Folding type specific secondary structure propensities of synonymous codons

Wanjun Gu, Tong Zhou, Jianmin Ma, Xiao Sun, Zuhong Lu

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

We have proposed new amino acid secondary structure propensities in proteins with different folding types based on synonymous codons. They have been derived from 200 all alpha, all beta, alpha/beta, and alpha + beta proteins of known structures and their coding genes. The secondary structure propensities of the same codon in gene coding for different folding type proteins are not the same. For instance, amino acid He coded by AUU is indifferent to form the alpha unit in the alpha + beta protein class, but it is a former and a breaker for the alpha unit in the all alpha protein class and the alpha/beta class, respectively. On the other hand, the secondary structure propensities of different synonymous codons in the coding genes with the same folding type are also not all the same. As an example, CGU, CGG, and AGA, which are synonymous codons of Arg, are preferential to form the alpha unit in all alpha proteins, while CGA is an alpha unit breaker and the other two synonymous codons, CGC and AGG, are indifferent to form or break the alpha unit. As a result, protein secondary structure information contained both in mRNA sequences and in amino acid sequences has been introduced in these codon-based amino acid secondary structure propensities. These codon-based amino acid secondary structure propensities are helpful to in vitro protein design and protein secondary structure prediction.

Original languageEnglish (US)
Pages (from-to)150-157
Number of pages8
JournalIEEE Transactions on Nanobioscience
Volume2
Issue number3
DOIs
StatePublished - Sep 2003
Externally publishedYes

Fingerprint

Codon
Proteins
Imino Acids
Amino acids
Secondary Protein Structure
Genes
Protein Folding
Amino Acids
Amino Acid Sequence
Messenger RNA

Keywords

  • Protein design
  • Protein folding type
  • Protein secondary structure prediction
  • Secondary structure propensity
  • Synonymous codon usage

ASJC Scopus subject areas

  • Engineering(all)
  • Bioengineering
  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Pharmaceutical Science
  • Medicine (miscellaneous)
  • Biotechnology
  • Biomedical Engineering

Cite this

Folding type specific secondary structure propensities of synonymous codons. / Gu, Wanjun; Zhou, Tong; Ma, Jianmin; Sun, Xiao; Lu, Zuhong.

In: IEEE Transactions on Nanobioscience, Vol. 2, No. 3, 09.2003, p. 150-157.

Research output: Contribution to journalArticle

Gu, Wanjun ; Zhou, Tong ; Ma, Jianmin ; Sun, Xiao ; Lu, Zuhong. / Folding type specific secondary structure propensities of synonymous codons. In: IEEE Transactions on Nanobioscience. 2003 ; Vol. 2, No. 3. pp. 150-157.
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