Synonymous codon usage influences the local protein structure observed
Open Access
- 8 June 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (19), 6719-6728
- https://doi.org/10.1093/nar/gkq495
Abstract
Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding.This publication has 76 references indexed in Scilit:
- tRNA over-expression in breast cancer and functional consequencesNucleic Acids Research, 2009
- Universal function-specificity of codon usageNucleic Acids Research, 2009
- Translationally Optimal Codons Associate with Structurally Sensitive Sites in ProteinsMolecular Biology and Evolution, 2009
- The Universal Protein Resource (UniProt) 2009Nucleic Acids Research, 2009
- Progress and challenges in protein structure predictionCurrent Opinion in Structural Biology, 2008
- The Universal Protein Resource (UniProt)Nucleic Acids Research, 2006
- [19] Gene Expression Omnibus: Microarray Data Storage, Submission, Retrieval, and AnalysisMethods in Enzymology, 2006
- UCSF Chimera?A visualization system for exploratory research and analysisJournal of Computational Chemistry, 2004
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- CATH – a hierarchic classification of protein domain structuresStructure, 1997