title: Choice of synonymous codons associated with protein folding.
abstract: Bioinformatical studies suggest that additional information provided by nucleic acids is necessary to construct protein three-dimensional structures. We find underlying correlations between the contents of bases. All correlations occur at the third codon position of a gene sequence. Four inverse relationships are observed between u(3) and c(3), between a(3) and g(3), between u(3) and g(3), and between c(3) and a(3); and two positive relationships are apparent between u(3) and a(3), and between c(3) and g(3). Their correlation coefficients reach -0.92, -0.89, -0.83, -0.85, 0.83, and 0.66, respectively, for large proteins with multistate folding kinetics. The interconnection of bases can be ascribed to choice of synonymous codons associated with protein folding in vivo. In this study, the refolding rate constants of large proteins correlate with the contents of the third base, suggesting that there is underlying biochemical rationale of guiding protein folding in choosing synonymous codons.
authors.affiliation: Department of Chemistry and State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China. jthuang@nankai.edu.cn
authors.forename: Jitao T
authors.initials: JT
authors.lastname: Huang
authors.forename: Dajie J
authors.initials: DJ
authors.lastname: Xing
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001483:Base Sequence / Q000235:genetics; D003062:Codon / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D008962:Models, Theoretical; D008968:Molecular Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013223:Statistics as Topic
chemical_list: D003062:Codon; D011506:Proteins