Associate Professor,
Biochemistry and Molecular Biology
Faculty of Medicine
Michael Smith Laboratories
Osaka University, Osaka, Japan, 2004, PhD
Weizmann Institute of Science, Rehovot, Israel, 2004, Postdoctoral Fellow
University of Cambridge, UK,, 2009, Postdoctoral Fellow
phone: 6048228156
phone: 6048274365
fax: 6048222114
Michael Smith Laboratories Office 327
2185 East Mall
Vancouver, BC V6T 1Z4
Canada

Molecular Mechanisms of Protein Evolution

How has the repertoire of remarkably diverse protein functions evolved in nature? We are interested in understanding the evolutionary dynamics of biological molecules and systems and, in particular, how evolution has generated the diverse array of genes (proteins and enzymes) that cohesively work together to function as complex cells and organisms. Current knowledge of the molecular mechanisms of protein evolution is limited: What drives the generation of a new protein function? How many mutations are required to change one enzyme to another? Is the order of mutations important for the course of evolution? What makes a sequence (gene) particularly “evolvable” for the generation of new functions? We aim to understand the molecular basis of evolution, i.e., how a mutation causes structural and biophysical changes to a protein, and eventually leads to functional changes. Understanding the molecular mechanisms of evolution addresses, not only 3 billion years of evolutionary history on earth, but also on-going evolution of extant proteins (e.g., drug resistance, and the degradation of xenobiotic compounds).

Our scientific approach is interdisciplinary, we employ a wide variety of research techniques, including laboratory evolution and protein engineering techniques, molecular and structural biology, protein biochemistry and biophysics, and bioinformatics. We extensively employ an “experimental evolution” approach, a technique that is used to mimic evolutionary processes in the laboratory, and to reconstruct the evolutionary trajectories of biological molecules. In doing so, we study the molecular mechanisms of protein evolution that underlie the diverse range of functions that are observed in modern enzymes. Furthermore, we utilize and apply the knowledge gained from evolutionary biochemistry to generate and engineer novel proteins, metabolic pathways and organisms.

Please visit our homepage (http://tokurikilab.msl.ubc.ca) to see more about our research program.

We are looking for graduate students to start in the fall of 2018. Please email me if you are interested in applying.

Selected Publications

Clifton BF, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ “Evolution of an enzyme from a solute-binding protein”, submitted

Akiva E†, Copp JN†, Tokuriki N*, Babbitt PC* “Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily” submitted.

Baier F, Copp JN, Tokuriki N* “Evolution of enzyme superfamilies: comprehensive exploration of sequence-function relationships” Biochemistry, 2016, 55 (46), 6375-6388

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

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

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)

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.

Miton CM & Tokuriki N* “How mutational epistasis impairs predictability in protein evolution and design” Protein Sci, 2016, 25 (7): 1260-72 (This paper is selected as 2017 Best Paper in Protein Science!)

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.

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

Kaltenbach M &Tokuriki N* “Generation of effective libraries by neutral drift” Methods Mol Biol,  2014, 1179: 69-81

Tokuriki N & Jackson CJ “Enzyme dynamics and engineering: one step at a time” Chem Biol,  2014, 21(10): 1259-60

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

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

Kaltenbach M & Touriki N* “Dynamics and constraints of enzyme evolution” J Exp Zool B Mol Dev Evol, 2014, 322(7): 468-87

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

Socha RD, Tokuriki N* “Modulating protein stability: Directed evolution strategies for improved protein function.” FEBS Journal, 2013, 280: 5582-5595

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 Comm, 2012 3: 1257

Tokuriki N & Tawfik DS “Stability effect of mutations and protein evolvability” Curr Opin Struct Biol, 2009, 5: 596-604

Tokuriki N & Tawfik DS “Chaperonin overexpression promote genetic variation and enzyme evolution” Nature, 2009, 459: 668-673

Tokuriki N & Tawfik DS “Protein dynamism and evolvability” Science, 2009, 324: 203-207

Please see the full list of our publications, http://tokurikilab.msl.ubc.ca/publications/