Kinetic Proofreading

Literature Cited

1. 1.

   Wong F, Gunawardena J. 2020. Gene regulation in and out of equilibrium. Annu. Rev. Biophys. 49:199–226
   [Google Scholar]
2. 2.

   Pauling L. 1957. The probability of errors in the process of synthesis of protein molecules. Festschrift Arthur Stoll zum siebzigsten Geburtstag, 8. Januar 1957597–602 Basel, Switz.: Birkhäuser
   [Google Scholar]
3. 3.

   Gamow G. 1954. Possible relation between deoxyribonucleic acid and protein structures. Nature 173:318
   [Google Scholar]
4. 4.

   Watson JD, Crick FH. 1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–38
   [Google Scholar]
5. 5.

   McKeithan TW. 1995. Kinetic proofreading in T-cell receptor signal transduction. PNAS 92:115042–46
   [Google Scholar]
6. 6.

   Hopfield JJ. 1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. PNAS 71:4135–39
   [Google Scholar]
7. 7.

   Ninio J. 1975. Kinetic amplification of enzyme discrimination. Biochimie 57:587–95
   [Google Scholar]
8. 8.

   Schnakenberg J. 1976. Network theory of microscopic and macroscopic behavior of master equation systems. Rev. Mod. Phys. 48:4571–85
   [Google Scholar]
9. 9.

   Van den Broeck C. 2013. Stochastic thermodynamics: a brief introduction. Proc. Int. Sch. Phys. “Enrico Fermi” 184:155–93
   [Google Scholar]
10. 10.

    Mackey MC. 1992. Time's Arrow: The Origins of Thermodynamic Behavior Mineola, NY: Dover Publ.
    [Google Scholar]
11. 11.

    Grimmet G, Stirzaker D. 2001. Probability and Random Processes Oxford, UK: Oxford Univ. Press. , 3rd ed..
    [Google Scholar]
12. 12.

    Kolmogorov AN. 1956. Foundations of the Theory of Probability New York: Chelsea Publ. Co. , 2nd ed..
    [Google Scholar]
13. 13.

    Cinlar E. 2013. Introduction to Stochastic Processes Mineola, NY: Dover Publ.
    [Google Scholar]
14. 14.

    Mirzaev I, Gunawardena J. 2013. Laplacian dynamics on general graphs. Bull. Math. Biol. 75:112118–49
    [Google Scholar]
15. 15.

    Perko L. 2001. Differential Equations and Dynamical Systems New York: Springer. , 3rd ed..
    [Google Scholar]
16. 16.

    Gunawardena J. 2012. A linear framework for time-scale separation in nonlinear biochemical systems. PLOS ONE 7:5e36321
    [Google Scholar]
17. 17.

    Gunawardena J. 2012. Some lessons about models from Michaelis and Menten. Mol. Biol. Cell 23:517–19
    [Google Scholar]
18. 18.

    Esposito M, Van Den Broeck C. 2010. Three faces of the second law. I. Master equation formulation. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 82:1011143
    [Google Scholar]
19. 19.

    Kelly FP. 1979. Reversibility and Stochastic Networks Hoboken, NJ: John Wiley and Sons Ltd.
    [Google Scholar]
20. 20.

    Seifert U. 2005. Entropy production along a stochastic trajectory and an integral fluctuation theorem. Phys. Rev. Lett. 95:4040602
    [Google Scholar]
21. 21.

    Crooks GE. 1999. Entropy production fluctuation theorem and the nonequilibrium work relation. Phys. Rev. E 60:32721–26
    [Google Scholar]
22. 22.

    Banerjee K, Kolomeisky AB, Igoshin OA. 2017. Elucidating interplay of speed and accuracy in biological error correction. PNAS 114:205183–88
    [Google Scholar]
23. 23.

    Estrada J, Wong F, DePace A, Gunawardena J. 2016. Information integration and energy expenditure in gene regulation. Cell 166:1234–44
    [Google Scholar]
24. 24.

    Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. 2006. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127:5941–54
    [Google Scholar]
25. 25.

    Mallory JD, Igoshin OA, Kolomeisky AB. 2020. Do we understand the mechanisms used by biological systems to correct their errors?. J. Phys. Chem. B 124:429289–96
    [Google Scholar]
26. 26.

    Murugan A, Huse DA, Leibler S. 2012. Speed, dissipation, and error in kinetic proofreading. PNAS 109:3012034–39
    [Google Scholar]
27. 27.

    Wong F, Amir A, Gunawardena J. 2018. Energy-speed-accuracy relation in complex networks for biological discrimination. Phys. Rev. E 98:112420
    [Google Scholar]
28. 28.

    Shelansky R, Boeger H. 2020. Nucleosomal proofreading of activator–promoter interactions. PNAS 117:52456–61
    [Google Scholar]
29. 29.

    Nicholls DG, Ferguson SJ. 2013. Bioenergetics London: Academic. , 4th ed..
    [Google Scholar]
30. 30.

    Esposito M, Van Den Broeck C. 2010. Three detailed fluctuation theorems. Phys. Rev. Lett. 104:9090601
    [Google Scholar]
31. 31.

    Jakubowski H, Goldman E. 1992. Editing of errors in selection of amino acids for protein synthesis. Microbiol. Rev. 56:3412–29
    [Google Scholar]
32. 32.

    Loftfield RB, Hecht LI, Eigner EA. 1963. The measurement of amino acid specificity of transfer ribonucleic acid. Biochim. Biophys. Acta Sect. Nucleic Acids Protein Synth. 72:383–90
    [Google Scholar]
33. 33.

    Baldwin AN, Berg P. 1966. Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase. J. Biol. Chem. 241:4839–45
    [Google Scholar]
34. 34.

    Fersht AR, Dingwall C. 1979. Evidence for the double-sieve editing mechanism in protein synthesis. Steric exclusion of isoleucine by valyl-tRNA synthetases. Biochemistry 18:122627–31
    [Google Scholar]
35. 35.

    Hussain T, Kamarthapu V, Kruparani SP, Deshmukh MV, Sankaranarayanan R. 2010. Mechanistic insights into cognate substrate discrimination during proofreading in translation. PNAS 107:5122117–21
    [Google Scholar]
36. 36.

    Hopfield JJ, Yamane T, Yue V, Courts SM. 1976. Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. PNAS 73:41164–68
    [Google Scholar]
37. 37.

    Martinis SA, Boniecki MT. 2010. The balance between pre- and post-transfer editing in tRNA synthetases. FEBS Lett 584:2455–59
    [Google Scholar]
38. 38.

    Oertell K, Harcourt EM, Mohsen MG, Petruska J, Kool ET, Goodman MF. 2016. Kinetic selection versus free energy of DNA base pairing in control of polymerase fidelity. PNAS 113:16E2277–85
    [Google Scholar]
39. 39.

    Goodman MF. 1997. Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. PNAS 94:2010493–95
    [Google Scholar]
40. 40.

    Morales JC, Kool ET. 1998. Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat. Struct. Biol. 5:11950–54
    [Google Scholar]
41. 41.

    McCulloch SD, Kunkel TA. 2008. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res 18:1148–61
    [Google Scholar]
42. 42.

    Bębenek A, Ziuzia-Graczyk I. 2018. Fidelity of DNA replication—a matter of proofreading. Curr. Genet. 64:5985–96
    [Google Scholar]
43. 43.

    Liu X, Bushnell DA, Kornberg RD. 2013. RNA polymerase II transcription: structure and mechanism. Biochim. Biophys. Acta Gene Regul. Mech. 1829:12–8
    [Google Scholar]
44. 44.

    Sydow JF, Cramer P. 2009. RNA polymerase fidelity and transcriptional proofreading. Curr. Opin. Struct. Biol. 19:6732–39
    [Google Scholar]
45. 45.

    Mellenius H, Ehrenberg M. 2017. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Res 45:11582–93
    [Google Scholar]
46. 46.

    Astatke M, Ng K, Grindley NDF, Joyce CM. 1998. A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. PNAS 95:73402–7
    [Google Scholar]
47. 47.

    DeLucia AM, Grindley NDF, Joyce CM. 2003. An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a ‘steric gate’ residue for discrimination against ribonucleotides. Nucleic Acids Res 31:144129–37
    [Google Scholar]
48. 48.

    Rich A. 2003. The double helix: a tale of two puckers. Nat. Struct. Biol. 10:4247–49
    [Google Scholar]
49. 49.

    Xu L, Butler KV, Chong J, Wengel J, Kool ET, Wang D. 2014. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues. Nucleic Acids Res 42:95863–70
    [Google Scholar]
50. 50.

    Zhang N, Zhang S, Szostak JW. 2012. Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template. J. Am. Chem. Soc. 134:83691–94
    [Google Scholar]
51. 51.

    Noller HF. 2013. How does the ribosome sense a cognate tRNA?. J. Mol. Biol. 425:203776–77
    [Google Scholar]
52. 52.

    Pavlov MY, Liljas A, Ehrenberg M. 2017. A recent intermezzo at the Ribosome Club. Philos. Trans. R. Soc. B 372:171620160185
    [Google Scholar]
53. 53.

    Rodnina MV, Wintermeyer W. 2001. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem. 70:415–35
    [Google Scholar]
54. 54.

    Prabhakar A, Choi J, Wang J, Petrov A, Puglisi JD. 2017. Dynamic basis of fidelity and speed in translation: coordinated multistep mechanisms of elongation and termination. Protein Sci 26:71352–62
    [Google Scholar]
55. 55.

    Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD 2004. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11:101008–14
    [Google Scholar]
56. 56.

    Ieong KW, Uzun Ü, Selmer M, Ehrenberg M. 2016. Two proofreading steps amplify the accuracy of genetic code translation. PNAS 113:4813744–49
    [Google Scholar]
57. 57.

    Maerkl SJ, Quake SR. 2007. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315:233–37
    [Google Scholar]
58. 58.

    Geertz M, Shore D, Maerkl SJ. 2012. Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. PNAS 109:4116540–45
    [Google Scholar]
59. 59.

    Kaffman A, Rank NM, O'Shea EK 1998. Phosphorylation regulates association of the transcription factor Pho4 with its import receptor Pse1/Kap121. Genes Dev 12:172673–83
    [Google Scholar]
60. 60.

    Mao C, Brown CR, Falkovskaia E, Dong S, Hrabeta-Robinson E et al. 2010. Quantitative analysis of the transcription control mechanism. Mol. Syst. Biol. 6:1431
    [Google Scholar]
61. 61.

    Zhou CY, Johnson SL, Gamarra NI, Narlikar GJ. 2016. Mechanisms of ATP-dependent chromatin remodeling motors. Annu. Rev. Biophys. 45:153–81
    [Google Scholar]
62. 62.

    Boeger H. 2014. Nucleosomes, transcription, and probability. Mol. Biol. Cell 25:223451–55
    [Google Scholar]
63. 63.

    Kornberg RD. 1974. Chromatin structure: a repeating unit of histones and DNA. Science 184:868–71
    [Google Scholar]
64. 64.

    Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–60
    [Google Scholar]
65. 65.

    Kornberg RD, Lorch Y. 2020. Primary role of the nucleosome. Mol. Cell 79:3371–75
    [Google Scholar]
66. 66.

    Almer A, Rudolph H, Hinnen A, Hörz W. 1986. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J 5:102689–96
    [Google Scholar]
67. 67.

    Ptashne M, Gann A. 1997. Transcriptional activation by recruitment. Nature 386:569–77
    [Google Scholar]
68. 68.

    Yudkovsky N, Logie C, Hahn S, Peterson CL. 1999. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev 13:2369–74
    [Google Scholar]
69. 69.

    Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. 2003. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11:61587–98
    [Google Scholar]
70. 70.

    Boeger H, Griesenbeck J, Kornberg RD. 2008. Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133:4716–26
    [Google Scholar]
71. 71.

    Brown CR, Mao C, Falkovskaia E, Jurica MS, Boeger H. 2013. Linking stochastic fluctuations in chromatin structure and gene expression. PLOS Biol 11:e1001621
    [Google Scholar]
72. 72.

    Brown CR, Boeger H. 2014. Nucleosomal promoter variation generates gene expression noise. PNAS 111:5017893–98
    [Google Scholar]
73. 73.

    Workman JL. 2006. Nucleosome displacement in transcription. Genes Dev 20:152009–17
    [Google Scholar]
74. 74.

    Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM et al. 2013. Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342:1238724
    [Google Scholar]
75. 75.

    Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. 2002. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296:55711285–90
    [Google Scholar]
76. 76.

    Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD. 2011. Initiation complex structure and promoter proofreading. Science 333:633–37
    [Google Scholar]
77. 77.

    Carpousis AJ, Gralla JD. 1980. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry 19:143245–53
    [Google Scholar]
78. 78.

    Henderson KL, Felth LC, Molzahn CM, Shkel I, Wang S et al. 2017. Mechanism of transcription initiation and promoter escape by E. coli RNA polymerase. PNAS 114:15E3032–40
    [Google Scholar]
79. 79.

    Mayas RM, Maita H, Staley JP. 2006. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat. Struct. Mol. Biol. 13:6482–90
    [Google Scholar]
80. 80.

    Blossey R, Schiessel H. 2008. Kinetic proofreading of gene activation by chromatin remodeling. HFSP J. 2:3167–70
    [Google Scholar]
81. 81.

    Narlikar GJ. 2010. A proposal for kinetic proof reading by ISWI family chromatin remodeling motors. Curr. Opin. Chem. Biol. 14:660–65
    [Google Scholar]