Mathematical and computational modelling of ribosomal movement and protein synthesis: An overview

Computational and Structural Biotechnology Journal

Volumn 1, Issue 1, 2012, Pages e201204002-

  Von Der Haar, Tobias ^a  

^a UNIVERSITY OF KENT   (United Kingdom)

Author keywords

Biosynthesis; Gene expression; MRNA; Polysome; Ribosome; Translation

Indexed keywords

EID: 84873429816     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201204002     Document Type: Review

References (91)

1. Mathews MB, Sonenberg N, Hershey JWB (2007) Translational Control in Biology and Medicine. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. 934 p.
2. Warner JR, Rich A, Hall CE (1962) Electron Microscope Studies of Ribosomal Clusters Synthesizing Hemoglobin. Science 138:1399-1403.
3. Naughton MA, Dhitzis HM (1962) Sequential biosynthesis of the peptide chains of hemoglobin. Proc Natl Acad Sci U S A 48:1822-1830.
4. Wettstein FO, Staehelin T, Noll H (1963) Ribosomal aggregate engaged in protein synthesis: characterization of the ergosome. Nature 197:430-435-
5. Englander SW, Page LA (1965) Interpretation of data on sequential labeling of growing polypeptides. Biochem Biophys Res Commun 19:565-570.
6. de Lorenzo V, Galperin M (2009) Microbial systems biology: bottom up and top down. FEMS Microbiol Rev 33:1-2.
7. Tuller T, Kupiec M, Ruppin E (2007) Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol 3:e248.
8. von der Haar T (2008) A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol 2:87-
9. Siwiak M, Zielenkiewicz P (2010) A comprehensive, quantitative, and genome-wide model of translation. PLoS Comput Biol 6:e1000865.
10. Barnes DJ, Chu DF (2010) Introduction to Modeling for Biosciences. London: Springer.
11. Gerst I, Levine SN (1965) Kinetics of protein synthesis by polyribosomes. J TheorBiol 9:16-36.
12. Garrick MD (1967) The kinetics of the translation of messenger RNA into protein. J Theor Biol 17:19-30.
13. Simha R, Zimmerman JM, Moacanin J (1963) Polymerization kinetics of biological macromolecules on templates. J Chem Phys 39:1239-1246.
14. Zimmerman JM, Simha R (1965) The kinetics of multicenter macromolecule growth along a template. J Theor Biol 9:156-185-
15. MacDonald CT, Gibbs JH, Pipkin AC (1968) Kinetics of Biopolymerization on Nucleic Acid Templates. Biopolymers 6:1-25.
16. MacDonald CT, Gibbs JH (1969) Concerning the Kinetics of Polypeptide Synthesis of Polyribosomes. Biopolymers 7:707-725.
17. Hiernaux J (1974) On some stochastic models for protein biosynthesis. Biophys Chem 2:70-75.
18. Lodish HF (1974) Model for the regulation of mRNA translation applied to haemoglobin synthesis. Nature 251:385-388.
19. Heinrich R, Rapoport TA (1980) Mathematical modelling of translation of mRNA in eucaryotes; steady state, time-dependent processes and application to reticulocytes. J Theor Biol 86:279-313. (Pubitemid 11255651)
20. Godefroy-Colburn T, Thach RE (1981) The role of mRNA competition in regulating translation. IV. Kinetic model. J Biol Chem 256:11762-11773.
21. Mehra A, Hatzimanikatis V (2006) An algorithmic framework for genomewide modeling and analysis of translation networks. Biophys J 90:1136-1146.
22. Zouridis H, Hatzimanikatis V (2008) Effects of codon distributions and tRNA competition on protein translation. Biophys J 95:1018-1033.
23. Rapoport TA, Heinrich R, Walter P, Schulmeister T (1987) Mathematical modeling of the effects of the signal recognition particle on translation and translocation of proteins across the endoplasmic reticulum membrane. J Mol Biol 195:621-636.
24. Schadschneider A (2000) Statistical physics of traffic flow. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 285:101-120.
25. Chou T (2003) Ribosome recycling, diffusion, and mRNA loop formation in translational regulation. Biophys J 85:755-773. (Pubitemid 36909643)
26. Shaw LB, Zia RK, Lee KH (2003) Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys Rev E Stat Nonlin Soft Matter Phys 68:021910.
27. Chou T, Lakatos G (2004) Clustered bottlenecks in mRNA translation and protein synthesis. Phys Rev Lett 93:198101.
28. Lakatos G, Chou T, Kolomeisky A (2005) Steady-state properties of a totally asymmetric exclusion process with periodic structure. Phys Rev E Stat Nonlin Soft Matter Phys 71:011103.
29. Basu A, Chowdhury D (2007) Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis. Phys Rev E Stat Nonlin Soft Matter Phys 75:021902.
30. Dong JJ, Schmittmann B, Zia RK (2007) Towards a Model for Protein Production Rates. J Stat Phys 128:21-34.
31. Cook LJ, Zia RK, Schmittmann B (2009) Competition between multiple totally asymmetric simple exclusion processes for a finite pool of resources. Phys Rev E Stat Nonlin Soft Matter Phys 80:031142.
32. Garai A, Chowdhury D, Chowdhury D, Ramakrishnan TV (2009) Stochastic kinetics of ribosomes: single motor properties and collective behavior. Phys Rev E Stat Nonlin Soft Matter Phys 80:011908.
33. Garai A, Chowdhury D, Ramakrishnan TV (2009) Fluctuations in protein synthesis from a single RNA template: stochastic kinetics of ribosomes. Phys Rev E Stat Nonlin Soft Matter Phys 79:011916.
34. Romano MC, Thiel M, Stansfield I, Grebogi C (2009) Queueing phase transition: theory of translation. Phys Rev Lett 102:198104.
35. Brackley CA, Romano MC, Grebogi C, Thiel M (2010) Limited resources in a driven diffusion process. Phys Rev Lett 105:078102.
36. Ciandrini L, Stansfield I, Romano MC (2010) Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation. Phys Rev E Stat Nonlin Soft Matter Phys 81:051904.
37. Cook LJ, Zia RK (2010) Power spectra of a constrained totally asymmetric simple exclusion process. J Stat Mech: P07014.
38. Mier-y-Teran-Romero L, Silber M, Hatzimanikatis V (2010) The origins of time-delay in template biopolymerization processes. PLoS Comput Biol 6:e1000726.
39. Sharma AK, Chowdhury D (2010) Quality control by a mobile molecular workshop: Quality versus quantity. Phys Rev E Stat Nonlin Soft Matter Phys 82:031912.
40. Krakauer DC, Jansen VA (2002) Red queen dynamics of protein translation. J Theor Biol 218:97-109. (Pubitemid 35217570)
41. Singh UN (1969) Polyribosomes and unstable messenger RNA: a stochastic model of protein synthesis. J Theor Biol 25:444-460.
42. Singh UN, Gupta RS (1971) Polyribosomes and unstable messenger RNA. II. Some further implications of the tape theory of protein synthesis. J Theor Biol 30:603-619.
43. Singh UN (1973) Polyribosomes and unstable messenger RNA. 3. Temporal relationship between the syntheses of mRNA and inducible enzyme. J Theor Biol 40:553-569.
44. Valleriani A, Ignatova Z, Nagar A, Lipowsky R (2010) Turnover of messenger RNA: Polysome statistics beyond the steady state. EPL - Europhys Lett 89:58003.
45. Varenne S, Lazdunski C (1986) Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism. J Theor Biol 120:99-110. (Pubitemid 16081275)
46. Bulmer M (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
47. Gilchrist MA, Wagner A (2006) A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 239:417-434.
48. Pienaar E, Viljoen HJ (2008) The tri-frame model. J Theor Biol 251:616-627.
49. Gordon R (1969) Polyribosome dynamics at steady state. J Theor Biol 22:515-532.
50. Singh UN (1996) Polyribosome dynamics: size-distribution as a function of attachment, translocation and release of ribosomes. J Theor Biol 179:147-159. (Pubitemid 26150992)
51. Heyd A, Drew DA (2003) A mathematical model for elongation of a peptide chain. Bull Math Biol 65:1095-1109. (Pubitemid 37446846)
52. Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, et al. (2010) Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Res 38:4778-4787.
53. Zouridis H, Hatzimanikatis V (2007) A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. Biophys J 92:717-730. (Pubitemid 46203205)
54. Bi X, Goss DJ (2000) Kinetic proofreading scanning models for eukaryotic translational initiation: the cap and poly (A) tail dependency of translation. J Theor Biol 207:145-157.
55. Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarthy JE (2004) Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Mol Microbiol 51:987-1001. (Pubitemid 38270794)
56. Dimelow RJ, Wilkinson SJ (2009) Control of translation initiation: a model-based analysis from limited experimental data. J R Soc Interface 6:51-61.
57. You T, Coghill GM, Brown AJ (2010) A quantitative model for mRNA translation in Saccharomyces cerevisiae. Yeast 27:785-800.
58. de Silva E, Krishnan J, Betney R, Stansfield I (2010) A mathematical modelling framework for elucidating the role of feedback control in translation termination. J Theor Biol 264:808-821.
59. Vassart G, Dumont JE, Cantraine FR (1971) Translational control of protein synthesis: a simulation study. Biochim Biophys Acta 247:471-485.
60. Li K, Kisilevsky R, Wasan MT, Hammond G (1972) A computer simulation of in vivo protein synthesis. Biochim Biophys Acta 272:451-462.
61. von Heijne G, Nilsson L, Blomberg C (1977) Translation and messenger RNA secondary structure. J Theor Biol 68:321-329. (Pubitemid 8209854)
62. Bergmann JE, Lodish HF (1979) A kinetic model of protein synthesis. Application to hemoglobin synthesis and translational control. J Biol Chem 254:11927-11937.
63. Harley CB, Pollard JW, Stanners CP, Goldstein S (1981) Model for messenger RNA translation during amino acid starvation applied to the calculation of protein synthetic error rates. J Biol Chem 256:10786-10794.
64. Menninger JR (1983) Computer simulation of ribosome editing. J Mol Biol 171:383-399. (Pubitemid 14191429)
65. Zhang S, Goldman E, Zubay G (1994) Clustering of low usage codons and ribosome movement. J Theor Biol 170:339-354. (Pubitemid 24339399)
66. Mitarai N, Sneppen K, Pedersen S (2008) Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol 382:236-245.
67. Fluitt A, Pienaar E, Viljoen H (2007) Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 31:335-346. (Pubitemid 47531990)
68. Macal CM, North MJ (2010) Tutorial on agent-based modelling and simulation. J Simul 4:151-162.
69. Chu DF, Barnes DJ, von der Haar T (2011) The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Res 39:6705-6714.
70. Sangthong P, Hughes J, McCarthy JE (2007) Distributed control for recruitment, scanning and subunit joining steps of translation initiation. Nucleic Acids Res 35:3573-3580. (Pubitemid 47244652)
71. Hiremath LS, Webb NR, Rhoads RE (1985) Immunological detection of the messenger RNA cap-binding protein. J Biol Chem 260:7843-7849. (Pubitemid 15228219)
72. Duncan R, Milburn SC, Hershey JW (1987) Regulated phosphorylation and low abundance of HeLa cell initiation factor eIF-4F suggest a role in translational control. Heat shock effects on eIF-4F. J Biol Chem 262:380-388. (Pubitemid 17000032)
73. Rati M, Ohlmann T, Morley SJ, Pain VM (1996) A revaluation of the capbinding protein, eIF4E, as a rate-limiting factor for initiation of translation in reticulocyte lysate. J Biol Chem 271:8983-8990. (Pubitemid 26123327)
74. Gray NK, Wickens M (1998) Control of translation initiation in animals. Annu Rev Cell Dev Biol 14:399-458. (Pubitemid 29001460)
75. Raught B, Gingras AC (1999) eIF4E activity is regulated at multiple levels. Int J Biochem Cell Biol 31:43-57. (Pubitemid 29094789)
76. Hayashi S, Nishimura K, Fukuchi-Shimogori T, Kashiwagi K, Igarashi K (2000) Increase in cap- and IRES-dependent protein synthesis by overproduction of translation initiation factor eIF4G. Biochem Biophys Res Commun 277:117-123.
77. von der Haar T, McCarthy JE (2002) Intracellular translation initiation factor levels in Saccharomyces cerevisiae and their role in cap-complex function. Mol Microbiol 46:531-544. (Pubitemid 35340962)
78. Kopeina GS, Afonina ZA, Gromova KV, Shirokov VA, Vasiliev VD, et al. (2008) Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA. Nucleic Acids Res 36:2476-2488. (Pubitemid 351659564)
79. Liljenstrom H, von Heijne G (1987) Translation rate modification by preferential codon usage: intragenic position effects. J Theor Biol 124:43-55. (Pubitemid 17002611)
80. Waldron C, Jund R, Lacroute F (1974) The elongation rate of proteins of different molecular weight classes in yeast. FEBS Lett 46:11-16.
81. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, et al. (2003) Genomewide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100:3889-3894. (Pubitemid 36418127)
82. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223.
83. Arava Y, Boas FE, Brown PO, Herschlag D (2005) Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 33:2421-2432. (Pubitemid 41511261)
84. Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, et al. (2010) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141:344-354.
85. Kitano H (2002) Systems biology: a brief overview. Science 295:1662-1664. (Pubitemid 34202893)
86. Klumpp S, Hwa T (2008) Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci USA 105:18159-18164.
87. Bai L, Fulbright RM, Wang MD (2007) Mechanochemical principles of transcription elongation. Phys Rev Lett 98:068103.
88. Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML et al. (2010) Synergistic action of RNA polymerases in overcoming the nucleosomal barrier. Nat Struct Mol Biol 17:745-752.
89. Tinoco I Jr, Gonzalez RL Jr (2011) Biological Mechanisms, one molecule at a time. Genes Dev 25:1205-1231.
90. Nayak S, Siddiqui JK, Varner JD (2011) Modelling and analysis of an ensemble of eukaryotic translation initiation models. IET Syst Biol 5:2.
91. Rheinberger HJ, Nierhaus KH (1986) Allosteric interactions between the ribosomal transfer RNA-binding sites A and E. J Biol Chem 261:9133-9139. (Pubitemid 17218183)