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Updated: Jul 20, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Evolution of protein structural classes and protein sequence families
1Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, CA 94720, USA.
Summary
Protein structures naturally cluster into four main classes, suggesting "structural selection" guides gene evolution. Earliest proteins evolved into these four classes, with a "multiple birth model" explaining diverse protein family origins.
Area of Science:
- Structural biology
- Evolutionary biology
- Bioinformatics
Background:
- Protein structures exhibit distinct clustering in 3D space.
- These clusters correspond to the four major protein classes based on secondary structure and topology.
Purpose of the Study:
- To investigate the evolutionary pathways of protein structures.
- To understand the role of structural constraints in gene evolution.
- To propose a model for the origin of protein families.
Main Methods:
- Analysis of protein structure similarity in 3D space.
- Tracing common structural ancestors for protein sequence families.
- Mapping protein evolution onto structural classes.
Main Results:
- Protein structures naturally form four distinct clusters, reflecting major protein classes.
- Evolutionary analysis indicates proteins emerged and diversified across these classes over time.
- The fourth protein class became the most dominant.
- Evidence suggests multiple origins for ancestral proteins, not a single common ancestor.
Conclusions:
- Gene evolution is likely constrained by "structural selection" favoring stable protein structures within the four major classes.
- The evolution of protein families follows a "multiple birth model" with origins at different evolutionary times.
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Overview