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Protein Networks02:26

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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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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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.
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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MultifacetedProtDB: a database of human proteins with multiple functions.

Elisa Bertolini1, Giulia Babbi1, Castrense Savojardo1

  • 1Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy.

Nucleic Acids Research
|October 4, 2023
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Summary

MultifacetedProtDB is a novel database for identifying human proteins with multiple functions, such as moonlighting or pleiotropic proteins. This resource aids research into complex biological processes and diseases.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Genomics

Background:

  • Multifunctional proteins, including pleiotropic, multidomain, promiscuous, and moonlighting proteins, are crucial for complex biological processes in humans.
  • These proteins play significant roles in signal transduction, metabolism, gene regulation, cellular communication, and disease development.
  • Existing databases often struggle to retrieve these multifaceted proteins through direct searches.

Purpose of the Study:

  • To develop and present MultifacetedProtDB, a specialized database for cataloging and accessing information on multifunctional human proteins.
  • To provide a centralized resource for researchers studying protein multitasking and its implications in human biology and disease.

Main Methods:

  • Integrated data from multiple reputable sources: UniProt, GeneCards, Human Protein Atlas (HPA), Human Phenotype Ontology (HPO), and MONDO.
  • Developed a web server enabling searches by gene, protein, and associated structural/functional data using various filters.
  • Enriched protein entries with comprehensive annotations: EC numbers, Gene Ontology (GO) terms, Reactome pathways, subcellular localization, tissue expression (HPA), and disease associations (MONDO, Orphanet, OMIM).

Main Results:

  • Successfully created MultifacetedProtDB, a curated database specifically for multifunctional human proteins.
  • The web server offers advanced search capabilities and detailed annotations for each protein entry.
  • The database consolidates information previously dispersed across multiple resources, enhancing accessibility.

Conclusions:

  • MultifacetedProtDB serves as a valuable, freely accessible resource for the scientific community.
  • Facilitates in-depth investigation into the roles of multifunctional proteins in human health and disease.
  • Enhances the study of protein complexity and its impact on biological systems.