Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome
Data(s) |
01/01/2006
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Resumo |
High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms. (c) 2005 Elsevier Ltd. All rights reserved. |
Identificador | |
Idioma(s) |
eng |
Publicador |
Academic Press Ltd Elsevier Science Ltd |
Palavras-Chave | #Synonymous Codon Usage #Cysteine #Escherichia Coli #Disulfide Bonding State #Information Theory #Statistical Correlation #Biology #Secondary Structure #Bonding State #Connectivity Prediction #Evolutionary Information #Neural-networks #In-vivo #Proteins #Translation #Patterns #Rna #Mathematical & Computational Biology #C1 #249901 Biophysics #250302 Biological and Medical Chemistry #270101 Analytical Biochemistry #270199 Biochemistry and Cell Biology not elsewhere classified #780101 Mathematical sciences #780103 Chemical sciences #780105 Biological sciences |
Tipo |
Journal Article |