Literature DB >> 19519001

Queueing phase transition: theory of translation.

M Carmen Romano1, Marco Thiel, Ian Stansfield, Celso Grebogi.   

Abstract

We study the current of particles on a lattice, where to each site a different hopping probability has been associated and the particles can move only in one direction. We show that the queueing of the particles behind a slow site can lead to a first-order phase transition, and derive analytical expressions for the configuration of slow sites for this to happen. We apply this stochastic model to describe the translation of mRNAs. We show that the first-order phase transition, uncovered in this work, is the process responsible for the classification of the proteins having different biological functions.

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Year:  2009        PMID: 19519001      PMCID: PMC3639427          DOI: 10.1103/PhysRevLett.102.198104

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  13 in total

1.  Totally asymmetric exclusion process with extended objects: a model for protein synthesis.

Authors:  Leah B Shaw; R K P Zia; Kelvin H Lee
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-08-18

2.  Dynamic scaling of growing interfaces.

Authors: 
Journal:  Phys Rev Lett       Date:  1986-03-03       Impact factor: 9.161

3.  Clustered bottlenecks in mRNA translation and protein synthesis.

Authors:  Tom Chou; Greg Lakatos
Journal:  Phys Rev Lett       Date:  2004-11-01       Impact factor: 9.161

4.  Inhomogeneous exclusion processes with extended objects: the effect of defect locations.

Authors:  J J Dong; B Schmittmann; R K P Zia
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-11-13

5.  Mutations in ribosomal proteins L7/L12 perturb EF-G and EF-Tu functions.

Authors:  N Bilgin; L A Kirsebom; M Ehrenberg; C G Kurland
Journal:  Biochimie       Date:  1988-05       Impact factor: 4.079

6.  Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.

Authors:  R Percudani; A Pavesi; S Ottonello
Journal:  J Mol Biol       Date:  1997-05-02       Impact factor: 5.469

7.  Disordered asymmetric simple exclusion process: mean-field treatment.

Authors:  R J Harris; R B Stinchcombe
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-07-02

8.  Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome.

Authors:  T Pape; W Wintermeyer; M V Rodnina
Journal:  EMBO J       Date:  1998-12-15       Impact factor: 11.598

9.  Ribosome pausing and stacking during translation of a eukaryotic mRNA.

Authors:  S L Wolin; P Walter
Journal:  EMBO J       Date:  1988-11       Impact factor: 11.598

10.  Reinitiation and recycling are distinct processes occurring downstream of translation termination in yeast.

Authors:  Lukas Rajkowitsch; Cristina Vilela; Karine Berthelot; Carmen Velasco Ramirez; John E G McCarthy
Journal:  J Mol Biol       Date:  2004-01-02       Impact factor: 5.469

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  17 in total

1.  Processivity and coupling in messenger RNA transcription.

Authors:  Stuart Aitken; Marie-Cécile Robert; Ross D Alexander; Igor Goryanin; Edouard Bertrand; Jean D Beggs
Journal:  PLoS One       Date:  2010-01-28       Impact factor: 3.240

2.  A comprehensive, quantitative, and genome-wide model of translation.

Authors:  Marlena Siwiak; Piotr Zielenkiewicz
Journal:  PLoS Comput Biol       Date:  2010-07-29       Impact factor: 4.475

3.  Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation.

Authors:  L Ciandrini; I Stansfield; M C Romano
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-05-05

4.  Limited resources in a driven diffusion process.

Authors:  Chris A Brackley; M Carmen Romano; Celso Grebogi; Marco Thiel
Journal:  Phys Rev Lett       Date:  2010-08-11       Impact factor: 9.161

5.  Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation.

Authors:  Barbara Gorgoni; Luca Ciandrini; Matthew R McFarland; M Carmen Romano; Ian Stansfield
Journal:  Nucleic Acids Res       Date:  2016-07-12       Impact factor: 16.971

6.  Synonymous codon usage influences the local protein structure observed.

Authors:  Rhodri Saunders; Charlotte M Deane
Journal:  Nucleic Acids Res       Date:  2010-06-08       Impact factor: 16.971

7.  The dynamics of supply and demand in mRNA translation.

Authors:  Chris A Brackley; M Carmen Romano; Marco Thiel
Journal:  PLoS Comput Biol       Date:  2011-10-13       Impact factor: 4.475

8.  The role of codon selection in regulation of translation efficiency deduced from synthetic libraries.

Authors:  Sivan Navon; Yitzhak Pilpel
Journal:  Genome Biol       Date:  2011-02-01       Impact factor: 13.583

9.  The architecture of eukaryotic translation.

Authors:  Dominique Chu; Tobias von der Haar
Journal:  Nucleic Acids Res       Date:  2012-09-10       Impact factor: 16.971

10.  Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.

Authors:  Luca Ciandrini; Ian Stansfield; M Carmen Romano
Journal:  PLoS Comput Biol       Date:  2013-01-31       Impact factor: 4.475

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