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Updated: Jun 26, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
The origin, evolution and structure of the protein world
Gustavo Caetano-Anollés1, Minglei Wang, Derek Caetano-Anollés
1Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W. Peabody Drive, Urbana, IL 61801, USA. gca@illinois.edu
The Biochemical Journal
|January 13, 2009
Summary
Protein architectures act as molecular fossils, revealing evolutionary history. Analyzing proteomes and genomes uncovered ancient enzyme origins and the diversification of life.
Area of Science:
- Evolutionary Biology
- Structural Bioinformatics
- Biochemistry
Background:
- Protein architectures serve as molecular fossils, reflecting evolutionary history.
- Protein structure is constrained by folding energy, sequence exploration, and cellular machinery.
- Existing classification schemes and bioinformatic approaches explore protein fold space.
Purpose of the Study:
- To unify protein architectural complexity using evolutionary principles ('shared and derived').
- To uncover global evolutionary patterns by analyzing protein structures across fully sequenced genomes.
- To reconstruct timelines of protein architecture and function discovery.
Main Methods:
- Shifted focus from individual proteins to proteomes.
- Conducted a census of protein structures within fully sequenced genomes.
- Applied bioinformatic approaches to explore protein structure and evolutionary relationships.
Main Results:
- Revealed global evolutionary patterns in protein structures.
- Identified specialization, reductive tendencies, and modularity in protein repertoires.
- Uncovered evidence for a complex ancestral proteome and early archaeal lineage origins.
- Pinpointed the P-loop-containing triphosphate hydrolase fold as an origin point for the protein world.
- Documented the recruitment of structures and functions in early metabolic pathways.
Conclusions:
- Protein architecture analysis provides insights into the history and diversification of life.
- The study sheds light on the origins of modern biochemistry and early life evolution.
- Understanding protein evolution is crucial for deciphering life's complex molecular history.
Related Concept Videos
01:13Protein Organization
Overview
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
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.
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...
02:15Protein and Protein Structure
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 can...
A protein's shape is critical to its function. For example, an enzyme can...