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Network analysis of synonymous codon usage
- Source :
- Bioinformatics
- Publication Year :
- 2019
-
Abstract
- Motivation Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionarily conserved. Analyses of their positions in protein 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. Results We model protein structures as networks and use network centrality to measure the structural position of an amino acid. We first validate that amino acids buried within the structural core are network-central, and those on the surface are not. Then, we study potential differences between network centralities and thus structural positions of amino acids encoded by conserved rare, non-conserved rare and commonly used codons. We find that in 84% of proteins, the three codon categories occupy significantly different structural positions. We examine protein groups showing different codon centrality trends, i.e. different relationships between structural positions of the three codon categories. We see several cases of all proteins from our data with some structural or functional property being in the same group. Also, we see a case of all proteins in some group having the same property. Our work shows that codon usage is linked to the final protein structure and thus possibly to co-translational protein folding. Availability and implementation https://nd.edu/∼cone/CodonUsage/. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Protein Folding
Molecular Networks (q-bio.MN)
Computational biology
Biology
Biochemistry
03 medical and health sciences
0302 clinical medicine
Protein structure
Quantitative Biology - Molecular Networks
Amino Acid Sequence
Codon
Codon Usage
Molecular Biology
Peptide sequence
030304 developmental biology
Supplementary data
chemistry.chemical_classification
0303 health sciences
Proteins
Model protein
Original Papers
Computer Science Applications
Amino acid
Computational Mathematics
Computational Theory and Mathematics
chemistry
FOS: Biological sciences
Codon usage bias
Protein folding
030217 neurology & neurosurgery
Network analysis
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....4963887ccbd86a5c4bdeb3d8b1905634