Identification of several types of periodicities in the collagens and their simulation

International Journal of Biological Macromolecules

Volumn 19, Issue 2, 1996, Pages 131-138

  Arquès, Didier G ^a   Fallott, Jean Paul ^b   Michel, Christian J ^b  

^a Université de Marne la Vallée   (France)

^b UNIVERSITÉ DE FRANCHE COMTÉ   (France)

Author keywords

Autocorrelation function; Automaton; Collagens; Identification; Modelling

Indexed keywords

ALANINE; AMINO ACID; ARGININE; ASPARTIC ACID; COLLAGEN; GLUTAMIC ACID; GLUTAMINE; LEUCINE; LYSINE; PROLINE; SERINE; TRIPEPTIDE;

ARTICLE; CLASSIFICATION; MODEL;

EID: 0030221634     PISSN: 01418130     EISSN: None     Source Type: Journal    
DOI: 10.1016/0141-8130(96)01115-4     Document Type: Article

References (21)

1. [1] Vuorio, E. and de Crombrugghe, B. The family of collagen genes. Annu. Rev. Biochem. 1990; 59: 837-872.
2. [2] Arquès, D.G. and Michel, C.J. A purine-pyrimidine motif verifying an identical presence in almost all gene taxonomic groups. J. Theor. Biol. 1987; 128: 457-461.
3. [3] Arquès, D.G. and Michel, C.J. Study of a perturbation in the coding periodicity. Math. Biosci. 1987; 86: 1-14.
4. [4] Arquès, D.G. and Michel, C.J. Periodicities in coding and noncoding regions of the genes. J. Theor. Biol. 1990; 143: 307-318.
5. [5] Arquès, D.G., Lapayre, J.-C. and Michel, C.J. Deux classes de periodicités non en phase de lecture identifiées dans les gènes codants des eucaryotes et simulées à l'aide d'un automate stochastique. Tech. Sci. Informat. 1995; 14: 197-216.
6. [6] Arquès, D.G. and Michel, C.J. A model of DNA sequence evolution, Part 1 Statistical features and classification of gene populations 743-753, Part 2 Simulation model 753-766, Part 3 Return of the model to the reality 766-770. Bull. Math. Biol. 1990; 52: 741-772.
7. [7] Arquès, D.G., Michel, C.J. and Orieux, K. Analysis of Gene Evolution: the software AGE. Comput. Applic. Biosci. 1992; 8: 5-14.
8. [8] Arquès, D.G. and Michel, C.J. A model of gene evolution based on recognizable languages and on insertion and deletion operations. Model. Simulat. 1993; 13:110-113.
9. [9] Benne, R., Van Den Burg, J., Brakenhoff, J.P.J., Sloof, P., Van Boom, J.H. and Tromp, M.C. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 1986; 46: 819-826.
10. [10] Covello, P.S. and Gray, M.W. On the evolution of RNA editing. Trends Genet. 1993; 9: 265-268.
11. [11] Gromiha, M.M. and Ponnuswamy, P.K. Relationship between amino acids properties and protein compressibility. J. Theor. Biol. 1993; 165: 87-100.
12. [12] Creighton, T.E. Proteins, Structures and Molecular Properties, W.H. Freeman and Company, New York, 1993.
13. [13] McLachlan, A.D. Evidence for gene duplication in collagen. J. Mol. Biol. 1976; 107: 159-174.
14. [14] Salem, G. and Traub, W. Conformational implications of amino acid sequence regularities in collagen. FEBS Lett. 1975; 51: 94-99.
15. [15] Traub, W. and Fietzek, P.P. Contribution of the α2 chain to the molecular stability of collagen. FEBS Lett. 1976; 68: 245-249.
16. [16] Katz, E.P. and David, C.W. Energetics of intrachain salt-linkage formation in collagen. Biopolymers 1990; 29: 791-798.
17. [17] Katz, E.P. and David, C.W. Unique side-chain conformation encoding for chirality and azimuthal orientation in the molecular packing of skin collagen. J. Mol. Biol. 1992; 228: 963-969.
18. [18] Traub, W. and Piez, K.A. The chemistry and structure of collagen. Adv. Protein Chem. 1971; 25: 243-352.
19. [19] Hulmes, D.J.S., Miller, A., Parry, D.A.D., Piez, K.A. and Woodhead-Galloway, J. Analysis of the primary structure of collagen for the origins of molecular packing. J. Mol. Biol. 1973; 79: 137-148.
20. [20] Hulmes, D.J.S., Miller, A., Parry, D.A.D. and Woodhead-Galloway, J. Fundamental periodicities in the amino acid sequence of the collagen α1. Biochem. Biophys. Res. Comm. 1977; 77: 574-580.
21. [21] Yamada, Y., Avvedimento, V.E., Mudryi, M., Ohkubo, H., Vogeli, G., Irani, M., Pastan, I. and de Crombrugghe, B. The collagen gene: evidence for its evolutionary assembly by amplification of a DNA segment containing an exon of 54 bp. Cell 1980; 22: 887-892.