Enzyme engineering: reaching the maximal catalytic efficiency peak

被引:93
作者
Goldsmith, Moshe [1 ]
Tawfik, Dan S. [1 ]
机构
[1] Weizmann Inst Sci, Dept Biomol Sci, Rehovot, Israel
关键词
STRUCTURE-BASED REDESIGN; DIRECTED EVOLUTION; SUBSTRATE-SPECIFICITY; COMPUTATIONAL DESIGN; TRIOSEPHOSPHATE ISOMERASE; CYTOCHROME-P450; ENZYMES; LABORATORY EVOLUTION; PROTEIN STABILITY; BINDING PROTEINS; SITE;
D O I
10.1016/j.sbi.2017.09.002
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The practical need for highly efficient enzymes presents new challenges in enzyme engineering, in particular, the need to improve catalytic turnover (k(cat)) or efficiency (k(cat)/K-M) by several orders of magnitude. However, optimizing catalysis demands navigation through complex and rugged fitness landscapes, with optimization trajectories often leading to strong diminishing returns and dead-ends. When no further improvements are observed in library screens or selections, it remains unclear whether the maximal catalytic efficiency of the enzyme (the catalytic 'fitness peak') has been reached; or perhaps, an alternative combination of mutations exists that could yield additional improvements. Here, we discuss fundamental aspects of the process of catalytic optimization, and offer practical solutions with respect to overcoming optimization plateaus.
引用
收藏
页码:140 / 150
页数:11
相关论文
共 139 条
[1]   The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase [J].
Afriat, Livnat ;
Roodveldt, Cintia ;
Manco, Giuseppe ;
Tawfik, Dan S. .
BIOCHEMISTRY, 2006, 45 (46) :13677-13686
[2]   Robust design and optimization of retroaldol enzymes [J].
Althoff, Eric A. ;
Wang, Ling ;
Jiang, Lin ;
Giger, Lars ;
Lassila, Jonathan K. ;
Wang, Zhizhi ;
Smith, Matthew ;
Hari, Sanjay ;
Kast, Peter ;
Herschlag, Daniel ;
Hilvert, Donald ;
Baker, David .
PROTEIN SCIENCE, 2012, 21 (05) :717-726
[3]   Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas [J].
Alvizo, Oscar ;
Nguyen, Luan J. ;
Savile, Christopher K. ;
Bresson, Jamie A. ;
Lakhapatri, Satish L. ;
Solis, Earl O. P. ;
Fox, Richard J. ;
Broering, James M. ;
Benoit, Michael R. ;
Zimmerman, Sabrina A. ;
Novick, Scott J. ;
Liang, Jack ;
Lalonde, James J. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (46) :16436-16441
[4]  
Amitai G, 2007, HFSP J, V1, P67, DOI [10.2976/1.2739115, 10.2976/1.2739115/10.2976/1]
[5]   Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance [J].
Badran, Ahmed H. ;
Guzov, Victor M. ;
Huai, Qing ;
Kemp, Melissa M. ;
Vishwanath, Prashanth ;
Kain, Wendy ;
Nance, Autumn M. ;
Evdokimov, Artem ;
Moshiri, Farhad ;
Turner, Keith H. ;
Wang, Ping ;
Malvar, Thomas ;
Liu, David R. .
NATURE, 2016, 533 (7601) :58-+
[6]  
Bar-Even A, TAWFIK DS MODERATELY
[7]   The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters [J].
Bar-Even, Arren ;
Noor, Elad ;
Savir, Yonatan ;
Liebermeister, Wolfram ;
Davidi, Dan ;
Tawfik, Dan S. ;
Milo, Ron .
BIOCHEMISTRY, 2011, 50 (21) :4402-4410
[8]   Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols [J].
Barajas, Jesus F. ;
Phelan, Ryan M. ;
Schaub, Andrew J. ;
Kliewer, Jaclyn T. ;
Kelly, Peter J. ;
Jackson, David R. ;
Luo, Ray ;
Keasling, Jay D. ;
Tsai, Shiou-Chuan .
CHEMISTRY & BIOLOGY, 2015, 22 (08) :1018-1029
[9]   FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants [J].
Bednar, David ;
Beerens, Koen ;
Sebestova, Eva ;
Bendl, Jaroslav ;
Khare, Sagar ;
Chaloupkova, Radka ;
Prokop, Zbynek ;
Brezovsky, Jan ;
Baker, David ;
Damborsky, Jiri .
PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (11)
[10]   Directed evolution of cytochrome P450 enzymes for biocatalysis: exploiting the catalytic versatility of enzymes with relaxed substrate specificity [J].
Behrendorff, James B. Y. H. ;
Huang, Weiliang ;
Gillam, Elizabeth M. J. .
BIOCHEMICAL JOURNAL, 2015, 467 :1-15