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The distribution of structures in evolving protein populations
1Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055, USA.
Biopolymers
|January 25, 2000
Summary
The uneven distribution of protein structures arises from evolution and population dynamics interacting with protein designability. This interplay results in a more pronounced unevenness in observed protein structures than in their inherent designability.
Area of Science:
- Structural biology
- Computational biology
- Evolutionary biology
Background:
- Proteins display a non-uniform distribution of structures.
- Existing models consider protein designability (fraction of sequences folding to a structure) to explain this.
- The precise relationship between designability and structure frequency remains unclear.
Purpose of the Study:
- To investigate the relationship between protein structure distribution and designability.
- To explain the observed nonuniformity of protein structures through evolutionary and dynamic factors.
Main Methods:
- Analysis of protein designability distributions.
- Modeling the interplay of evolution and population dynamics with designability.
- Investigating the influence of sequence space topology and structural similarity.
Main Results:
- The nonuniform distribution of natural protein structures is explained by the combined effects of evolution, population dynamics, and designability.
- The frequency of protein structures depends on designability with a greater-than-linear relationship.
- Sequence space topology and structural similarity also influence structure distribution.
Conclusions:
- Evolution and population dynamics amplify the effect of designability on protein structure frequency.
- The observed unevenness in protein structures is a consequence of these combined factors.
- Understanding these relationships is key to predicting protein structure prevalence.