Dark Proteome Database: Studies on Dark Proteins
Nelson Perdigão1,2, Agostinho Rosa3,4
1Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal. p3rdigao@isr.tecnico.ulisboa.pt.
High-Throughput
|April 3, 2019
Summary
The human proteome remains largely uncharacterized, with over 50% of proteins lacking 3D structural data. This study maps the dark proteome, identifying dark genes and tissues in humans and model organisms.
Area of Science:
- Proteomics
- Structural Biology
- Bioinformatics
Background:
- The "dark proteome" comprises proteins lacking observed 3D structures, hindering functional understanding.
- Existing data shows significant portions of viral and eukaryotic proteomes are "dark".
Purpose of the Study:
- To map the dark proteome in humans and key model organisms.
- To identify "dark" genes and tissues associated with uncharacterized proteins in humans.
Main Methods:
- Analysis of protein structural data from Swiss-Prot.
- Comparative proteomic analysis across different species.
- Identification of gene and tissue-specific enrichment of dark proteins.
Main Results:
- Approximately 40-50% of proteins in model organisms, including humans, lack structural characterization.
- Higher eukaryotes, like humans and mice, exhibit higher percentages of dark proteomes.
- Over 50% of the human proteome is "dark", with enrichment in heart, cervical mucosa, and natural killer cells.
Conclusions:
- A significant portion of the human proteome remains structurally uncharacterized.
- Mapping the dark proteome is crucial for advancing our understanding of protein function and human biology.
- Further research into dark genes and tissues is needed to elucidate their roles.
Related Concept Videos
01:29Dark Triad and Person Perception
285
Person perception is influenced by both external behaviors and the observer’s internal characteristics, including personality traits. Individuals with dark personality traits, comprising psychopathy, Machiavellianism, and narcissism — collectively known as the dark triad – exhibit manipulative and exploitative tendencies in social contexts. These traits affect how they perceive others and how they are perceived.The Role of Dark Personality Traits in Person PerceptionBlack et...
285
01:33Proteomics
9.5K
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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.5K
02:26Protein Networks
4.5K
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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
02:04Protein-protein Interfaces
14.6K
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...
14.6K
02:15Protein and Protein Structure
87.2K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
87.2K
02:26Conservation of Protein Domains Over Different Proteins
14.1K
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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
14.1K