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Circular permutations of natural protein sequences: structural evidence
1Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden. ylva@alfa.mbb.ki.se
Current Opinion in Structural Biology
|June 1, 1997
Summary
Circularly permuted proteins, arising from gene permutations, occur naturally. Detecting these protein sequence variations can be challenging using only sequence alignment methods, as seen with transaldolase.
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- Circularly permuted proteins arise from gene permutations.
- Natural occurrence of these proteins is increasingly documented.
- Sequence alignment is a common detection method.
Purpose of the Study:
- To highlight the natural occurrence of circularly permuted proteins.
- To discuss the limitations of sequence alignment in detecting these proteins.
- To present transaldolase as a case study.
Main Methods:
- Review of accumulated evidence on protein circular permutation.
- Analysis of sequence alignment techniques for protein comparison.
- Case study involving transaldolase and class I aldolase family.
Main Results:
- Evidence confirms the natural occurrence of circularly permuted proteins.
- Sequence alignment may fail to detect certain circular permutations.
- Transaldolase exemplifies a protein where permutation was not initially detected by sequence comparison.
Conclusions:
- Circularly permuted proteins are a natural biological phenomenon.
- Detection methods need to account for potential limitations of sequence alignment.
- Further investigation into alternative detection strategies is warranted.