TY - JOUR
T1 - The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens
AU - Gu, Wanjun
AU - Zhou, Tong
AU - Ma, Jianmin
AU - Sun, Xiao
AU - Lu, Zuhong
N1 - Funding Information:
This research is funded by the National Grand Fundamental Research Project and the National Natural Science Foundation of China Project 60121101.
PY - 2004/2
Y1 - 2004/2
N2 - The role of silent position in the codon on the protein structure is an interesting and yet unclear problem. In this paper, 563 Homo sapiens genes and 417 Escherichia coli genes coding for proteins with four different folding types have been analyzed using variance analysis, a multivariate analysis method newly used in codon usage analysis, to find the correlation between amino acid composition, synonymous codon, and protein structure in different organisms. It has been found that in E. coli, both amino acid compositions in differently folded proteins and synonymous codon usage in different gene classes coding for differently folded proteins are significantly different. It was also found that only amino acid composition is different in different protein classes in H. sapiens. There is no universal correlation between synonymous codon usage and protein structure in these two different organisms. Further analysis has shown that GC content on the second codon position can distinguish coding genes for different folded proteins in both organisms.
AB - The role of silent position in the codon on the protein structure is an interesting and yet unclear problem. In this paper, 563 Homo sapiens genes and 417 Escherichia coli genes coding for proteins with four different folding types have been analyzed using variance analysis, a multivariate analysis method newly used in codon usage analysis, to find the correlation between amino acid composition, synonymous codon, and protein structure in different organisms. It has been found that in E. coli, both amino acid compositions in differently folded proteins and synonymous codon usage in different gene classes coding for differently folded proteins are significantly different. It was also found that only amino acid composition is different in different protein classes in H. sapiens. There is no universal correlation between synonymous codon usage and protein structure in these two different organisms. Further analysis has shown that GC content on the second codon position can distinguish coding genes for different folded proteins in both organisms.
KW - Amino acid composition
KW - Protein folding type
KW - Synonymous codon usage
KW - Variance analysis
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U2 - 10.1016/j.biosystems.2003.10.001
DO - 10.1016/j.biosystems.2003.10.001
M3 - Article
C2 - 15013221
AN - SCOPUS:0842307105
VL - 73
SP - 89
EP - 97
JO - Currents in modern biology
JF - Currents in modern biology
SN - 0303-2647
IS - 2
ER -