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

Wanjun Gu, Tong Zhou, Jianmin Ma, Xiao Sun, Zuhong Lu

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)89-97
Number of pages9
JournalBioSystems
Volume73
Issue number2
DOIs
StatePublished - Feb 2004
Externally publishedYes

Fingerprint

Protein Structure
protein structure
codons
Codon
Escherichia coli
Escherichia Coli
Proteins
Protein
protein
Gene
Amino Acids
amino acid composition
Coding
Genes
Amino acids
proteins
amino acid
gene
organisms
genes

Keywords

  • Amino acid composition
  • Protein folding type
  • Synonymous codon usage
  • Variance analysis

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Drug Discovery

Cite this

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. / Gu, Wanjun; Zhou, Tong; Ma, Jianmin; Sun, Xiao; Lu, Zuhong.

In: BioSystems, Vol. 73, No. 2, 02.2004, p. 89-97.

Research output: Contribution to journalArticle

Gu, Wanjun ; Zhou, Tong ; Ma, Jianmin ; Sun, Xiao ; Lu, Zuhong. / The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. In: BioSystems. 2004 ; Vol. 73, No. 2. pp. 89-97.
@article{afd0a62a8c4d485b882edd39d33ca2a6,
title = "The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens",
abstract = "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.",
keywords = "Amino acid composition, Protein folding type, Synonymous codon usage, Variance analysis",
author = "Wanjun Gu and Tong Zhou and Jianmin Ma and Xiao Sun and Zuhong Lu",
year = "2004",
month = "2",
doi = "10.1016/j.biosystems.2003.10.001",
language = "English (US)",
volume = "73",
pages = "89--97",
journal = "BioSystems",
issn = "0303-2647",
publisher = "Elsevier Ireland Ltd",
number = "2",

}

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

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

UR - http://www.scopus.com/inward/record.url?scp=0842307105&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0842307105&partnerID=8YFLogxK

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 - BioSystems

JF - BioSystems

SN - 0303-2647

IS - 2

ER -