Analysis of the distribution of functionally relevant rare codons.

ABSTRACT:

Background

The substitution of rare codons with more frequent codons is a commonly applied method in heterologous gene expression to increase protein yields. However, in some cases these substitutions lead to a decrease of protein solubility or activity. To predict these functionally relevant rare codons, a method was developed which is based on an analysis of multisequence alignments of homologous protein families.

Results

The method successfully predicts functionally relevant codons in fatty acid binding protein and chloramphenicol acetyltransferase which had been experimentally determined. However, the analysis of 16 homologous protein families belonging to the alpha/beta hydrolase fold showed that functionally rare codons share no common location in respect to the tertia

SUBMITTER: Widmann M 

PROVIDER: S-EPMC2391168 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature