The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens

Adzhubei, 1996, Non-random usage of ‘degenerate’ codons is related to protein three-dimensional structure, FEBS Lett., 399, 78, 10.1016/S0014-5793(96)01287-2 Basharov, 2000, Cotranslational folding of proteins, Biochemistry (Moscow), 65, 1380, 10.1023/A:1002800822475 Berman, 2000, The Protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Brenner, 2000, The ASTRAL compendium for protein structure and sequence analysis, Nucleic Acids Res., 28, 254, 10.1093/nar/28.1.254 Brunak, 1996, Protein structure and the sequential structure of mRNA: alpha helix and beta sheet signals at the nucleotide level, Proteins, 25, 237, 10.1002/(SICI)1097-0134(199606)25:2<237::AID-PROT9>3.3.CO;2-Y Chiapello, 1998, Codon usage and gene function are related in sequences of Arabidopsis thaliana, Gene, 209, GC1, 10.1016/S0378-1119(97)00671-9 Chou, 1974, Prediction of protein conformation, Biochemistry, 13, 222, 10.1021/bi00699a002 Comeron, 1998, An evaluation of measure of synonymous codon usage bias, J. Mol. Evol., 47, 268, 10.1007/PL00006384 Conte, 2002, SCOP database in 2002: refinements accommodate structural genomics, Nucleic Acids Res., 30, 264, 10.1093/nar/30.1.264 Crombie, 1994, The folding of the bifunctional TRP3 protein in yeast is influenced by a translational pause which lies in a region of structural divergence with Escherichia coli indoleglycerol-phosphate synthase, Eur. J. Biochem., 226, 657, 10.1111/j.1432-1033.1994.tb20093.x David, 2001, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 29, 11, 10.1093/nar/29.1.11 Dong, 1996, Co-variation of tRNA abundance and codon usage in E. coli at different growth rates, J. Mol. Biol., 260, 649, 10.1006/jmbi.1996.0428 Ghosh, 2000, Studies on codon usage in Entamoeba histolytica, Int. J. Parasitol., 30, 715, 10.1016/S0020-7519(00)00042-4 Gouy, 1982, Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Res., 10, 7055, 10.1093/nar/10.22.7055 Grantham, 1980, Codon catalog usage and the genome hypothesis, Nucleic Acids Res., 8, 49r, 10.1093/nar/8.1.197-c Grantham, 1981, Codon catalog usage is a genome strategy modulated for gene expressivity, Nucleic Acids Res., 9, 43r, 10.1093/nar/9.1.213-b Gupta, 2000, Studies on the relationships between the synonymous codon usage and protein secondary structural units, Biochem. Biophys. Res. Commun., 269, 692, 10.1006/bbrc.2000.2351 Ikemura, 1981, Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J. Mol. Biol., 151, 389, 10.1016/0022-2836(81)90003-6 Ikemura, 1985, Codon usage and tRNA content in unicellular and multicelluar organisms, Mol. Biol. Evol., 2, 13 Irwin, 1995, Codon pair utilization biases influence translational elongation step times, J. Biol. Chem., 270, 22801, 10.1074/jbc.270.39.22801 Karlin, 1996, What drives codon choices in human genes?, J. Mol. Biol., 262, 459, 10.1006/jmbi.1996.0528 Komar, 1999, Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation, FEBS Lett., 462, 387, 10.1016/S0014-5793(99)01566-5 Lesnik, 2000, Ribosome traffic in E. coli and regulation of gene expression, J. Theor. Biol., 202, 175, 10.1006/jtbi.1999.1047 Liu, 1999, The relationship between mRNA’s sequence, structure, translational rate and protein structure, Zool. Res. (Chinese), 20, 457 Luo, 1995, Some physical problems in protein folding, J. Neimongu Univ. (Chinese), 26, 172 Ma, 2002, Cluster analysis of the codon use frequency of MHC genes from different species, Biosystems, 65, 199, 10.1016/S0303-2647(02)00016-3 Majumdar, 1999, Compositional correlation studies among the three different codon positions in 12 bacterial genomes, Biochem. Biophys. Res. Commun., 266, 66, 10.1006/bbrc.1999.1774 Makhoul, 2002, Distribution of rare triplets along mRNA and their relation to protein folding, J. Biomol. Struct. Dyn., 20, 413, 10.1080/07391102.2002.10506859 Mardia, K.V., Kent, J.T., Bibby, J.M., 1979. Multivariate Analysis. Academic Press, New York, pp. 305–378. Oresic, 1998, Specific correlations between relative synonymous codon usage and protein secondary structure, J. Mol. Biol., 281, 31, 10.1006/jmbi.1998.1921 Patricia, 2002, Silent mutations affect in vivo protein folding in Escherichia coli, Biochem. Biophys. Res. Commun., 293, 537, 10.1016/S0006-291X(02)00226-7 Richard, 2000, A functional significance for codon third bases, Gene, 245, 291, 10.1016/S0378-1119(00)00042-1 Rost, 2001, Protein secondary structure prediction continues to rise, J. Struct. Biol., 134, 204, 10.1006/jsbi.2001.4336 Sharp, 1986, Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes, Nucleic Acids Res., 14, 125, 10.1093/nar/14.13.5125 Su, J.M., Fu, R.H., Zhou, J.B., Zhang, L.H., 2000. Practical Guide for the Statistical Software of SPSS for Windows. Publishing House of Electronic Industry, Beijing, pp. 478–503. Thanaraj, 1996, Ribosome-mediated translational pause and protein domain organization, Protein Sci., 5, 1594, 10.1002/pro.5560050814 Thanaraj, 1996, Protein secondary structural types are differentially coded on messenger RNA, Protein Sci., 5, 1973, 10.1002/pro.5560051003 Xie, 1998, The relationship between synonymous codon usage and protein structure, FEBS Lett., 434, 93, 10.1016/S0014-5793(98)00955-7