Movable Finite Automaton Models for mRNA Translation

Toyomasa Hatakeyama; Takashi Miyagoshi

doi:10.1541/ieejeiss1987.120.12_1940

Toyomasa Hatakeyama, Takashi Miyagoshi

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Keywords: mRNA

JOURNAL FREE ACCESS

2000 Volume 120 Issue 12 Pages 1940-1947

DOI https://doi.org/10.1541/ieejeiss1987.120.12_1940

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Published: December 01, 2000 Received: January 20, 1999 Available on J-STAGE: December 19, 2008 Accepted: - Advance online publication: - Revised: -
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Date of correction: December 19, 2008 Reason for correction: - Correction: CITATION Details: Wrong : (1) B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson: ⌈Molecular Biology of THE CELL Third Edition⌋, Garland Publishing, New York, 1994.
(2) B. Lewin: _??_Genes VI_??_, Oxford University Press, 1997.
(4) C. G. Langton:_??_Studying artificial life with cellular automata_??_, Physica, IOD (22), pp. 120-149, 1986.
(5) S. R. Hameroff, S. A. Smith, and R. C. Watt:_??_Automaton model of dynamic organization in microtubules_??_, Ann. NY Acad. Sci., no. 466, pp. 949-952, 1986.
(6) G. Zou and G. N. Phillips:_??_A cellular automaton model for the regulatory behavior of muscle thin filaments_??_, Biophysical J., vol. 67, pp. 11-28, 1994.
(7) R. L. Thompson and N. S. Goel:_??_A simulation of T4 bacteriophage assembly and operation_??_, BioSystems, vol. 18, pp. 23-45, 1985.
(8) R. L. Thompson and N. S. Goel:_??_Movable finite automata (MFA) models for biological systems: Bacteriophage assembly and operation_??_, J. Theor. Biol., vol. 131, pp. 351-385, 1988.
(11) A. Rich and S. H. Kim:_??_The three-dimensional structure of transfer RNA_??_, Sci. Am., vol. 238, no. 1, pp. 52-62, 1978.
(12) P. Schimmel:_??_Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs_??_, Annu Rev Biochem, vol.56, pp. 125-158, 1987.
(13) W. Freist:_??_Mechanisms of aminoacyl-tRNA synthetases: a critical consideration of recent results_??_, Biochemistry, vol. 28, no. 17, pp. 6787-6795, 1989.
(14) W. J. Craigen, C. C. Lee, and C. T. Caskey:_??_Recent advances in peptide chain termination_??_, Mol. Microbiol., vol. 4, no. 6, pp. 861-865, 1990.
(15) K. H. Nierhaus:_??_The allosteric three-site model for the ribosomal elongation cycle: features and future_??_, Biochemistry, vol. 29, no. 21, pp. 4997-5008, 1990.
(16) W. C. Merrick:_??_Overview: mechanism of translation initiation in eukaryotes_??_, Enzyme, vol. 44, pp. 1-4, 1990.
(17) P. Schimmel:_??_Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code_??_, Trends Biochem Sci., vol. 16, no. 1, pp. 1-3, 1991.
(18) J. Cavarelli and D. Moras:_??_Recognition of tRNAs by aminoacyl-tRNA synthetases_??_, FASEB J., vol. 7, no. 1, pp. 79-86, 1993.
(19) H. O. Voorma, A. A. Thomas, and H. A. Van Heugten:_??_Initiation of protein synthesis in eukaryotes_??_, Mol Biol Rep., vol. 19, no. 3, pp. 139-145, May 1994.
(20) T. C. Evans, S. L. Crittenden, V. Kodoyianni, and J. Kimble:_??_Translational control of maternal glp-1 mRNA establishes an asymmetry in the C. Elegans embryo_??_, Cell, vol. 77, pp. 183-194, 1994.
(21) D. St Johnston:_??_The intracellular localization of messenger RNAs_??_, Cell, vol. 81, pp. 161-170, 1995.
(22) V. M. Pain:_??_Initiation of protein synthesis in eukaryotic cells_??_, Eur J Biochem, vol. 236, no. 3, pp. 747-771 1996.

Right : (1) B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson: ⌈Molecular Biology of THE CELL Third Edition⌋, Garland Publishing, New York, 1994.
(2) B. Lewin: ⌈Genes VI⌋, Oxford University Press, 1997.
(4) C. G. Langton:⌈Studying artificial life with cellular automata⌋, Physica, IOD (22), pp. 120-149, 1986.
(5) S. R. Hameroff, S. A. Smith, and R. C. Watt:⌈Automaton model of dynamic organization in microtubules⌋, Ann. NY Acad. Sci., no. 466, pp. 949-952, 1986.
(6) G. Zou and G. N. Phillips:⌈A cellular automaton model for the regulatory behavior of muscle thin filaments⌋, Biophysical J., vol. 67, pp. 11-28, 1994.
(7) R. L. Thompson and N. S. Goel:⌈A simulation of T4 bacteriophage assembly and operation⌋, BioSystems, vol. 18, pp. 23-45, 1985.
(8) R. L. Thompson and N. S. Goel:⌈Movable finite automata (MFA) models for biological systems: Bacteriophage assembly and operation⌋, J. Theor. Biol., vol. 131, pp. 351-385, 1988.
(11) A. Rich and S. H. Kim:⌈The three-dimensional structure of transfer RNA⌋, Sci. Am., vol. 238, no. 1, pp. 52-62, 1978.
(12) P. Schimmel:⌈Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs⌋, Annu Rev Biochem, vol.56, pp. 125-158, 1987.
(13) W. Freist:⌈Mechanisms of aminoacyl-tRNA synthetases: a critical consideration of recent results⌋, Biochemistry, vol. 28, no. 17, pp. 6787-6795, 1989.
(14) W. J. Craigen, C. C. Lee, and C. T. Caskey:⌈Recent advances in peptide chain termination⌋, Mol. Microbiol., vol. 4, no. 6, pp. 861-865, 1990.
(15) K. H. Nierhaus:⌈The allosteric three-site model for the ribosomal elongation cycle: features and future⌋, Biochemistry, vol. 29, no. 21, pp. 4997-5008, 1990.
(16) W. C. Merrick:⌈Overview: mechanism of translation initiation in eukaryotes⌋, Enzyme, vol. 44, pp. 1-4, 1990.
(17) P. Schimmel:⌈Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code⌋, Trends Biochem Sci., vol. 16, no. 1, pp. 1-3, 1991.
(18) J. Cavarelli and D. Moras:⌈Recognition of tRNAs by aminoacyl-tRNA synthetases⌋, FASEB J., vol. 7, no. 1, pp. 79-86, 1993.
(19) H. O. Voorma, A. A. Thomas, and H. A. Van Heugten:⌈Initiation of protein synthesis in eukaryotes⌋, Mol Biol Rep., vol. 19, no. 3, pp. 139-145, May 1994.
(20) T. C. Evans, S. L. Crittenden, V. Kodoyianni, and J. Kimble:⌈Translational control of maternal glp-1 mRNA establishes an asymmetry in the C. Elegans embryo⌋, Cell, vol. 77, pp. 183-194, 1994.
(21) D. St Johnston:⌈The intracellular localization of messenger RNAs⌋, Cell, vol. 81, pp. 161-170, 1995.
(22) V. M. Pain:⌈Initiation of protein synthesis in eukaryotic cells⌋, Eur J Biochem, vol. 236, no. 3, pp. 747-771 1996.

Date of correction: December 19, 2008 Reason for correction: - Correction: PDF FILE Details: -

Abstract

We propose a movable finite automaton (MFA) models for describing the translation process based on biological findings, in which the sequence of nucleotides in the mRNA molecule is translated into a corresponding sequence of amino acids to produce a distinctive protein chain. We have constructed the MFA models of mRNA, tRNA contained the end factor, the amino acids, and the small and the large ribosomal subunits concerned with the translation process. Using these quasi-bioelements, an algorithm of the protein elongation is developed, and then the computer simulation is performed. Results obtained is discussed from the biological studies.

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