Linked Life Data

15376949

Source:http://linkedlifedata.com/resource/pubmed/id/15376949

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2004-9-20
pubmed:abstractText
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 Ile 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.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1536-1241
pubmed:author
pubmed:issnType
Print
pubmed:volume
2
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
150-7
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2003
pubmed:articleTitle
Folding type specific secondary structure propensities of synonymous codons.
pubmed:affiliation
Key Laboratory of Molecular and Biomolecular Electronics, Southeast University, Ministry of Education, Nanjing 210096, China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't