Simplified amino acid alphabets for protein fold recognition and implications for folding
| Autor: | Anders Wallqvist, Lynne Reed Murphy, Ronald M. Levy |
|---|---|
| Rok vydání: | 2000 |
| Předmět: |
chemistry.chemical_classification
Protein Folding Sequence database Protein family Protein design Proteins Bioengineering Sequence alignment Computational biology Biology Biochemistry Amino acid chemistry Protein folding Amino Acid Sequence Amino Acids Molecular Biology Peptide sequence Sequence Alignment Algorithms Software Biotechnology Sequence (medicine) |
| Zdroj: | Protein engineering. 13(3) |
| ISSN: | 0269-2139 |
| Popis: | Protein design experiments have shown that the use of specific subsets of amino acids can produce foldable proteins. This prompts the question of whether there is a minimal amino acid alphabet which could be used to fold all proteins. In this work we make an analogy between sequence patterns which produce foldable sequences and those which make it possible to detect structural homologs by aligning sequences, and use it to suggest the possible size of such a reduced alphabet. We estimate that reduced alphabets containing 10-12 letters can be used to design foldable sequences for a large number of protein families. This estimate is based on the observation that there is little loss of the information necessary to pick out structural homologs in a clustered protein sequence database when a suitable reduction of the amino acid alphabet from 20 to 10 letters is made, but that this information is rapidly degraded when further reductions in the alphabet are made. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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