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Updated: Jul 18, 2026
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Modeling the evolution of protein domain architectures using maximum parsimony
Jessica H Fong1, Lewis Y Geer, Anna R Panchenko
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
Journal of Molecular Biology
|December 15, 2006
Summary
Protein domain architectures evolve through gene fusion and fission events. Most architectures gain complexity over time, with fusion being more common than fission, offering insights into protein evolution.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational biology
Background:
- Proteins are composed of domains, the basic units of evolution.
- Protein domain architectures link related proteins and their functions.
- Understanding the evolutionary pathways of these architectures is crucial.
Purpose of the Study:
- To identify evolutionary pathways of protein domain architectures.
- To model architecture evolution via rearrangements and domain acquisition.
- To rank evolutionary scenarios using a parsimony principle.
Main Methods:
- Analysis of domain architectures across 159 proteomes.
- Modeling evolution using fission and fusion operations.
- Employing a parsimony principle to infer likely evolutionary pathways.
Main Results:
- Over 85% of known protein architectures' histories were estimated.
- Architecture evolution is robust to alternative parsimony rules.
- 87% of architectures increase in complexity, with fusion events 5.6 times more frequent than fission.
Conclusions:
- Protein domain architectures predominantly evolve towards increased complexity.
- The proposed model accurately estimates evolutionary histories.
- Results enable computation of domain architecture similarities and new functional insights.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
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 form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:26Conservation of Protein Domains
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 form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview