不能成肽，DL-α-氨基酸成肽困难；在SOCl2存在下，α-氨基酸也不能成肽，用电喷雾质谱研究了氨基酸的自组装反应，反应过程中有五元环状的氨基酸五配位磷中间体生成，使用硅烷基保护的氨基酸，在^31PNMR中可观察到五配位磷中间体。     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

A sequence and structural study of transmembrane helices

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the -branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.     

The use of glass capillary columns for the analysis of polar natural products

Two published procedures for glass capillary column production are applied to produce capillaries for chromatography of polar natural compounds. Soda lime glass capillaries, after leaching with aqueous HCL, are either treated with colloidal silicic acid or with barium carbonate and coated with either Silar 7CP or SE 52. A test mixture as well as polar carbohydrate and peptide mixtures are chromatographed on the different columns and their chromatographic properties are evaluated. Combined capillary gas chromatography-electron impact and chemical ionization mass spectrometry are used for identification of the peptide sequence.     

LyP-1 peptide-functionalized gold nanoprisms for SERRS imaging and tumor growth suppressing by PTT induced-hyperthermia

The gold nanoprisms (GNPs) have exhibited special plasmonic properties for biomedical applications because of their unique shapes and dimensions. Based on their optical performance, the NIR dye IR780 not only enabled the GNPs-based nanosystem as SERRS nanoparticles for Raman-encoded molecular imaging, but also enhanced the plasmonic photothermal property by laser irradiation. Meanwhile, the GNPs/IR780-Lyp-1 by introduction of tumor-homing peptide segment LyP-1, which presents high affinity to p32 protein, demonstrated the increased enrichment in tumor region and enhanced photothermal therapy efficacy.     

THPep: A machine learning-based approach for predicting tumor homing peptides

In the present era, a major drawback of current anti-cancer drugs is the lack of satisfactory specificity towards tumor cells. Despite the presence of several therapies against cancer, tumor homing peptides are gaining importance as therapeutic agents. In this regard, the huge number of therapeutic peptides generated in recent years, demands the need to develop an effective and interpretable computational model for rapidly, effectively and automatically predicting tumor homing peptides. Therefore, a sequence-based approach referred herein as THPep has been developed to predict and analyze tumor homing peptides by using an interpretable random forest classifier in concomitant with amino acid composition, dipeptide composition and pseudo amino acid composition. An overall accuracy and Matthews correlation coefficient of 90.13% and 0.76, respectively, were achieved from the independent test set on an objective benchmark dataset. Upon comparison, it was found that THPep was superior to the existing method and holds high potential as a useful tool for predicting tumor homing peptides. For the convenience of experimental scientists, a web server for this proposed method is provided publicly at http://codes.bio/thpep/.     

Synthesis and antiangiogenic activities of 5-amino-1,3-dihydro-1, 3-dioxo-2H-isoindole-2-propanoic acid derivatives

Based on the structure-activity relationships and antiangiogenic mechanism of RGD-containing peptides,a series of 5-amino- 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized.The structures were characterized by ~1H NMR,MS and elementary analysis.There ability to inhibit angiogenesis were evaluated by chick embryo chorioallantoic membrane assay at 10~(-5) mol/L.Compounds 7a and 7b displayed obvious antiangiogenic activity.     

Synthesis of protected peptides from the human IgG1 hinge region on PEG support using disulfide bond synthons and alkaline or enzymatic detachment

Peptides from the hinge region of human IgG1 are potential defined carriers of synthetic immunogens. Their synthesis was carried out on the soluble support—PEG-OMe 2000 using disulfide bond synthons. The loading capacity of the polymer was increased twofold by anchoring the lysine as a simple branching unit. The amino acid leucine was used as an enzymatically cleavable linker. Peptide detachment from the polymer was performed either by classical ester bond saponification or newly by peptide bond cleavage catalyzed by thermolysin in water.