Epitope Mapping: Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of immunochemistry.Epitopes: Sites on an antigen that interact with specific antibodies.Antibodies, Monoclonal: Antibodies produced by a single clone of cells.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Antibody Specificity: The property of antibodies which enables them to react with some ANTIGENIC DETERMINANTS and not with others. Specificity is dependent on chemical composition, physical forces, and molecular structure at the binding site.Epitopes, B-Lymphocyte: Antigenic determinants recognized and bound by the B-cell receptor. Epitopes recognized by the B-cell receptor are located on the surface of the antigen.Binding Sites, Antibody: Local surface sites on antibodies which react with antigen determinant sites on antigens (EPITOPES.) They are formed from parts of the variable regions of FAB FRAGMENTS.Peptide Library: A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Neutralization Tests: The measurement of infection-blocking titer of ANTISERA by testing a series of dilutions for a given virus-antiserum interaction end-point, which is generally the dilution at which tissue cultures inoculated with the serum-virus mixtures demonstrate cytopathology (CPE) or the dilution at which 50% of test animals injected with serum-virus mixtures show infectivity (ID50) or die (LD50).Cross Reactions: Serological reactions in which an antiserum against one antigen reacts with a non-identical but closely related antigen.Enzyme-Linked Immunosorbent Assay: An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme-antibody-antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed.Antibodies, Neutralizing: Antibodies that reduce or abolish some biological activity of a soluble antigen or infectious agent, usually a virus.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Autoantibodies: Antibodies that react with self-antigens (AUTOANTIGENS) of the organism that produced them.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Surface Plasmon Resonance: A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.Antibodies, Viral: Immunoglobulins produced in response to VIRAL ANTIGENS.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Autoantigens: Endogenous tissue constituents that have the ability to interact with AUTOANTIBODIES and cause an immune response.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Antibody Affinity: A measure of the binding strength between antibody and a simple hapten or antigen determinant. It depends on the closeness of stereochemical fit between antibody combining sites and antigen determinants, on the size of the area of contact between them, and on the distribution of charged and hydrophobic groups. It includes the concept of "avidity," which refers to the strength of the antigen-antibody bond after formation of reversible complexes.Immunoglobulin Fab Fragments: Univalent antigen-binding fragments composed of one entire IMMUNOGLOBULIN LIGHT CHAIN and the amino terminal end of one of the IMMUNOGLOBULIN HEAVY CHAINS from the hinge region, linked to each other by disulfide bonds. Fab contains the IMMUNOGLOBULIN VARIABLE REGIONS, which are part of the antigen-binding site, and the first IMMUNOGLOBULIN CONSTANT REGIONS. This fragment can be obtained by digestion of immunoglobulins with the proteolytic enzyme PAPAIN.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Mice, Inbred BALB CImmunodominant Epitopes: Subunits of the antigenic determinant that are most easily recognized by the immune system and thus most influence the specificity of the induced antibody.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.HIV Envelope Protein gp120: External envelope protein of the human immunodeficiency virus which is encoded by the HIV env gene. It has a molecular weight of 120 kDa and contains numerous glycosylation sites. Gp120 binds to cells expressing CD4 cell-surface antigens, most notably T4-lymphocytes and monocytes/macrophages. Gp120 has been shown to interfere with the normal function of CD4 and is at least partly responsible for the cytopathic effect of HIV.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Antibodies, Bacterial: Immunoglobulins produced in a response to BACTERIAL ANTIGENS.Epitopes, T-Lymphocyte: Antigenic determinants recognized and bound by the T-cell receptor. Epitopes recognized by the T-cell receptor are often located in the inner, unexposed side of the antigen, and become accessible to the T-cell receptors after proteolytic processing of the antigen.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Immunoglobulin G: The major immunoglobulin isotype class in normal human serum. There are several isotype subclasses of IgG, for example, IgG1, IgG2A, and IgG2B.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Kinetics: The rate dynamics in chemical or physical systems.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Bacterial Proteins: Proteins found in any species of bacterium.Spectrometry, Fluorescence: Measurement of the intensity and quality of fluorescence.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.Hybridomas: Cells artificially created by fusion of activated lymphocytes with neoplastic cells. The resulting hybrid cells are cloned and produce pure MONOCLONAL ANTIBODIES or T-cell products, identical to those produced by the immunologically competent parent cell.Antigen-Antibody Reactions: The processes triggered by interactions of ANTIBODIES with their ANTIGENS.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Antigens, Bacterial: Substances elaborated by bacteria that have antigenic activity.Antigens, Viral: Substances elaborated by viruses that have antigenic activity.HIV Antibodies: Antibodies reactive with HIV ANTIGENS.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Antigen-Antibody Complex: The complex formed by the binding of antigen and antibody molecules. The deposition of large antigen-antibody complexes leading to tissue damage causes IMMUNE COMPLEX DISEASES.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Viral Envelope Proteins: Layers of protein which surround the capsid in animal viruses with tubular nucleocapsids. The envelope consists of an inner layer of lipids and virus specified proteins also called membrane or matrix proteins. The outer layer consists of one or more types of morphological subunits called peplomers which project from the viral envelope; this layer always consists of glycoproteins.HIV Antigens: Antigens associated with specific proteins of the human adult T-cell immunodeficiency virus (HIV); also called HTLV-III-associated and lymphadenopathy-associated virus (LAV) antigens.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Antibodies: Immunoglobulin molecules having a specific amino acid sequence by virtue of which they interact only with the ANTIGEN (or a very similar shape) that induced their synthesis in cells of the lymphoid series (especially PLASMA CELLS).Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Antigens, Plant: Substances found in PLANTS that have antigenic activity.Immunoblotting: Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Oligopeptides: Peptides composed of between two and twelve amino acids.Protein Denaturation: Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.Allergens: Antigen-type substances that produce immediate hypersensitivity (HYPERSENSITIVITY, IMMEDIATE).Immunization: Deliberate stimulation of the host's immune response. ACTIVE IMMUNIZATION involves administration of ANTIGENS or IMMUNOLOGIC ADJUVANTS. PASSIVE IMMUNIZATION involves administration of IMMUNE SERA or LYMPHOCYTES or their extracts (e.g., transfer factor, immune RNA) or transplantation of immunocompetent cell producing tissue (thymus or bone marrow).Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Membrane Glycoproteins: Glycoproteins found on the membrane or surface of cells.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Immune Sera: Serum that contains antibodies. It is obtained from an animal that has been immunized either by ANTIGEN injection or infection with microorganisms containing the antigen.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.T-Lymphocytes: Lymphocytes responsible for cell-mediated immunity. Two types have been identified - cytotoxic (T-LYMPHOCYTES, CYTOTOXIC) and helper T-lymphocytes (T-LYMPHOCYTES, HELPER-INDUCER). They are formed when lymphocytes circulate through the THYMUS GLAND and differentiate to thymocytes. When exposed to an antigen, they divide rapidly and produce large numbers of new T cells sensitized to that antigen.Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Molecular Weight: The sum of the weight of all the atoms in a molecule.Brain Mapping: Imaging techniques used to colocalize sites of brain functions or physiological activity with brain structures.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Protein Array Analysis: Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.Viral Proteins: Proteins found in any species of virus.Immunoglobulin E: An immunoglobulin associated with MAST CELLS. Overexpression has been associated with allergic hypersensitivity (HYPERSENSITIVITY, IMMEDIATE).Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Solutions: The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Body Surface Potential Mapping: Recording of regional electrophysiological information by analysis of surface potentials to give a complete picture of the effects of the currents from the heart on the body surface. It has been applied to the diagnosis of old inferior myocardial infarction, localization of the bypass pathway in Wolff-Parkinson-White syndrome, recognition of ventricular hypertrophy, estimation of the size of a myocardial infarct, and the effects of different interventions designed to reduce infarct size. The limiting factor at present is the complexity of the recording and analysis, which requires 100 or more electrodes, sophisticated instrumentation, and dedicated personnel. (Braunwald, Heart Disease, 4th ed)Allosteric Regulation: The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Nucleocapsid Proteins: Viral proteins found in either the NUCLEOCAPSID or the viral core (VIRAL CORE PROTEINS).
... linear epitope - linkage - linker protein - lipofectin - locus - LOD score - lymphocyte - M13 phage - malformation - mapping - ... conformational epitope - congenital - consensus sequence - conservative substitution - conserved - contig - cosmid - ... gene mapping - gene pool - gene therapy - gene transfer - genetic code - genetic counseling - genetic map - genetic marker - ... physical map - plasmid - point mutation - poly-A track - polyA tail - polyacrylamide gel - polyclonal antibodies - polydactyly ...
... an epitope mapping strategy developed to improve rapid mapping of conformational epitopes on structurally complex proteins. MHC ... The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their ... The proportion of epitopes that are conformational is unknown.[citation needed] By contrast, linear epitopes interact with the ... A conformational epitope is composed of discontinuous sections of the antigen's amino acid sequence. These epitopes interact ...
These are known as linear epitopes. Antigen Linear epitope Epitope mapping, finding (on an antigen protein) the epitope(s) for ... A conformational epitope is a sequence of sub-units (usually amino acids) composing an antigen that come in direct contact with ... Such segments are called epitopes. Likewise, it is only paratope of the receptor that comes in contact with the epitope. ... a new method to predict conformational epitopes using phage display peptide sequences. ...
As a result, mAb epitopes on these types of targets are often conformational, making them difficult to map. Epitope mapping has ... Epitope mapping is also crucial to developing vaccines against prevalent viral diseases such as Dengue virus. Epitope mapping ... "Epitope Mapping". www.covalx.com/epitope2. Retrieved 2017-02-23. Epitope mapping at the US National Library of Medicine Medical ... discontinuous epitopes have been mapped on CD20. The epitope mapping resolution here depends on the number of overlapping ...
The Pepitope Server is used to map epitopes using affinity-selected peptides. Her work with autism genetic sequencing which won ... "Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm". Proteins: Structure, ... epitope mapping from affinity-selected peptides". Bioinformatics. 23 (23): 3244-3246. doi:10.1093/bioinformatics/btm493. ISSN ...
Ansari, HR; Raghava, Gajendra PS (2010). "Identification of conformational B-cell Epitopes in an antigen from its primary ... The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein ... Prediction of Conformational B-cell epitope in a sequence from its amino acid sequence. DesiRM: Designing of Complementary and ... of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post ...
The epitopes which bind neutralizing antibodies are both linear and conformational. All extant rabies viruses appear to have ... Apr 2005). "Novel rabies virus-neutralizing epitope recognized by human monoclonal antibody: fine mapping and escape mutant ... These antigenic sites, or epitopes, are categorized into regions I-IV and minor site a. Previous work has demonstrated that ...
... neutralizing epitopes map in regions of continuous and discontinuous residues". Virology. 172 (1): 11-24. doi:10.1016/0042-6822 ... pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1". J. Virol. 84 (24): 12924-33. doi: ... In HSV, neutralizing monoclonal antibodies map to structural domains I, II, IV and V. Due to its unique structure, herpesvirus ...
Sugaya K, Matsubara S, Miyamoto K, Kawata A, Hayashi H (2004). "An aggregate-prone conformational epitope in trinucleotide ... "The oculopharyngeal muscular dystrophy locus maps to the region of the cardiac alpha and beta myosin heavy chain genes on ...
Serke S, Schwaner I, Yordanova M, Szczepek A, Huhn D (April 2001). "Monoclonal antibody FMC7 detects a conformational epitope ... Szepetowski P, Perucca-Lostanlen D, Gaudray P (June 1993). "Mapping genes according to their amplification status in tumor ... ISBN 1-84110-100-1. Polyak MJ, Ayer LM, Szczepek AJ, Deans JP (July 2003). "A cholesterol-dependent CD20 epitope detected by ... Deans JP, Polyak MJ (February 2008). "FMC7 is an epitope of CD20". Blood. 111 (4): 2492; author reply 2493-4. doi:10.1182/blood ...
"The N-ethylmaleimide-sensitive fusion protein and alpha-SNAP induce a conformational change in syntaxin". J. Biol. Chem. 270 ( ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... of SNAP receptors in rat adipose cell membrane fractions and in SNARE complexes co-immunoprecipitated with epitope-tagged N- ... "The N-ethylmaleimide-sensitive fusion protein and alpha-SNAP induce a conformational change in syntaxin". J. Biol. Chem. 270 ( ...
Functional mapping of the surface residues of human thrombin. The Journal of Biological Chemistry 270, 16854-16863 PubMed ID: ... The residues His71, Arg75, Tyr76, Arg77, Asn78, Ile79, Tyr117 in the exosite I epitope are involved in the interaction with TBA ... Once the TBA part interacts with thrombin, the conformational change would change the distance between the FRET pair and lead ... which results in conformational change. Some groups use this property to develop aptamer-based thrombin sensors. For this ...
... and nucleic acid-and recognize conformational epitopes, which have three-dimensional structure.) MHC molecules enable immune ... MHC Sequencing Consortium (1999). "Complete sequence and gene map of a human major histocompatibility complex". Nature. 401 ( ... On the cell's surface, the epitope can contact its cognate region on immunologic structures recognizing that epitope. That ... The TCRs of T lymphocytes recognise only sequential epitopes, also called linear epitopes, of only peptides and only if coupled ...
Negi SS, Braun W (2009). "Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences". Bioinform Biol ... can use three dimensional structure of a protein and the peptides selected from phage display experiment to map conformational ... Explanation of "Protein interaction mapping" from The Wellcome Trust Lunder M, Bratkovic T, Doljak B, Kreft S, Urleb U, ... characterize small molecules-protein interactions and map protein-protein interactions. Users ...
MCV is a common human infection that can be detected by conformational capsid epitope immunoassays". International Journal of ... "The interaction of SV40 small tumor antigen with protein phosphatase 2A stimulates the map kinase pathway and induces cell ...
Natural rubber latex contains several conformational epitopes located on several enzymes such as Hev b 1, Hev b 2, Hev b 4, Hev ... "Mapping of IgE-binding epitopes on the major latex allergen Hev b 2 and the cross-reacting 1,3β-glucanase fruit allergens as a ... "Insights into a conformational epitope of Hev b 6.02 (hevein)". Biochemical and Biophysical Research Communications. 314 (1): ... Beezhold, Donald H.; Hickey, Vicky L.; Slater, Jay E.; Sussman, Gordon L. (1999). "Human IgE-binding epitopes of the latex ...
Wade R, Eddy R, Shows TB, Kedes L (Jul 1990). "cDNA sequence, tissue-specific expression, and chromosomal mapping of the human ... Chong SM, Jin JP (May 2009). "To investigate protein evolution by detecting suppressed epitope structures". Journal of ... 3) was proposed to show the conformational changes in troponin during muscle activation and relaxation. Phosphorylation: Ser118 ... Sequence analysis, immunological distance, and examination of evolutionarily suppressed conformational states showed that the ...
Zhang Z, Akhter S, Mottl S, Jin JP (Sep 2011). "Calcium-regulated conformational change in the C-terminal end segment of ... Chong SM, Jin JP (May 2009). "To investigate protein evolution by detecting suppressed epitope structures". Journal of ... to chromosome 19q13.4 by radiation hybrid mapping". Cytogenetics and Cell Genetics. 79 (3-4): 272-3. doi:10.1159/000134740. ...
"Fate mapping of IL-17-producing T cells in inflammatory responses". Nature Immunology. 12 (3): 255-63. doi:10.1038/ni.1993 ... Epitope *Linear. *Conformational. *Mimotope. *Antigen presentation/Professional APCs: Dendritic cell. *Macrophage. *B cell ... "Interleukin-10 production by Th1 cells requires interleukin-12-induced STAT4 transcription factor and ERK MAP kinase ...
Its epitope straddles β-strands A and G of ED3 as does the epitope of 1A1D-2. The structures at 2.0 Å resolution have enabled ... This acidic environment causes a conformational change in the E protein which disassociates it from the prM protein and causes ... Lisova, O; Hardy, F; Petit, V; Bedouelle, H (Sep 2007). "Mapping to completeness and transplantation of a group-specific, ... Its epitope is included in domain 1 (ED1) of the E protein. The human antibodies Ede1-C10, Ede2-A11 and Ede2-B7 potently ...
Tiso N, Rampoldi L, Pallavicini A, Zimbello R, Pandolfo D, Valle G, Lanfranchi G, Danieli GA (Jan 1997). "Fine mapping of five ... The rise of cytosolic Ca2+ results in binding to the N-terminal domain of troponin C and induces conformational changes in ... Chong SM, Jin JP (May 2009). "To investigate protein evolution by detecting suppressed epitope structures". Journal of ... and chromosomal mapping of the human slow-twitch skeletal muscle isoform of troponin I". Genomics. 7 (3): 346-57. doi:10.1016/ ...
The Hsp90 protein can adopt two major conformational states. The first is an open ATP-bound state and the second is a closed ... Fontana J, Fulton D, Chen Y, Fairchild TA, McCabe TJ, Fujita N, Tsuruo T, Sessa WC (May 2002). "Domain mapping studies reveal ... The decapeptide EP6 (380-389)is a major immunogenic epitope of HSP90 followed by EP1 (1-12) and EP8 (488-498). Knowledge of ... Thus, ATP hydrolysis drives what is commonly referred to as a "pincer-type" conformational change in the protein binding site. ...
Runge S, Gram C, Brauner-Osborne H, Madsen K, Knudsen LB, Wulff BS (Jul 2003). "Three distinct epitopes on the extracellular ... map of full length glucagon receptor have been determined. Furthermore, the structural dynamics of an active state complex of ... "Conformational states of the full-length glucagon receptor". Nat. Communications. 6: 7859. doi:10.1038/ncomms8859. PMC 4532856 ...
Dulubova I, Sugita S, Hill S, Hosaka M, Fernandez I, Südhof TC, Rizo J (Aug 1999). "A conformational switch in syntaxin during ... VAMP2 is a likely candidate gene for familial infantile myasthenia (FIMG) because of its map location and because it encodes a ... of SNAP receptors in rat adipose cell membrane fractions and in SNARE complexes co-immunoprecipitated with epitope-tagged N- ...
Wang J, Jin JP (Oct 1998). "Conformational modulation of troponin T by configuration of the NH2-terminal variable region and ... 1). Sequence homology and protein epitope allosteric similarity data suggest that TnT gene was originated by duplication of a ... "To investigate protein evolution by detecting suppressed epitope structures". Journal of Molecular Evolution. 68 (5): 448-60. ...
Expression of HLA-E at the cell surface is dependent on the presence of nonamer peptide epitope derived from the signal ... Using discontinuous density centrifugation, and later monoclonal antibodies, natural killing ability was mapped to the subset ...
... Biochemistry. 2007 Nov ... and epitope mapping of VL Len using wild-type and alanine-mutated Len peptides where it was shown that the antibody epitope was ... bound to a non-native conformational epitope located within the N-terminal 18 residues of fibrillar, as well as partially ...
... engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of ... engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of ... engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of ...
However, many epitopes rely on protein folding and form so-called conformational epitopes. Such conformational epitopes can ... Download the detailed report Characterization of Rituximab by Conformational Epitope Mapping and Epitope Substitution Scan ... Download the Application Note: Characterization of Rituximab by Conformational Epitope Mapping and Epitope Substitution Scan ... The epitope was further characterized by a full conformational epitope substitution scan with 20 L-amino acids to identify ...
Conformational epitope mapping of Pru du 6, a major allergen from almond nut. Molecular Immunology. 2013 Oct;55(3-4):253-263. ... Conformational epitope mapping of Pru du 6, a major allergen from almond nut. / Willison, LeAnna N.; Zhang, Qian; Su, Mengna; ... Willison, L. N., Zhang, Q., Su, M., Teuber, S. S., Sathe, S. K., & Roux, K. H. (2013). Conformational epitope mapping of Pru du ... Willison, LN, Zhang, Q, Su, M, Teuber, SS, Sathe, SK & Roux, KH 2013, Conformational epitope mapping of Pru du 6, a major ...
We attempted to map conformational epitopes and analyze IgG subclass distribution against Dsg3 in PNP. Method: Epitopes on Dsg3 ... We attempted to map conformational epitopes and analyze IgG subclass distribution against Dsg3 in PNP. Method: Epitopes on Dsg3 ... We attempted to map conformational epitopes and analyze IgG subclass distribution against Dsg3 in PNP. Method: Epitopes on Dsg3 ... We attempted to map conformational epitopes and analyze IgG subclass distribution against Dsg3 in PNP. Method: Epitopes on Dsg3 ...
... after linear epitope mapping is completed ... then i wont have any feeling at all just plain persuadive data:) , , , Peter , ... already done , , It is likely not the case, but theoretically your epitope still can be , conformational - protein can refold ... Linear_``,,´ ´_Conformational_``,,´´_Epitope _ ` `,,´´_Retrieval. redeamer alion85 at hotmail.com Tue Feb 10 16:37:16 EST 2004 ... Previous message: ``,,´´_Linear_``,,´ ´_Conformational_``,,´´_Epitope_ ` `,,´´_Retrieval *Next message: Everywhere life is full ...
The immediate application of the server is the mapping of antibody epitopes, however the system is sufficiently flexible for ... The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues involved ... One of the most interesting problems in molecular immunology is epitope mapping, i.e. the identification of the regions of ... Schreiber A, Humbert M, Benz A, Dietrich U: 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three- ...
All XLAS alloantibodies recognized conformational epitopes in the NC1 domain of alpha5(IV) collagen, which were mapped using ... Allograft-eluted alloantibodies mainly targeted two conformational alloepitopes mapping to alpha5NC1 residues 1-45 and 114-168 ... Cuvinte cheie: Alport syndrome, post-transplant nephritis, collagen IV, alloantibodies, epitope mapping ... pathogenic X-linked alport alloantibodies target two accessible conformational epitopes in the alpha5NC1 domain.. Domenii ...
Conclusion: Conformational epitopes may be mapped through screening of clones from random peptide phage display libraries and ... Conclusion: Conformational epitopes may be mapped through screening of clones from random peptide phage display libraries and ... Conclusion: Conformational epitopes may be mapped through screening of clones from random peptide phage display libraries and ... Conclusion: Conformational epitopes may be mapped through screening of clones from random peptide phage display libraries and ...
Combinatorial peptide-based epitope mapping from Ebola virus DNA vaccines and infections reveals residue-level determinants of ... Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to ... Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16.". Cancers attributable to human papillomavirus (HPV) ... Conformational Occlusion of Blockade Antibody Epitopes, a Novel Mechanism of GII.4 Human Norovirus Immune Evasion. ...
1998) Sequence diversity, predicted two-dimensional protein structure, and epitope mapping of neisserial Opa proteins. J. ... Identification of surface-exposed conformational epitopes.To determine the nature (linear or conformational) of surface-exposed ... The conclusion that the surface-exposed MOMP epitopes are conformational in nature was based on several pieces of evidence. ... 6I). Together, these results indicated that the surface-exposed epitopes of MOMP are predominantly conformational in nature. ...
Mapping of a conformational epitope by homologue scanning. L Wang, P J Hertzog, M Galanis, M L Overall, G J Waine and A W ... V. Mapping of a dominant immunopathologic VP2 T cell epitope in susceptible SJL/J mice. S J Gerety, W J Karpus, A R Cubbon, R G ... Identification of autoantibody epitopes of glutamic acid decarboxylase in stiff-man syndrome patients. L Li, W A Hagopian, H R ... Direct sequence identification and kinetic analysis of an MHC class I-restricted Listeria monocytogenes CTL epitope. E G Pamer ...
A linear region of a monoclonal antibody conformational epitope mapped on p185HER2 oncoprotein. ... Cytotoxic T-lymphocytes derived from patients with breast adenocarcinoma recognize an epitope present on the protein core of a ... Relative cytotoxic activity of immunotoxins reactive with different epitopes on the extracellular domain of the c-erbB-2 (HER-2 ... Antibody-induced growth inhibition is mediated through immunochemically and functionally distinct epitopes on the extracellular ...
Traditionally, protein epitopes have been divided into discontinuous/conformational epitopes, which require that the native ... Epitope context and structure. Epitopes identified by the peptide microarray approach and reported in Fig. 4 were mapped onto ... Epitope Mapping Using Cell-surface Display. Mapping using cell-surface display was performed as described elsewhere (28). ... Two alternative epitope mapping approaches identified similar, although not necessarily identical, epitopes. These results show ...
These are known as linear epitopes. Antigen Linear epitope Epitope mapping, finding (on an antigen protein) the epitope(s) for ... A conformational epitope is a sequence of sub-units (usually amino acids) composing an antigen that come in direct contact with ... Such segments are called epitopes. Likewise, it is only paratope of the receptor that comes in contact with the epitope. ... a new method to predict conformational epitopes using phage display peptide sequences. ...
Mapping and molecular characterization of novel monoclonal antibodies to conformational epitopes on NH2 and COOH termini of ... Epitope mapping: the first step in developing epitope-based vaccines.. Gershoni JM, Roitburd-Berman A, Siman-Tov DD, ... The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. ... Pepitope: epitope mapping from affinity-selected peptides.. Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Freund NT, ...
Finer epitope mapping, using GST-L1 fusion proteins, mapped the 16A epitope to the L1 variable regions I and possibly II within ... The efficacy of these vaccines is critically dependent upon L1 type-specific conformational epitopes. To investigate the ... molecular determinants of the HPV16 L1 conformational epitope recognized by monoclonal antibody 16A, we utilized a domain- ... These results suggest that non-contiguous loop regions of L1 display critical components of a type-specific, conformational ...
The epitope was mapped by using sera from patients with neuroborreliosis from a B. garinii infection, but it was not within the ... Conformational Nature of the Borrelia burgdorferi B31 Outer Surface Protein C Protective Epitope. Robert D. Gilmore, Jr., M. ... 3A). If MAb B5 recognized a conformational epitope, then one would not expect these OspC proteins to be immunoreactive on blots ... It remains to be determined if OspC molecules from other strains ofB. burgdorferi have conformational protective epitope ...
... an epitope mapping strategy developed to improve rapid mapping of conformational epitopes on structurally complex proteins. MHC ... The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their ... The proportion of epitopes that are conformational is unknown.[citation needed] By contrast, linear epitopes interact with the ... A conformational epitope is composed of discontinuous sections of the antigens amino acid sequence. These epitopes interact ...
Use of domain-swapped molecules for conformational epitope mapping of desmoglein 3 in pemphigus vulgaris. J Invest Dermatol. ... For mapping of calcium-dependent conformational epitopes, domain-swapped DSG3 recombinant molecules (DSG3 EC1-EC5 in the ... consistent with the recognition of calcium-dependent conformational epitopes. Figure 1. Human antibodies bind conformational ... Epitope mapping of 3 pathogenic antibodies. (A) Alignment of DSG3 amino acid sequence 1-232 with C-cadherin, DSG1, DSG2, and ...
GAD65Ab in autoimmune diabetes are dependent on the conformational integrity of the antigen. Traditional epitope mapping assays ... We developed a novel epitope mapping assay that depends on competition of the serum antibodies with recombinant Fab derived ... Masked and Overt Autoantibodies Specific to the DPD Epitope of 65-kDa Glutamate Decarboxylase (GAD65-DPD) Are Associated With ... Using this novel technique, we identified disease-specific GAD65Ab epitopes. We also succeeded to detect antibody maturation ...
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acid Research. 35(1):69-78. [pdf] ... Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 10;68(1):294-304 [ ... Pepitope: Inferring epitopes based on affinity-selected peptides. Bioinformatics. 23(23):3244-3246. [pdf] [abs] ... Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics. 10:287. [pdf] [abs] ...
Phage display and peptide mapping of an immunoglobulin light chain fibril-related conformational epitope. Biochemistry. 2007 ... Conformational conversion during amyloid formation at atomic resolution. Mol Cell. 2011 Jan 21;41(2):161-72. PubMed. ... established specific conformational changes in full-length β2m that arose from bimolecular interactions with ΔN6 that ...
Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes. Sci. Rep. 2:706. doi ... Epitope Mapping. Phage libraries are useful for mapping antibody epitopes, and display millions of peptides/proteins with ... for the epitope mapping of polysaccharides in L. pneumophila and the epitope mapping of various low affinity peptide/protein ... Phage display and peptide mapping of an immunoglobulin light chain fibril-related conformational epitope. Biochem. Mol. Biol. ...
Petit, M.A.; Jolivet-Reynaud, C.; Peronnet, E.; Michal, Y.; Trepo, C. Mapping of a conformational epitope shared between E1 and ... Recently, epitopes have been identified in the E2 protein at residues 412-426 (epitope I) and 434-446 (epitope II). ... conformational and widely conserved epitopes were identified in E1 and E2 [38,43,44,45]. The human mAb AR3, which defines one ... Similar antibodies recognizing conformational epitopes, in this case defined by the mouse mAb D32.10 (aa 297-306; 480-494 and ...
  • The MAbs in this group were thermostable and bound different epitopes in the highly conserved HA stalk region. (asm.org)
  • The ability of MAbs to block the conformational change of HA at the low pH of the endosomal compartment appears to be the key attribute of stalk-binding neutralizing MAbs responsible for preventing influenza viral infectivity ( 19 ). (asm.org)
  • Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning against unwanted ( e.g. autoimmune) reactivities. (mcponline.org)
  • The Immune Epitope Database (IEDB) is a freely available repository of epitope data from infectious disease agents, as well as epitopes defined for allergy, autoimmunity, and transplantation. (karger.com)
  • For the very first time, the new PEPperCHIP® Human Epitome Microarray covers all linear human B-cell epitopes of the Immune Epitope Database including all epitopes of the most common vaccines. (pepperprint.com)
  • Background: Bla g 2, one of the major cockroach allergens, induces a strong IgE response against conformational epitopes, and on reexposure, sensitized individuals often display symptoms of allergic rhinitis and asthma. (utmb.edu)
  • www.iedb.org) was created by the National Institute of Allergy and Infectious Disease (NIAID) to provide a freely accessible repository of immune epitope data encompassing infectious disease, allergy, autoimmunity, and transplant-related reactivity. (karger.com)
  • In these studies, only highly homologous HPVs, such as HPV6/11 and HPV18/45, induced cross-neutralizing sera and type-common epitopes were found to be less immunogenic than type-specific epitopes. (biomedcentral.com)
  • Likewise, recognition of specific epitopes by T cells leads to secretion of soluble mediators directly contributing to immunopathology. (karger.com)
  • We are also investigating conformational states of the C-terminal region of the PrP protein associated with differential exposure of specific epitopes, in order to provide clues on regions of the protein undergoing conformational transitions leading to aggregation. (wodaklab.org)
  • Relative cytotoxic activity of immunotoxins reactive with different epitopes on the extracellular domain of the c-erbB-2 (HER-2/neu) gene product p185. (nih.gov)
  • Both kidney-eluted and circulating alloantibodies to alpha5NC1 distinctively targeted epitopes accessible in the alpha3alpha4alpha5NC1 hexamers of human GBM, unlike anti-GBM autoantibodies, which targeted sequestered alpha3NC1 epitopes. (ad-astra.ro)
  • To analyze the fine specificity of IgG autoantibodies in sera from rheumatoid arthritis (RA) patients for type II collagen (CII) epitopes that are arthritogenic in collagen-induced arthritis (CIA), a relevant murine model of RA. (docme.ru)
  • In recent years, interest has shifted to uncover the target epitopes of these autoantibodies. (biomedcentral.com)
  • We demonstrated that the mutant represents an intermediate in a series of conformational changes leading to amyloid. (pnas.org)
  • Two cryptic epitopes were mapped to a domain of TTR, where most mutations associated with amyloidosis occur and which we propose is displaced at the initial phase of amyloid formation, opening up new surfaces necessary for autoaggregation of TTR monomers. (pnas.org)
  • Posttranslational modifications are observed in some cases associated with the formation of amyloid fibrils, including conformational changes and proteolytic cleavage ( 3 ). (pnas.org)
  • An HLA-directed molecular and bioinformatics approach identifies new HLA-A11 HIV-1 subtype E cytotoxic T lymphocyte epitopes in HIV-1-infected Thais," AIDS Research and Human Retroviruses , vol. 17, no. 8, pp. 703-717, 2001. (hindawi.com)
  • HLA-A2-restricted CD8-cytotoxic-T-Cell responses to novel epitopes in mycobacterium tuberculosis superoxide dismutase, alanine dehydrogenase, and glutamine synthetase," Infection and Immunity , vol. 72, no. 4, pp. 2412-2415, 2004. (hindawi.com)