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[The relation between translation speed and protein secondary structure]
Xiao-Qin Li1, Liao-Fu Luo, Ci-Quan Liu
1Kunming Institute of Zoology, the Chinese Academy of Sciences, China.
Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao Acta Biochimica Et Biophysica Sinica
|January 25, 2003
Summary
Fast-translating mRNA codons preferentially encode alpha helices in human and E. coli proteins. Codon usage for beta strands varies with translation speed, suggesting non-random selection.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Context:
- Investigating the relationship between mRNA sequence, translation speed, and protein secondary structure.
- Analyzing codon usage patterns in human and Escherichia coli (E. coli) proteomes.
- Exploring potential non-random selection mechanisms in protein biosynthesis.
Purpose:
- To determine if specific codon types and translation speeds correlate with the formation of alpha helices, beta strands, or coils.
- To identify non-homogeneous codon usage within specific secondary structures.
- To assess if observed patterns can be explained by random fluctuations.
Summary:
- Statistical analysis of 119 human and 92 E. coli proteins revealed that mRNA sequences with high translation speeds, particularly tri-codons and tetra-codons, preferentially code for alpha helices over coils.
- Beta strand formation shows an oscillating preference or avoidance depending on translation speed.
- Non-uniform usage of codons with varying translation speeds within the same secondary structure was observed, indicating a complex regulatory mechanism.
Impact:
- Suggests that translation speed is a significant factor influencing protein secondary structure.
- Challenges simple explanations based on stochastic fluctuations, pointing towards more sophisticated biological regulation.
- Provides insights into the intricate relationship between the genetic code, translation dynamics, and protein folding.