中国物理B ›› 2009, Vol. 18 ›› Issue (1): 363-369.doi: 10.1088/1674-1056/18/1/059

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The structural analysis of protein sequences based on the quasi-amino acids code

朱平1, 徐振源1, 唐旭清2   

  1. (1)School of Science, Jiangnan University, Wuxi 214122, China; (2)School of Science, Jiangnan University, Wuxi 214122, China;Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Anhui University, Hefei 230039, China
  • 收稿日期:2008-03-18 修回日期:2008-04-12 出版日期:2009-01-20 发布日期:2009-01-20
  • 基金资助:
    Project supported in part by the International Technology Collaboration Research Program of China (Grant No 2007DFA706700).

The structural analysis of protein sequences based on the quasi-amino acids code

Zhu Ping(朱平)a)†, Tang Xu-Qing(唐旭清)a)b), and Xu Zhen-Yuan(徐振源)a)   

  1. a School of Science, Jiangnan University, Wuxi 214122, China; b Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Anhui University, Hefei 230039, China
  • Received:2008-03-18 Revised:2008-04-12 Online:2009-01-20 Published:2009-01-20
  • Supported by:
    Project supported in part by the International Technology Collaboration Research Program of China (Grant No 2007DFA706700).

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摘要： Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑,+,*) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑,+,*), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕,○x) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of `the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).

关键词: algebraic operation, quasi-amino acids code, protein sequences, structural analysis

Abstract: Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system ($\varSigma$,+,*) is introduced, where $\varSigma$ is the set of 64 codons. According to the characteristics of ($\varSigma$,+,*), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕, $\otimes$) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of `the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).

Key words: algebraic operation, quasi-amino acids code, protein sequences, structural analysis

中图分类号:  (Structure of biomolecules)

  • 87.15.B-
87.14.E- (Proteins) 87.14.G- (Nucleic acids) 87.15.A- (Theory, modeling, and computer simulation) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.15.K- (Molecular interactions; membrane-protein interactions)