`a`
Mathematical Biosciences and Engineering (MBE)
 

Formulation of the protein synthesis rate with sequence information
Pages: 507 - 522, Issue 2, April 2018

doi:10.3934/mbe.2018023      Abstract        References        Full text (1150.6K)           Related Articles

Wenjun Xia - Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013, China (email)
Jinzhi Lei - Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084, China (email)

1 M. M. Babu, N. M. Luscombe, L. Aravind, M. Gerstein and S. A. Teichmann, Structure and evolution of transcriptional regulatory networks, Curr. Opin. Struct. Biol., 14 (2004), 283-291.
2 G. Cannarozzi, N. N. Schraudolph, M. Faty, P. von Rohr, M. T. Friberg, A. C. Roth, P. Gonnet, G. Gonnet and Y. Barral, A role for codon order in translation dynamics, Cell, 141 (2010), 355-367.
3 D. Chu, D. J. Barnes and T. von der Haar, The role of tRNA and ribosome competition in coupling the expression of different mRNAs in saccharomyces cerevisiae, Nucleic. Acids. Res., 39 (2011), 6705-6714.
4 L. J. Core, A. L. Martins, C. G. Danko, C. T. Waters, A. Siepel and J. T. Lis, Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers, Nat. Genet., 46 (2014), 1311-1320.
5 H. Dong, L. Nilsson and C. G. Kurland, Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates, J. Mol. Biol., 260 (1996), 649-663.
6 A. Fluitt, E. Pienaar and H. Viljoen, Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis, Comput. Biol. Chem., 31 (2007), 335-346.
7 D. T. Gilliespie, Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem., 81 (1977), 2340-2361.
8 K. B. Gromadski and M. V. Rodnina, Kinetic determinants of high-fidelity tRNA discrimination on the ribosome, Mol. Cell, 13 (2004), 191-200.
9 M. Guttman, P. Russell, N. T. Ingolia, J. S. Weissman and E. S. Lander, Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins, Cell, 154 (2013), 240-251.
10 N. T. Ingolia, S. Ghaemmaghami, J. R. Newman and J. S. Weissman, Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, 324 (2009), 218-223.
11 N. T. Ingolia, L. F. Lareau and J. S. Weissman, Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes, Cell, 147 (2011), 789-802.
12 R. J. Jackson, C. U. Hellen and T. V. Pestova, The mechanism of eukaryotic translation initiation and principles of its regulation, Nat. Rev. Mol. Cell Biol., 11 (2010), 113-127.
13 G.-W. Li and X. S. Xie, Central dogma at the single-molecule level in living cells, Nature, 475 (2011), 308-315.
14 E. Limpert, W. Stahel and M. Abbt, Log-normal distributions across the sciences: Keys and clues, BioScience, 51 (2001), 341-352.
15 Y. Mao, H. Liu, Y. Liu and S. Tao, Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in saccharomyces cerevisiae, Nucleic. Acids. Res., 42 (2014), 4813-4822.
16 N. Mitarai, K. Sneppen and S. Pedersen, Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization, J. Mol. Biol., 382 (2008), 236-245.
17 J. Ninio, Ribosomal kinetics and accuracy: sequence engineering to the rescue, J. Mol. Biol., 422 (2012), 325-327.
18 J. B. Plotkin and G. Kudla, Synonymous but not the same: The causes and consequences of codon bias, Nat. Rev. Genet., 12 (2010), 32-42.
19 S. Proshkin, A. R. Rahmouni, A. Mironov and E. Nudler, Cooperation between translating ribosomes and RNA polymerase in transcription elongation, Science, 328 (2010), 504-508.
20 A. Savelsbergh, V. Katunin, D. Mohr, F. Peske, M. Rodnina and W. Wintermeyer, An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation, Mol. Cell, 11 (2003), 1517-1523.
21 P. Shah, Y. Ding, M. Niemczyk, G. Kudla and J. B. Plotkin, Rate-limiting steps in yeast protein translation, Cell, 153 (2013), 1589-1601.
22 P. Shah and M. A. Gilchrist, Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift, Proc. Natl. Acad. Sci. USA, 108 (2011), 10231-10236.
23 M. Siwiak and P. Zielenkiewicz, A comprehensive, quantitative, and genome-wide model of translation, PLoS Comput. Biol., 6 (2010), e1000865.
24 S. S. Sommer and N. A. Rin, The lognormal distribution fits the decay profile of eukaryotic mRNA, Biochem Biophys Res Commun, 90 (1979), 135-141.
25 T. Tian, K. Burrage, P. M. Burrage and M. Carletti, Stochastic delay differential equations for genetic regulatory networks, J. Comput. Appl. Math., 205 (2007), 696-707.       
26 T. Tuller, A. Carmi, K. Vestsigian, S. Navon, Y. Dorfan, J. Zaborske, T. Pan, O. Dahan, I. Furman and Y. Pilpel, An evolutionarily conserved mechanism for controlling the efficiency of protein translation, Cell, 141 (2010), 344-354.
27 T. Tuller, Y. Y. Waldman, M. Kupiec and E. Ruppin, Translation efficiency is determined by both codon bias and folding energy, Proc. Natl. Acad .Sci. USA, 107 (2010), 3645-3650.
28 G. von Heijne, Membrane-protein topology, Nat. Rev. Mol. Cell Biol., 7 (2006), 909-918.
29 X. S. Xie, P. J. Choi, G.-W. Li, N. K. Lee and G. Lia, Single-molecule approach to molecular biology in living bacterial cells, Annual review of biophysics, 37 (2008), 417-444.
30 L. M. y TerĂ¡n-Romero, M. Silber and V. Hatzimanikatis, The origins of time-delay in template biopolymerization processes, PLoS Comput. Biol., 6 (2010), e1000726, 15pp.       
31 E. Zavala and T. T. Marquez-Lago, Delays induce novel stochastic effects in negative feedback gene circuits, Biophys. J., 106 (2014), 467-478.

Go to top