Biological Components Design for Engineering Requirements

Authors

CUI Yinglu, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
WU Bian, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

Keywords

computational enzyme design; protein engineering; artificial metalloenzymes; substrate selectivity; thermosability

Document Type

Article

Abstract

Understanding life from the perspective of synthetic biology centers on the design, construction, and characterization of novel biological systems under the engineering design principles. Most catalytic functions in living organisms are performed by enzymes, which serve as one of the most important components in synthetic biology. While the amino acid sequence makes up the primary structure of the protein, the three-dimensional structure of protein determines its biochemical properties. Therefore, researches on biological functionality based on protein structure have become frontiers of the emerging field of synthetic biology. Meanwhile, the development of computational enzyme design algorithms can provide large amounts of prototype molecules for the synthetic biological devices, especially for new chemical catalytic devices, and provide design templates and guidelines for important components in synthetic biology. This study provides a brief overview of new advances in the construction and design of biological components, especially synthetic biological devices in recent years.

First page

1150

Last Page

1157

Language

Chinese

Publisher

Bulletin of Chinese Academy of Sciences

References

Elowitz M B, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature, 2000, 403(6767):335-338.

Gardner T S, Cantor C R, Collins J J. Construction of a genetic toggle switch in Escherichia coli. Nature, 2000, 403:339-342.

Meng H L, Wang J F, Xiong Z Q, et al. Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network. PLoS One, 2013, 8:e60288.

Rackham O, Chin J W. A network of orthogonal ribosome x mRNA pairs. Nature Chemical Biology, 2005, 1, 3:159-166.

Kiss G, Çelebi N, Moretti R, et al. Computational enzyme design. Angewandte Chemie International Edition, 2013, 52:5700-5725.

Huang P S, Boyken S E, Baker D. The coming of age of de novo protein design. Nature, 2016, 537:320-327.

Jacoby M. Computer-driven research reached new milestones. Chemical & Engineering News, 2017, 95(49):20.

Giger L, Caner S, Obexer R, et al. Evolution of a designed retroaldolase leads to complete active site remodeling. Nature Chemical Biology, 2013, 9:494-498.

Siegel J B, Zanghellini A, Lovick H M, et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science, 2010, 329:309-313.

Röthlisberger D, Khersonsky O, Wollacott A M, et al. Kemp elimination catalysts by computational enzyme design. Nature, 2008, 453:190-195.

Frushicheva M P, Cao J, Warshel A. Challenges and advances in validating enzyme design proposals:The case of Kemp eliminase catalysis. Biochemistry, 2011, 50:3849-3858.

Privett H K, Kiss G, Lee T M, et al. Iterative approach to computational enzyme design. PNAS, 2012, 109:3790-3795.

Eiben C B, Siegel J B, Bale J B, et al. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 2012, 30:190-192.

Bos J, Fusetti F, Driessen A J, et al. Enantioselective artificial metalloenzymes by creation of a novel active site at the protein dimer interface. Angewandte Chemie International Edition, 2012, 51:7472-7475.

Valdez C E, Smith Q A, Nechay M R, et al. Mysteries of metals in metalloenzymes. Accounts of Chemical Research, 2014, 47:3110-3117.

Der B S, Machius M, Miley M J, et al. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. Journal of the American Chemical Society, 2011, 134:375-385.

Der B S, Edwards D R, Kuhlman B. Catalysis by a de novo zincmediated protein interface:implications for natural enzyme evolution and rational enzyme engineering. Biochemistry, 2012, 51:3933-3940.

Hyster T K, Knörr L, Ward T R, et al. Biotinylated Rh (Ⅲ) complexes in engineered streptavidin for accelerated asymmetric C-H activation. Science, 2012, 338:500-503.

Fujieda N, Hasegawa A, Ishihama K I, et al. Artificial Dicopper Oxidase:Rational Reprogramming of Bacterial Metallo-β-lactamase into a Catechol Oxidase. Chemistry-An Asian Journal, 2012, 7:1203-1207.

Yang W, Lai L H. Computational design of ligand-binding proteins. Current Opinion in Structural Biology, 2017, 45:67-73.

Siegel J B, Smith A L, Poust S, et al. Computational protein design enables a novel one-carbon assimilation pathway. PNAS, 2015, 112:3704-3709.

Wijma H J, Floor R J, Janssen D B. Structure-and sequenceanalysis inspired engineering of proteins for enhanced thermostability. Current Opinion in Structural Biology, 2013, 23:588-594.

Buß O, Rudat J, Ochsenreither K. FoldX as Protein Engineering Tool:Better Than Random Based Approaches? Computational and Structural Biotechnology Journal, 2018, 16:25-33.

Diaz J E, Lin C S, Kunishiro K, et al. Computational design and selections for an engineered, thermostable terpene synthase. Protein Science, 2011, 20:1597-1606.

Wijma H J, Floor R J, Jekel P A, et al. Computationally designed libraries for rapid enzyme stabilization. Protein Engineering, Design and Selection, 2014, 27:49-58.

Floor R J, Wijma H J, Colpa D I, et al. Computational library design for increasing haloalkane dehalogenase stability. ChemBioChem, 2014, 15:1660-1672.

Arabnejad H, Dal L M, Jekel P A, et al. A robust cosolvent-compatible halohydrin dehalogenase by computational library design. Protein Engineering, Design and Selection, 2016, 30:175-189.

Goldenzweig A, Goldsmith M, Hill S E, et al. Automated structure-and sequence-based design of proteins for high bacterial expression and stability. Molecular Cell, 2016, 63:337-346.

Wu B, Wijma H J, Song L, et al. Versatile peptide C-terminal functionalization via a computationally engineered peptide amidase. ACS Catalysis, 2016, 6:5405-5414.

Van D D, Koenigstein S, Reiss T. The development of synthetic biology:a patent analysis. Systems and Synthetic Biology, 2013, 7:209-220.

Global and China Industrial Enzyme Industry Report, 2014-2017.[2015-07-02]. https://www.reportlinker.com/p01037001/Globaland-China-Industrial-Enzyme-Industry-Report.html.

Constable D J C, Dunn P J, Hayler J D, et al. Key green chemistry research areas-a perspective from pharmaceutical manufacturers. Green Chemistry, 2007, 9(5):411-420.

Li R F, Wijma H J, Song L, et al. Computational redesign of enzymes for regio-and enantioselective hydroamination. Nature Chemical Biology, 2018, 14:664-670.

Recommended Citation

Yinglu, CUI and Bian, WU (2018) "Biological Components Design for Engineering Requirements," Bulletin of Chinese Academy of Sciences (Chinese Version): Vol. 33 : Iss. 11 , Article 2.
DOI: https://doi.org/10.16418/j.issn.1000-3045.2018.11.002
Available at: https://bulletinofcas.researchcommons.org/journal/vol33/iss11/2