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At least 37 records · Page 2Linked to original sources
PubMed1992

Photolabelling of Salmonella typhimurium LT2 sialidase. Identification of a peptide with a predicted structural similarity to the active sites of influenza-virus sialidases.

The sialidase from Salmonella typhimurium LT2 was characterized by using photoaffinity-labelling techniques. The well-known sialidase inhibitor 5-acetamido-2,6-anhydro-3,5-dideoxy-D-glycero-D-galacto-non- 2-enonic acid (Neu5Ac2en) was modified to contain an amino group at C-9, which permitted the incorporation of 4-azidosalicylic acid in amide linkage at this position. Labelling of the purified protein with the radioactive (125I) photoprobe was determined to be highly specific for a region within the active-site cavity. This conclusion was based on the observation that the competitive inhibitor Neu5Ac2en in the photolysis mixture prevented labelling of the protein. In contrast, compounds with structural and chemical features similar to the probe and Neu5Ac2en, but which were not competitive enzyme inhibitors, did not affect the photolabelling of the protein. The peptide interacting with the probe was identified by CNBr treatment of the labelled protein, followed by N-terminal sequence analysis. Inspection of the primary structure of the protein, predicted from the cloned structural gene for the sialidase [Hoyer, Hamilton, Steenbergen & Vimr (1992) Mol. Microbiol. 6, 873-884] revealed that the label was incorporated into a 9.6 kDa fragment situated within the terminal third of the molecule near the C-terminal end. Secondary-structural predictions using the Garnier-Robson algorithm [Garnier, Osguthorpe & Robson (1978) J. Mol. Biol. 120, 97-120] of the labelled peptide revealed a structural similarity to the active site of influenza-A- and Sendai-HN-virus sialidases with a repetitive series of alternating beta-sheets connected with loops.

Affinity Labels↗
PubMed1977

Characterization of a common precursor to corticotropin and beta-lipotropin: cell-free synthesis of the precursor and identification of corticotropin peptides in the molecule.

mRNA was isolated from cultures of AtT-20/D-16v tumor cells and translated in a mRNA-dependent reticulocyte cell-free system. The corticotropin (ACTH) product was purified by a double-antibody immunoprecipitation procedure using antisera specific for the alpha(1-24) sequence of ACTH. The product is shown by sodium dodecyl sulfate/gel electrophoresis and gel filtration on guanidine-HCl columns to be homogeneous with an apparent molecular weight (Mr) of 28,500. A product with the same molecular weight is synthesized when membrane-bound polysomes from D-16v cells are allowed to complete their nascent chains in a reticulocyte cell-free system. Mr 31,000 ACTH isolated from tumor cells has been separated into three proteins of different apparent Mr:29,000, 32,000, and 34,000. The cell-free product contains the same lysine-, methionine-, and phenylalanine-labeled tryptic peptides as the Mr 29,000 ACTH synthesized in the tumor cells. Tryptic peptide analysis also reveals the presence of the alpha(1-39) sequence in the Mr 28,500 cell-free product and suggests that there is only one copy of this sequence in the Mr 28,500 molecule.

Adrenocorticotropic Hormone↗
PubMed1979

Coexistence of desmin and the fibroblastic intermediate filament subunit in muscle and nonmuscle cells: identification and comparative peptide analysis.

Extraction of chicken embryo fibroblasts (CEF) or baby hamster kidney (BHK) cells with 1% Triton X-100 and 0.6 M KCl leaves an insoluble cytoskeletal residue composed primarily of the 52,000 Mr subunit of intermediate filaments (F-IFP). In addition, CEF cytoskeletons exhibit a minor component with Mr of 50,000, identified as alpha-desmin, one of the two major isoelectric variants of the intermediate filament subunit from smooth muscle. BHK cytoskeletons contain the 50,000 Mr mammalian desmin variant. Cytoskeletons prepared from chicken embryonic myotubes contain F-IFP and both alpha- and beta-desmin. These data suggest that two distinct 10-nm filament subunits coexist in a single cell. One-dimensional peptide analysis of F-IFP and desmin from avian and mammalian cells reveals significant interspecies homology, as well as homology between F-IFP and desmin from the same species. Peptide analyses of 32P-labeled intermediate filament subunits suggest that there is considerable similarity in the phosphorylation sites of these proteins. These results indicate that F-IFP and desmin might be evolutionally related.

Amino Acid Sequence↗
PubMed1977

Characterization of a common precursor to corticotropin and beta-lipotropin: identification of beta-lipotropin peptides and their arrangement relative to corticotropin in the precursor synthesized in a cell-free system.

Radioactive proteins synthesized in an mRNA-dependent reticulocyte cell-free system under the direction of mRNA from AtT-20/D-16v mouse cells were isolated by specific immunoprecipitation using antiserum to either alpha(1-24) corticotropin or beta-endorphin [beta(61-91) lipotropin]. Each immunoprecipitate was fractionated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis and shown to contain only one labeled protein with an apparent molecular weight of 28,500. Tryptic peptide analysis of the Mr 28,500 corticotropin and beta-lipotropin molecules isolated from the gels demonstrated that the two proteins had the same lysine, methionine, and tryptophan peptides. Four tryptic peptides from the cell-free product exhibited the same electrophoretic and chromatographic mobilities as marker tryptic peptides from bovine beta-melanotropin and porcine beta-endorphin. The identification of these peptides was confirmed by amino acid composition studies with a variety of labeled amino acids. The beta-lipotropin tryptic peptides were also shown to be located carboxy terminal to the corticotropin tryptic peptides.

Adrenocorticotropic Hormone↗
PubMed1978

Disulfide-linked cyanogen bromide peptides of bovine fibrinogen. III. Isolation and identification by sequence analysis of the chain constituents in peptides F-CB2, F-CB4 and F-CB5.

Three disulfide-linked peptides with molecular weights of about 6000, 7000 and 45000, respectively, were isolated from bovine fibrinogen cleaved with cyanogen bromide. The chain constituents of these peptides were separated after reduction and alkylation and identified by partial amino acid sequence analysis. Of the five polypeptide chains of the largest fragment F-CB2, three are derived from the central region of Bbeta chain, one from the Aalpha chain and one from the gamma chain. The smaller peptides F-CB4 and F-CB5 consist of one and two polypeptide chains and originate from central regions of the Bbeta and gamma chains, respectively, indicating that they represent intrachain disulfide loops. These and previous data show that the disulfide-bonded regions of bovine fibrinogen are similar to those in human fibrinogen.

Amino Acid Sequence↗
PubMed1977

Watery diarrhea syndrome in an adult with ganglioneuroma-pheochromocytoma: identification of vasoactive intestinal peptide, calcitonin, and catecholamines and assessment of their biologic activity.

A case of adult ganglioneuroma-pheochromocytoma with an associated watery diarrhea syndrome is reported. High levels of vasoactive intestinal peptide (VIP) were found in preoperative serum and in tumor tissue. The serum VIP levels fell to normal, and the watery diarrhae syndrome completely ceased following removal of the tumor. In addition to containing VIP, the tumor was rich in catecholamines, and calcitonin. Peptide hormone-containing extracts and catecholamine extracts from the tumor both activated the adenyl cyclase system and increased lipolytic activity in a preparation of isolated rat fat cells. The findings in this patient further link VIP with neural crest tissues, and suggest the importance of determining catecholamine levels in patients with the watery diarrhea syndrome.

Acidosis↗
PubMed2026

Identification of a Nonribosomal Peptide Analog With Activity Against Multiple Gram-Positive Bacteria via a Synthetic Bioinformatic Natural Product Discovery Approach.

Nonribosomal peptide (NRP) antibiotics exhibit potent biological activities and are broadly used in clinical therapy. Because most microorganisms are difficult to culture and many antibiotic biosynthetic genes are silent, traditional activity tracking approaches face major limitations in the discovery of novel NRPs. Here, based on a synthetic bioinformatic natural product (syn-BNP) discovery approach that integrates bioinformatics and chemical synthesis, a novel nonribosomal peptide synthetase (NRPS) gene cluster from the genome of Rhodococcus erythropolis D-1 was mined. A putative NRP scaffold synthesized by the NRPS encoded by this cluster was predicted. Through chemical synthesis and four rounds of structure-activity relationship (SAR) studies, 37 NRP analogs were ultimately generated. Among these analogs, ZURJC28 shows activity against multiple Gram-positive bacteria, including two drug-resistant strains. Mechanistic studies and metabolomics analyses revealed that ZURJC28 exerts membrane-disruptive activity associated with interaction with phosphatidylglycerol (PG)-enriched Gram-positive membranes, leading to membrane damage and widespread metabolic dysregulation. ZURJC28 also shows low cytotoxicity and low hemolytic activity, suggesting its preliminary in vitro safety profile.

Gram-Positive Bacteria↗
PubMed2026

Foundation model enables interpretable open and error-tolerant searching for mass spectrometry-based proteomics.

MOTIVATION: Mass spectrometry-based proteomics allows studying all proteins of a sample on a molecular level. However, mass spectra are noisy and contain complex patterns, making them inherently challenging to analyze with algorithmic approaches. In terms of the protein sequence landscape, most recent bottom-up MS-based proteomics studies consider either a diverse pool of post-translational modifications, employ large databases-as in metaproteomics or proteogenomics, study multiple isoforms of proteins, include unspecific cleavage sites or even combinations thereof. All this makes peptide and protein identifications challenging. RESULTS: Here, we present a foundation model, called yHydra, that jointly embeds spectra and peptides. This allows us to implement various downstream tasks and search modes in Euclidean space. We implement an open search which allows querying multiple ten-thousands of spectra against millions of peptides. Furthermore, we implement an error-tolerant search for identifying additional proteoforms that are not included in off-the-shelf reference proteomes. Our foundation model provides meaningful embeddings, as we interpret learned peptide embeddings in comparison to the peptide's physico-chemical properties. Hydra's open search, assigns delta masses to each identification which allows to unrestrictedly characterize post-translational modifications. The error-tolerant mode of yHydra can be used as post-processing to existing search engines or as a standalone. yHydra is evaluated on several real life data sets for the identification of modified peptide sequences and shows up to 25% increase in peptide identification at constant false discovery rate compared to the current state-of-the-art. AVAILABILITY AND IMPLEMENTATION: Code is available on Gitlab: https://gitlab.com/dacs-hpi/yHydra, and https://gitlab.com/dacs-hpi/yHydra_train.

Proteomics↗
PubMed2026

Immunopeptidomics in gliomas: Decoding antigen presentation for precision immunotherapy.

Gliomas and particularly glioblastomas, represent the most aggressive and treatment-resistant brain tumours. Current standard treatments, including surgical resection, radiotherapy and chemotherapy, offer only limited long-term survival benefits. The highly immunosuppressive tumour microenvironment that characterizes gliomas enables immune evasion and limits the effectiveness of anti-tumour immune response, indicating the urgent need for identification of tumour antigens with clinical relevance to improve current immunotherapeutic strategies and enhance glioma immunogenicity. Immunopeptidomics, a mass spectrometry-based identification of peptides presented by HLA molecules, is a growing field of research for understanding the immunosurveillance of gliomas. By enabling the direct identification of naturally presented HLA-bound peptides from tumour tissue for T cell recognition, immunopeptidomics provide valuable insights into tumour antigen presentation and immune targeting. This review highlights the emerging role of immunopeptidomics in gliomas, covering the mechanisms of antigen processing and presentation by HLA class I and II molecules, the identification of glioma-associated antigens, the development of personalised peptide vaccines and the discovery of new targets for T cell-based immunotherapies. The potential of plasma-derived soluble HLA (sHLA) peptidomes as minimally invasive liquid-biopsy biomarkers is further discussed for disease monitoring and response to treatment. Overall, immunopeptidomics are foreseen as a powerful tool for the discovery of new tumour antigens leading to the development of more effective personalised glioma immunotherapies.

Humans↗
PubMed2025

Improved Detection of Differentially Abundant Proteins through FDR-Control of Peptide-Identity-Propagation.

The goal of proteomics is to identify and quantify peptides and proteins within a biological sample. Almost all algorithms for the identification of peptides in LC-MS/MS data employ two steps: peptide/spectrum matching and peptide-identity-propagation (PIP), also known as match-between-runs. PIP can routinely account for up to 40% of all results, with that proportion rising as high as 75% in single-cell proteomics. Unlike peptide identities derived through peptide/spectrum matches, for which error estimation has been strictly enforced for decades, peptide identities derived through PIP have not historically been subject to statistical evaluation. As an indispensable component of label-free quantification, PIP needs a statistically rigorous method for estimating its false-discovery rate (FDR). We present a method for FDR control of PIP, called PIP-ECHO, and devise a rigorous protocol for evaluating FDR control of any PIP method. Using three different benchmark data sets, we evaluate PIP-ECHO alongside the PIP procedures implemented by FlashLFQ, IonQuant, and MaxQuant. These analyses show that only PIP-ECHO can accurately control the FDR of PIP at 1% across all data sets. When analyzing a spike-in data set, PIP-ECHO increases both the accuracy and sensitivity of differential expression analysis, yielding substantially more differentially abundant proteins than either MaxQuant or IonQuant.

Proteomics↗
PubMed1976

Incorporation of 14C-labelled amino acids into corticotrophin-like intermediate lobe peptide and alpha-melanocyte-stimulating hormone by the rat pituitary neurointermediate lobe in vitro, and the identification of four new pars intermedia peptides.

At least seven radioactive peptides, which fractionated on Biogel P6, were found in rat neurointermediate lobes after incubation for 6 h with [14C]proline. Only three of these could be tentatively identified; one as alpha-melanocyte-stimulating hormone (alpha-MSH) and two as forms of corticotrophin-like intermediate lobe peptide (CLIP). One other cross-reacted partially with a beta-malanocyte-stimulating hormone (beta-MSH) antiserum, was acidically charged and eluted on Biogel P6 in roughly the same position as ACTH. The other three peptides showed no resemblance to alpha-MSH, CLIP, beta-MSH or ACTH.

Adrenocorticotropic Hormone↗
PubMed1975

[Identification and biological activity of peptides containing a partially benzyloxycarbonylated L-arginine on their amino terminus (author's transl)].

Nomega-Z-L-Arg-L-Phe-L-Phe was shown to be the antibiotically active compound in a peptide mixture which was obtained by treating Z3-L-Arg-L-Phe-L-Phe with hydrogen bromide/trifluoroacetic acid or 4N HBr/glacial acetic acid, respectively. Identification of this compound was achieved by thin-layer chromatography, enzymatic digestion and autobiograms with fungi. The pure Nomega-Z-L-Arg-L-Phe-L-Phe was not the only compound with antibiotic qualities; generally it could be said that all peptides with the sequence Nomega-Z-L-Arg-X-L-Phe (X might be any amino acid) are antibiotically active. All of them are antagonized by L-aspartic acid and asparagine in the crossstrip test (on fungi). The antibiotical activity of all these peptides must be due to the Nomega-Z-L-Arg-residue provided that it is coupled to a dipeptide X-L-Phe, or to an aromatic system (e.g. L-Phe or benzyl amine).

Anti-Bacterial Agents↗
PubMed1978

Highly active position eight analogues of somatostatin and separation of peptide diastereomers by partition chromatography.

Six stereochemically pure analogues of somatostatin (SS), D- and L-5F-Trp8-SS, D- and L -6F-Trp8-SS, and D- and L-5Br-Trp8-SS, were synthesized and found to be more potent than somatostatin in suppressing the release of growth hormone from cultured rat pituitary cells. Two of the analogues, D-5F-Trp8- and D-5Br-Trp8-SS, were respectively 25 and 30 times more active than somatostatin in that assay. The analogues were prepared by solid phase synthesis of their corresponding diastereomeric mixtures, followed by their complete resolution by preparative partition chromatography. Reversed phase high pressure liquid chromatography (HPLC) was used to monitor the resolution and also to check the final purity of each peptide. Positive identification of each diastereoisomer was determined by amino acid analyses of their enzymatic digests, direct comparison with a known all-L standard in the case of the 5F-Trp8 analogues, and chromatographic separation of dansylated amino acids following enzymatic digestion of D- and L-5Br-Trp8-SS. The role of tryptophan in somatostatin is discussed and it is suggested that maintenance of physiological activity in somatostatin peptides, at least on the pituitary, is partially dependent upon the degree of resonance in the indole nucleus in position 8.

Cells, Cultured↗