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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Families02:47

Protein Families

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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Cross-reactivity00:42

Cross-reactivity

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Overview
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

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Classification epitopes in groups based on their protein family.

Edgar Kozlova, Benjamin Viart, Ricardo de Avila

    BMC Bioinformatics
    |December 24, 2015
    PubMed
    Summary

    Computational methods can now infer an antigen's protein family from linear epitopes. Physico-chemical properties of epitopes improve B-cell epitope prediction accuracy for vaccine design and diagnostics.

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    Area of Science:

    • Immunology
    • Bioinformatics
    • Computational Biology

    Background:

    • The humoral immune system relies on antibody-antigen interactions for pathogen clearance.
    • B-cell epitopes are specific binding sites, but experimental identification is costly and time-consuming.
    • In silico epitope prediction methods are valuable for biomedical applications but currently lack optimal accuracy.

    Purpose of the Study:

    • To investigate if linear epitopes from the same protein family share common properties.
    • To enhance the accuracy of B-cell epitope prediction by incorporating antigen family information.
    • To explore the potential of physico-chemical and predicted secondary structure features for epitope classification.

    Main Methods:

    • Analysis of physico-chemical (PCP) and predicted secondary structure (PSS) features of linear epitopes.
    • Utilized data mining techniques to identify distinguishing parameters between epitope groups.
    • Applied five-fold cross-validation to evaluate model performance using regression, decision tree, and support vector machine algorithms.

    Main Results:

    • Statistically significant parameters were identified to distinguish between metalloproteinase and neurotoxin epitopes, and from random sequences.
    • Physico-chemical property-based models achieved Area Under the Curve (AUC) and accuracy values exceeding 0.9.
    • Demonstrated that antigen family can be inferred from properties within linear epitope groups.

    Conclusions:

    • Antigen family can be inferred from the properties of linear epitopes, specifically metalloproteinases and neurotoxins.
    • Identified unique characteristics and similarities of these epitope groups compared to random peptides.
    • Findings suggest incorporating antigen protein family information can improve computational epitope prediction and discovery methods.