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PeptidesPeptide MappingPeptide FragmentsAmino Acid SequenceMolecular Sequence DataCross ReactionsEpitopesPeptide LibraryChromosome MappingAntimicrobial Cationic PeptidesTrypsinMolecular WeightPeptides, CyclicElectrophoresis, Polyacrylamide GelOligopeptidesAmino AcidsChromatography, High Pressure LiquidBinding SitesProtein BindingPeptide BiosynthesisNatriuretic Peptide, BrainBase SequenceMass SpectrometryProtein ConformationKineticsPeptide HydrolasesEpitope MappingCyanogen BromideVasoactive Intestinal PeptideModels, MolecularCell LineCalcitonin Gene-Related PeptideProtein PrecursorsCell-Penetrating PeptidesCattleRecombinant ProteinsCloning, MolecularSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationPeptide YYProtein Structure, SecondarySequence Homology, Amino AcidPeptide Nucleic AcidsStructure-Activity RelationshipNatriuretic Peptide, C-TypePhosphopeptidesPhosphorylationEscherichia coliSubstrate SpecificityNatriuretic PeptidesProteinsGastrin-Releasing PeptideAntibodies, MonoclonalReceptors, Formyl PeptidePeptide PHIPeptide SynthasesRabbitsProtein Structure, TertiaryReceptors, PeptideViral ProteinsAtrial Natriuretic FactorProtein Processing, Post-TranslationalCells, CulturedEndopeptidasesMutationDisulfidesIsoelectric FocusingSerine EndopeptidasesChromatography, AffinityChromatography, GelMembrane ProteinsSequence AlignmentChromatography, Ion ExchangeBinding, CompetitiveBacterial ProteinsCell MembraneCysteineRNA, MessengerProtein KinasesGlycoproteinsIntracellular Signaling Peptides and ProteinsSpecies SpecificityOpioid PeptidesHydrolysisMacromolecular SubstancesRecombinant Fusion ProteinsPeptide HormonesProtein BiosynthesisLysineAffinity LabelsIsoelectric PointChickensHydrogen-Ion ConcentrationCricetinaeElectrophoresis, Gel, Two-DimensionalGlycosylationIsoenzymesMolecular MimicryMagnetic Resonance SpectroscopyCarrier ProteinsAntibodies
ProteinsCross-reactivityEpitopeAntimicrobial peptidesGenesProteinGeneSequencesImmunogenicResiduesStructuresHumansNucleotideSimilarityMRNAEnzymeVitroGeneratesPartialCatalyticHumoralDemonstrateOccursHighHumanImmunePathwayDomainsPresenceStructuralAnalysisResultsSpecificPreviouslyExpressionModelsActivityHighlyAlphaEvidencePopulationCandidateGlobal
Proteins17
  • Prospectively applying our tools to SARS-CoV-2 proteins identified several epitopes and TCR sequencing revealed a monoclonal response in effector/memory CD8+ T cells against one of these epitopes with cross-reactivity against the homologous peptides from other coronaviruses. (ki.se)
  • We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. (elifesciences.org)
  • The resulting technique maps the location of most of the proteins in a human cancer cell line and, in addition, determines how many copies of each protein there are. (elifesciences.org)
  • Employing this map of SARS-CoV-2-non-homologous and homologous immunogenic peptides, we observe several immunogenic peptides with high similarity to human proteins, some of which have been reported to have elevated expression in severe COVID-19 patients. (ox.ac.uk)
  • Second, this MAP infection triggers a specific humoral response, as Sardinian T1D Olcegepant hydrochloride patients display high frequencies of antibodies (Abs) against mycobacterial proteins (heparin-binding hemagglutinin, glycosyl transferase) [17], whole MAP lysates (70% Ab+ T1D patients vs 7.6% Ab+ healthy controls) [16] and. (healthweblognews.info)
  • We also did selective epitope mapping using BLAST and showed similarities and homology between spike, nucleoprotein, and many other SARS-CoV-2 proteins with the human tissue antigens mitochondria M2, F-actin and TPO. (frontiersin.org)
  • SAR-CoV-2 spike proteins, and all other SARS-CoV-2 proteins, immunogenic epitopes in each SARS-CoV-2 protein were compared to human proteins in search of high local homologous matching. (danielsolis.cz)
  • If all of the parts of the epitopes that are homologous to human proteins are excluded from consideration due to risk of pathogenic priming, the remaining immunogenic parts of the epitopes may be still immunogenic and remain as potentially viable candidates for vaccine development. (danielsolis.cz)
  • If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC 5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. (iucr.org)
  • However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
  • Most commonly, this approach leverages high-resolution mass spectrometric measurements of proteolyzed proteins, combined with tandem peptide fragmentation to match observed spectra with those expected from their amino acid composition. (biorxiv.org)
  • Harnessing insights from our map of the global proteome, we're learning the fundamental design principles of proteins to bid farewell to trial and error and replace it with efficient and informed protein engineering. (basecamp-research.com)
  • We're on a mission to map the entire global proteome to derive the most in-depth understanding of how proteins function. (basecamp-research.com)
  • Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. (silverchair.com)
  • This technology is based on the capture of all proteins present in biological samples, and the normalization of their concentration via a combinatorial library of hexameric peptide ligands, used as baits for adsorbing all macromolecular species present in solution. (unict.it)
  • On the other hand, the large presence of known homologous proteins from the closest related specie (Equus caballus), allowed the cross-species identification for most of the proteins investigated. (unict.it)
  • Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)
Cross-reactivity3
  • In depth characterization of MHC motifs can help mapping the targets of T cells and understanding TCR cross-reactivity. (ki.se)
  • Overall, our work shows how in depth characterization of MHC motifs can help mapping the targets of T cells and understanding TCR cross-reactivity. (ki.se)
  • Type I hyper - sensitive reaction is induced by certain types of antigens referred to as allergens that elicit specific IgE antibodies or from cross reactivity between common homologous allergens from different sources (Santos et al 1999). (ispub.com)
Epitope2
  • was a linear correlation between titers of anti-MAP3865c and anti-ZnT8 Abs targeting these two homologous epitopes, and pre-incubation of sera with ZnT8 epitope peptides blocked binding to the corresponding MAP3865c peptides. (healthweblognews.info)
  • These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. (uthscsa.edu)
Antimicrobial peptides2
Genes4
  • The other gene, named RBD-2, was homologous to the HBD-2 and bovine tracheal antimicrobial peptide (TAP) genes. (lookformedical.com)
  • The beta-defensin genes mapped closely on rat chromosome 16 and were closely linked to the alpha-defensins genes, suggesting that they are part of a gene cluster, similar to the organization reported for humans. (lookformedical.com)
  • The associated genes with 2-Monoolein are Glucagon-Like Peptide 1, Homologous Gene, LIPG gene and Serum Albumin. (cmdm.tw)
  • Mapping of the genes encoding human protein matches to pathways point to targets that could explain the observed presentation of symptoms in COVID-19 disease. (danielsolis.cz)
Protein11
  • We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. (elifesciences.org)
  • Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. (elifesciences.org)
  • Methods: We have conducted a non-randomized, open-label and parallel-controlled phase 4 trial to evaluate the magnitude and longevity of immune responses to booster vaccination with intramuscular adenovirus vectored vaccine (Ad5-nCoV), aerosolized Ad5-nCoV, a recombinant protein subunit vaccine (ZF2001) or homologous inactivated vaccine (CoronaVac) in those who received two doses of inactivated COVID-19 vaccines. (bvsalud.org)
  • To use this resource, a user provides the sequence information for each protein building block and available partial or homologous structures. (asbmb.org)
  • Researchers must incubate individual peptide spots with the protein extract on a cellulose membrane and then retrieve them for further analysis. (asbmb.org)
  • To overcome these shortcomings, Evelyn Ramberger, Lorena Suarez-Artiles, Daniel Perez-Hernandez and colleagues at Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Germany, have developed an optimized method for using protein interaction screen on a peptide matrix, or PRISMA, in combination with quantitative mass spectrometry. (asbmb.org)
  • These assays demonstrated that, at least under the conditions used in this assay, binding to laminin was localized to domain 137-230, a region that encompasses a previously identified binding site known as Peptide G. This protein, like the full-length recombinant laminin binding protein, aggregated under conditions used for nuclear magnetic resonance experiments and therefore could not be analyzed with this technique. (montana.edu)
  • Chemical perturbation mapping performed on the copper(I)=protein defined regions of NosL potentially involved in copper binding, and thus allowed preliminary identification of the copper-binding ligand Met 109. (montana.edu)
  • Current approaches for peptide and protein identification use advanced statistical and graphical methods to match mass spectra and estimate their confidence. (biorxiv.org)
  • We thank Ross Tomaino at the Harvard Mass Spectrometry Core for assisting in the protein mass spectrometric peptide sequencing and phosphopeptide mapping experiments. (tecnoetica.org)
  • Notwithstanding this renewed growing interest, until today genome mapping of the Equus genus is largely uncompleted and the characterization at molecular level of DM only concerns the major protein components,3,4,5 whereas nothing is known about the minor or trace protein components. (unict.it)
Gene4
  • Database searches and analysis of available genomic DNA sequence from the region revealed the presence of the fibroblast growth factor homologous factor gene, FHF2, within the duplication breakpoint interval. (edu.au)
  • The FHF2 gene localisation and tissue-specific expression pattern suggest it to be a candidate gene for familial cases of the BFLS syndrome and other syndromal and non-specific forms of X-linked mental retardation mapping to the region. (edu.au)
  • We have cloned the NPFF gene from human, bovine, rat, and mouse, and show that the precursor mRNA encodes for all three of the biochemically identified peptides (NPFF, NPAF, and NPSF). (aspetjournals.org)
  • Exon 8 of the mouse α 6 subunit gene was disrupted by homologous recombination. (jneurosci.org)
Sequences2
  • The objective of the project is to discover the peptide sequences present in each venom, to map mutations of homologous sequences, to quantitatively analyze the peptides of males and females and to prospect in silico potential biological activities of new peptides. (fapesp.br)
  • Modified peptides showed enhanced binding to HLA-A2 compared with the native sequences and immunization of HLA-A2 transgenic mice generated high avidity modification specific CD8 responses that killed peptide expressing target cells. (bmj.com)
Immunogenic2
  • Using a pool of functionally evaluated SARS-CoV-2 peptides, we report a map of 126 immunogenic peptides with high similarity to 285 MHC-presented peptides from at least one HCoV. (ox.ac.uk)
  • The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. (uthscsa.edu)
Residues2
  • The alpha- and beta-subunits of spectrin are made of repeated homologous units of 106 residues. (embl.de)
  • Contrary to previous findings on a synthetic peptide corresponding to residues 205-229, this sequence within the context of the 200-295 construct demonstrated no laminin binding activity. (montana.edu)
Structures1
  • The newly described crystallographic structures of two consecutive homologous repeats of human alpha-actinin, a member of the spectrin superfamily, shed new light on alpha-actinin interchain binding properties. (embl.de)
Humans1
  • Although evidence for a cause-effect relationship is lacking, MAP transmission to humans has long been associated with Crohn's disease both in Sardinia [13] and elsewhere [14]. (healthweblognews.info)
Nucleotide1
  • Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (embl.de)
Similarity1
  • Neuropeptides FF (NPFF), AF (NPAF), and SF (NPSF) are homologous amidated peptides that were originally identified on the basis of similarity to the molluscan neuropeptide FMRF-amide. (aspetjournals.org)
MRNA1
  • We demonstrate that NPFF precursor mRNA expression by Northern analysis and map sites of expression by in situ hybridization. (aspetjournals.org)
Enzyme1
  • Simian immunodeficiency (SIV) multiple antigenic peptide-enzyme immunoassay (SMAP-EIA) seroreactivity trends to SIV immunodominant region (IDR) peptides in HIV-seronegative Cameroonian population groups with different levels of exposure (high exposure [HE], low exposure. (cdc.gov)
Vitro1
  • Methods Homocitrullinated peptides were identified and assessed in vitro for HLA-A2 binding and in vivo in human leukocyte antigen (HLA) transgenic mouse models for immunogenicity. (bmj.com)
Generates1
  • The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. (iucr.org)
Partial1
  • In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the internal repeat in spectrin occurs several times. (embl.de)
Catalytic2
  • 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. (uthscsa.edu)
  • The discovery of butelase-1, an extremely efficient AEP (catalytic efficiency of up to 1 340 000 M −1 s −1 on a non-native substrate) [ 6 , 7 ] that forms peptide bonds via a cleavage-coupled transpeptidation reaction, has led to a surge of interest in AEPs. (silverchair.com)
Humoral1
  • One person had strong humoral and weak cellular immune reactivity to SIVcol peptides. (cdc.gov)
Demonstrate1
Occurs1
  • Transpeptidation by plant AEPs is often intramolecular, in that the free N-terminal nucleophile originates from the same molecule in which the initial cleavage reaction occurs, resulting in peptide macrocyclisation. (silverchair.com)
High4
  • 1 of a panel of 9 SIV IDR MAPs ( Figure 1 ), 17.1% were seroreactive in the high exposure group, 7.8% in the low exposure group, and 2.3% in the general group. (cdc.gov)
  • Finally, we provide 10 SARS-CoV-2 peptides with known cognate TCRs that are conserved across multiple coronaviruses and are predicted to be recognised by a high proportion of the global population. (ox.ac.uk)
  • Counting 1.8 million inhabitants, 3.5 millions sheeps and approximately two hundred thousand cattle, MAP exposure may be particularly high in the Western Mediterranean island of Sardinia, where it is estimated that 60% of flocks may be contaminated. (healthweblognews.info)
  • The high-resolution structure of NosL consists of one four-strand antiparallel beta sheet, one three strand antiparallel beta sheet and two alpha-helices organized in a twisted butterfly-like fold that is structurally homologous to MerB, an alkyl mercury lyase. (montana.edu)
Human6
  • Börjeson-Forssman-Lehmann syndrome (BFLS) is a syndromal X-linked mental retardation, which maps by linkage to the q26 region of the human X chromosome. (edu.au)
  • Human tumor samples were analyzed by targeted mass spectrometry for presence of homocitrullinated peptides. (bmj.com)
  • Immunohistochemical analysis of paraffin-embedded human breast carcinoma using HER2/ErbB2 (29D8) RmAb in the presence of control peptide (left) or HER2/ErbB2 Blocking Peptide #1059 (right). (cellsignal.com)
  • Although transmitted to man, MAP infection is asymptomatic in human carriers and is not therefore regarded as a zoonosis, nor subjected Olcegepant hydrochloride to eradication in contaminated animals. (healthweblognews.info)
  • Western immunoblotting, liquid chromatography, and mass spectrometry were used to identify the HBD-1 and HBD-2 peptides in human saliva. (lookformedical.com)
  • Structural analysis by two-dimensional peptide maps (2D-PM) of the human Ia molecular pool expressed on the cell surface of two distinct lymphoblastoid cell line, LG-2 and Raji, revealed the existence of a novel MHC class II molecular heterodimer that differs at the level of both alpha and beta subunits from the previously described DP, DQ, and DR antigens. (silverchair.com)
Immune1
  • The new mapping method could be used in the future to analyse the anatomy of different cell types, such as nerve cells and cells of the immune system. (elifesciences.org)
Pathway1
  • Its function is homologous to that of C1s in the classical pathway. (lu.se)
Domains1
  • Villin-1 is made up of seven domains, six homologous domains make up the N-terminal core and the remaining domain makes up the C-terminal cap. (wikipedia.org)
Presence1
  • Furthermore, for the first time, we have shown that DP alpha chains display distinct peptide maps in LG-2 and Raji cells, thus suggesting the presence of structural polymorphism for these Ia subunits also. (silverchair.com)
Structural1
  • The DQ1 alpha and beta allelic products present in LG-2 cells (DQ homozygous) did not show appreciable structural variation when compared with the homologous allelic products present in Raji cells (DQ heterozygous). (silverchair.com)
Analysis2
  • In face of the potential richness of new active peptides still unexplored of the Naja kaouthia venom, we propose in this project the comparative peptidomic analysis of the venom of male and female specimens. (fapesp.br)
  • Further analysis suggests that this skewed distribution of TCRs cognate to homologous or non-homologous peptides in COVID-19 patients is likely to be HLA-dependent. (ox.ac.uk)
Results2
  • Our results support a model for the role of these peptides in pain regulation at the level of the spinal cord. (aspetjournals.org)
  • Results Homocitrullinated peptides from aldolase and cytokeratin were identified, that stimulated CD8-mediated responses in vivo. (bmj.com)
Specific3
  • The SMAP-EIA also detects other SIV strains not represented by specific SIV lineage-based peptides. (cdc.gov)
  • After combining our map with SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls, we show that public repertoires for the majority of convalescent patients are dominated by TCRs cognate to non-homologous SARS-CoV-2 peptides. (ox.ac.uk)
  • 50% of their public SARS-CoV-2-specific repertoires consist of TCRs cognate to homologous SARS-CoV-2-HCoV peptides. (ox.ac.uk)
Previously1
  • They also provide a context for the interpretation of the pain-sensitizing effects of injections of these peptides that have been previously reported. (aspetjournals.org)
Expression1
  • In this study, we characterized the expression of HBD-1 and HBD-2 mRNAs within the major salivary glands, tongue, gingiva, and buccal mucosa and detected beta-defensin peptides in salivary secretions. (lookformedical.com)
Models1
  • XL-MS can overcome ambiguity in modest-resolution cryo-EM density maps and add more information to extrapolate X-ray maps into more accurate models. (asbmb.org)
Activity1
  • beta-Defensins are cationic peptides with broad-spectrum antimicrobial activity that are produced by epithelia at mucosal surfaces. (lookformedical.com)
Highly1
Alpha2
  • The alpha and beta subunits are homologous with approximately 30% identity. (embl.de)
  • Furthermore, the peptide lacked the predicted alpha-helical content and tertiary structure as ascertained by nuclear magnetic resonance and by circular dichroism spectroscopy. (montana.edu)
Evidence1
  • Conclusion This is the first evidence that homocitrullinated peptides can be processed and presented via MHC-I and targeted for tumor therapy. (bmj.com)
Population1
  • It was because of the failure to produce a suitable mapping population for N. sylvestris that a mapping population of N. acuminata TA3460 × N. acuminata TA3461 was used instead. (biomedcentral.com)
Candidate2
  • We have recently proposed that MAP infection may be a potential candidate environmental trigger also for T1D. (healthweblognews.info)
  • Therefore, computationally predicted IgE epitopes from GMF allergen might be an ideal peptide-based novel candidate for immunotherapy. (ispub.com)
Global1
  • Brain Maps 4.0-Structure of the Rat Brain: An Open Access Atlas with Global Nervous System Nomenclature Ontology and Flatmaps. (neurotree.org)