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Published on: August 18, 2023
A possible molecular metric for biological evolvability.
1Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110 016, India. amittal@bioschool.iitd.ac.in
Journal of Biosciences
|July 4, 2012
Summary
Life's survival depends on functional proteins. A new metric, using the stoichiometric margin of life, quantifies evolvability and predicts extinction risk based on amino acid constraints and genetic code degeneracy.
Area of Science:
- Biochemistry
- Evolutionary Biology
- Molecular Biology
Background:
- Proteins determine phenotypic traits and are crucial for adaptation and survival.
- Loss of functional proteins can lead to extinction.
- Current metrics for 'evolvability' and extinction prediction at the molecular level are lacking.
Purpose of the Study:
- To introduce the first quantitative metric for measuring 'evolvability' and assessing extinction risk.
- To utilize the stoichiometric margin of life for all known functional proteins.
- To explore the relationship between genetic code degeneracy, amino acid stoichiometry, and protein functionality.
Main Methods:
- Analysis of the stoichiometric margin of life for naturally occurring proteins.
- Investigation of the genetic code's degeneracy and codon usage for 20 amino acids.
- Examination of amino acid proximity in protein backbones using crystal structure data.
Main Results:
- The stoichiometric margin of life metric was developed.
- 11 out of 20 amino acids require full codon degeneracy to maintain stoichiometric balance.
- Non-availability of codons for these 11 amino acids leads to non-functional proteins and extinction.
- The remaining 9 amino acids' stoichiometry is robust to codon availability, ensuring survivability.
Conclusions:
- A novel quantitative metric for evolvability and extinction risk has been established.
- Amino acid stoichiometry, influenced by codon availability, is a critical factor in protein functionality and survival.
- Protein structural proximity of amino acids dictates their dependence on codon degeneracy for maintaining functional stoichiometry.
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