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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 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.
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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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ProtMiscuity: a database of promiscuous proteins.

Ana Julia Velez Rueda1, Nicolas Palopoli1, Matías Zacarías1

  • 1Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD Buenos Aires, Argentina.

Database : the Journal of Biological Databases and Curation
|October 26, 2019
PubMed
Summary
This summary is machine-generated.

ProtMiscuity is a new database detailing protein catalytic promiscuity, offering insights into enzyme function. This curated resource aids researchers in understanding the complex structure-function relationships of promiscuous proteins.

Keywords:
databasepromiscuityproteins

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Understanding protein structure-function relationships is crucial, yet promiscuous protein behavior presents a significant challenge.
  • Catalytic promiscuity, where a single enzyme catalyzes multiple reactions, complicates traditional structure-function paradigms.

Purpose of the Study:

  • To introduce ProtMiscuity, a manually curated online database for proteins exhibiting catalytic promiscuity.
  • To provide a centralized, accessible resource for researchers studying enzyme promiscuity.

Main Methods:

  • Manual curation of experimental data from scientific literature.
  • Database development including search and browse functionalities.
  • Integration of detailed information on reactions, substrates, products, kinetics, and active site mapping.

Main Results:

  • ProtMiscuity contains data on 57 proteins across 40 organisms, detailing 88 distinct reactions.
  • The database includes information on canonical and promiscuous activities, kinetic parameters, and active site characteristics.
  • Entries link to external resources for comprehensive biological and functional annotations.

Conclusions:

  • ProtMiscuity offers a unique, curated collection of experimentally derived data on protein promiscuity.
  • The database facilitates the study of underlying mechanisms of promiscuous reactions by overcoming data retrieval challenges.
  • ProtMiscuity serves as a valuable tool for advancing the understanding of enzyme function and evolution.