All papers: Google Scholar, Download from ResearchGate
Preprint
48. Chen JZ, Fowler DM, Tokuriki N, “Environmental changes dictate selection and nonspecific epistasis in an empirical phenotype-environment-fitness landscape” doi: https://doi.org/10.1101/2021.04.14.439889
2021
47. Anderson DW, Baier F, Yang G, Tokuriki N “Secondary environmental variation creates a shifting evolutionary watershed for the methyl-parathion hydrolase enzyme” bioRxiv, 833764
46. Miton CM, Buta K, Tokuriki N “Epistasis and intramolecular networks in protein evolution” accepted, Current Opinion in Structural Biology
45. Frohlich C, Chen JZ, Gholipour S, Erdogan AN, Tokuriki N., “Evolution of beta-lactamases and enzyme promiscuity” accepted, Protein Engineering, Design and Selection
2020
44. Copp JN, Pletzer D, Brown A, Van der Heijden J, Miton CM, Edgar RJ, Rich M, Little R, Williams E, Hancock REW, Tokuriki N, Ackerley DF, “Mechanistic understanding enables the rational design of salicylanilide combination therapies for Gram-negative infections” mBio 202011 (5)
43. Yang G, Miton CM, Tokuriki N “A mechanistic view of enzyme evolution” Protein Science, 2020, 29 (8), 1724-1747
42. Miton CM, Chen JZ, Ost K, Anderson DW, Tokuriki N “Statistical analysis of mutational epistasis to reveal intramolecular interaction networks in proteins.” Methods in Enzymology, 2020, 643, 243-280
41. Chen JZ, Fowler DM , Tokuriki N “Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase” eLife, 2020, e56707
40. Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Holfellder F “Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis” Nature Communications, 2020, 11 (1), 1-14
2019
39. Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson CJ, Bornberg-Bauer E, Tokuriki N “Higher-order epistatic networks underlie the evolutionary fitness landscape of a xenobiotic-degrading enzyme” Nature Chem Biol, 2019, 15 (11), 1120-1128
38. Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N, “Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions” Methods in Enzymology, 2019, 620, 315-347
37. Bashiri G, Antoney JP, Jirgis NMH, Shah MV, Ney B, Copp J, Stutely SM, Sreebhavan S, Palmer B, Middleditch M, Tokuriki N, Greening C, Baker EN, Scott C, Jackson CJ “A revised biosynthetic pathway for the cofactor F420 in bacteria” Nature communications, 2019, 10 (1), 1558
36. Socha R, Chen J, Tokuriki N*, “The molecular mechanisms underlying hidden phenotypic variation among metallo-β-lactamases” J Mol Biol, 2019 Mar 15;431(6):1172-1185.
35. Baier F, Hong N, Yang G, Pabis A, Miton CM, Barrozo A, Carr PD, Lamerlin SCL, Jackosn CJ, Tokuriki N*, “Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes” eLife, 2019, 8, e40789
2018
34. Miton CM, Jonas S, Fischer G, Duarte F, Mohamed MF, van Loo B, Kintses B, Kamerlin SCL, Tokuriki N, Hyvönen M, Hollfelder F. “Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset” Proc Natl Acad Sci USA. 2018, 115 (31) E7293-E7302
33. Copp JN , Akiva E, Babbitt PC, Tokuriki N* “Revealing unexplored sequence-function space using sequence similarity networks” Biochemistry, 2018, 57 (31), 4651-4662
32. Clifton BF, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ “Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein” Nature Chem Biol, 2018, 14 (6), 542
31. Campbell E, Correy CJ, Mabbitt PD, Buckle AM, Tokuriki N, Jackson CJ “Laboratory and natural evolution of protein structural dynamics” Curr Opin Struct Biol, 2018 50: 49-57
2017
30. Akiva E†, Copp JN†, Tokuriki N*, Babbitt PC* “Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily” Proc Natl Sci USA, 2017, 114 (45): E9549-E9558
2016
29. Baier F, Copp JN, Tokuriki N* “Evolution of enzyme superfamilies: comprehensive exploration of sequence-function relationships” Biochemistry, 2016, 55 (46), 6375-6388
28. Kaltenbach M, Emond S, Hollfelder F & Tokuriki N* “Functional trade-offs in promiscuous enzymes cannot be explained by intrinsic mutational robustness of the native activity” PLoS Genet, 2016, 12 (10): e1006305
27. Yang G†, Hong N†, Baier F, Jackson CJ*. & Tokuriki N* “Conformational tinkering through indirect effects of mutations drives evolution of a promiscuous activity” Biochemistry, 2016, 55 (32): 4583-4593
26. Purg M, Pabis A, Baier F, Tokuriki N, Jackson C & Kamerlin SCL, “Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase” Philosophical Transactions A, 2016, 374 (2080)
25. Campbell E†, Kaltenbach M†, Carr P, Livingstone E, Jurnou L, Weik M, Tokuriki N* & Jackson CJ*, “The role of protein dynamics in the evolution of new enzyme function” Nature Chem Biol, 2016, 12(11): 944-950.
See also highlights of this article, Nature Chem Biol, 2016, 12(11):890-891 by Ma and Nussinov, and Chemical & Engineering News, 2016, 94(37):7.
24. Miton CM & Tokuriki N* “How mutational epistasis impairs predictability in protein evolution and design” Protein Sci, 2016, 25 (7): 1260-72
2015
23. Kaltenbach M, Campbell E, Hyvonen M, Jackson CJ, Hollfelder F, & Tokuriki N* “Reverse evolution leads to an efficient enzyme incompatible with its ancestor” eLife, 2015, 10.7554/eLife.06492.
See also”eLife Digest” for this article
22. Baier F, Chen J, Solomonson M, Strynadka N, & Tokuriki N* “Distinct metal isoforms underlie promiscuous activity profiles of metalloenzymes” ACS Chem Biol, 2015 10 (7): 1684-93
2014
21. Kaltenbach M &Tokuriki N* “Generation of effective libraries by neutral drift” Methods Mol Biol, 2014, 1179: 69-81
20. Tokuriki N & Jackson CJ “Enzyme dynamics and engineering: one step at a time” Chem Biol, 2014, 21(10): 1259-60
19. Emond S, Socha RS, Tokuriki N* “Strategies to overcome stability constraints in enzyme evolution and facilitate effective enzyme engineering” Industrial Biocatalysis (Pan Stanford), 2014, 115-160
18. Baier F & Tokuriki N* “Connectivity between the catalytic landscapes of various members of the metallo-β-lactamase superfamily” J Mol Biol, 2014, 426(13): 2442-56
17. Kaltenbach M & Touriki N* “Dynamics and constraints of enzyme evolution” J Exp Zool B Mol Dev Evol, 2014, 322(7): 468-87
2013
16. Wygnowski KT†, Kaltenbach M†, Tokuriki N* “GroEL/ES buffering and compensatory mutations promote protein evolution by stabilizing folding intermediates.” J Mol Biol, 2013, 425(18): 3403-14
15. Socha RD, Tokuriki N* “Modulating protein stability: Directed evolution strategies for improved protein function.” FEBS Journal, 2013, 280: 5582-5595
2012
14. Tokuriki N*, Jackson CJ, Afriat-Jurnou L, Wygnowski KT, Tang R & Tawfik DS* “Diminishing returns and tradeoffs constrain the evolutionary optimization of an enzyme” Nature Communications, 2012 3: 1257
13. Hornung G, Bar-Ziv R, Rosin D, Tokuriki N, Tawfik DS, Oren M, & Barkai N “Noise-mean relationship in mutated promoters.” Genome Res, 2012, 12: 2409-2417
2011 or earlier
12. Babtie A, Tokuriki N & Hollfelder F “What makes an enzyme promiscuous?” Curr Opin Chem Biol, 2010, 2: 200-207
11. Jackson CJ, Foo J-L, Tokuriki N, Afriat L, Carr PD, Kim H-K, Schenk G, Tawfik DS, Ollis DL “Conformational change, catalysis and evolution in the bacterial phosphotriesterase” Proc Natl Sci USA, 2009, 51: 21631-21636
10. Tokuriki N & Tawfik DS “Stability effect of mutations and protein evolvability” Curr Opin Struct Biol, 2009, 5: 596-604
9. Tokuriki N & Tawfik DS “Chaperonin overexpression promote genetic variation and enzyme evolution” Nature, 2009, 459: 668-673
8. Tokuriki N & Tawfik DS “Protein dynamism and evolvability” Science, 2009, 324: 203-207
7. Tokuriki N, Oldfield CJ, Uversky VN, Berezovsky IN & Tawfik DS “Do viral proteins possess unique biophysical features?” Trends Biochem Sci, 2009, 34 (2): 53-59
6. Tokuriki N, Stricher F, Serrano L, & Tawfik DS “How protein stability and new functions tradeoff” PLoS Computational Biol, 2008, 4 (2): e1000002
5. Tokuriki N, Stricher F, Schymkowitz J, Serrano L, & Tawfik DS “The stability effects of protein mutations appear to be universally distributed” J Mol Biol, 2007, 369: 1318-1322
4. Bershtein S, Segal M, Bekerman R, Tokuriki N, & Tawfik DS “Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein” Nature, 2006, 444 (7121): 929-932
3. Tokuriki N, Kinjo M, Negi S, Hoshi S, Goto Y, Urabe I & Yomo T “Protein folding by the effects of macromolecular crowding” Protein Sci, 2004 13, 125-133
2. Yamauchi A, Nakashima T, Tokuriki N, Hosokawa M, Nogami H, Arioka S, Urabe I & Yomo T “Evolvability of random polypeptides through functional selection within a small library” Protein Eng, 2002, 15 (7): 619-626
1. Tokuriki N, Sakamoto K, Waluyo D, Makino Y, Ogasawara K, Yutani K, Urabe I, & Yomo T “Effects of amino acid substitution on the Physicochemical Properties of Artificial Proteins with Random Sequences” J Biosci Bioeng, 2001, 92 (2): 167-172