Trends and Tips in Protein Engineering, A Review
DOI:
https://doi.org/10.11113/jt.v59.1574Keywords:
Protein mutagenesis, protein modification, site-directed mutagenesis, random mutagenesisAbstract
Protein engineering is widespread approach in the branch of protein science. It is a useful tool for elucidating function of a single or a stretch of amino acids. Some protein engineers use it to improve the properties of a protein. Despite protein engineering is a powerful tool; it remains an unexplored field in Southeast Asia, specifically in the developing countries. Therefore, this chapter aims to provide a basic overview on the tips, methods, applications, common problems and solutions, as well as the progress of protein engineering in Southeast Asia.References
Zhang, J., Chiodini, R., Badr, A., and Zhang, G. 2011. The Impact of
Next-generation Sequencing on Genomics. Journal of Genetics and
Genomics. 38(3): 95–109.
Benetti, F., and Legname, G. 2009. De Novo Mammalian Prion
Synthesis. Prion. 3(4): 213–219.
Declerck, N., Machius, M., Wiegand, G., Huber, R., and Gaillardin, C.
Probing Structural Determinants Specifying High
Thermostability in Bacillus Licheniformis α-amylase. Journal of
Molecular Biology. 301(4): 1041–1057.
Lin, K. F., Lee, T. R., Tsai, P. H., Hsu, M. P., Chen, C. S., and Lyu, P.
C. 2007. Structure-based Protein Engineering for α-amylase Inhibitory
Activity of Plant Defensin. Proteins: Structure, Function, and
Bioinformatics. 68(2): 530–554.
Glieder, A., Farinas, E. T. and Arnold, F. H. 2002. Laboratory
Evolution of a Soluble Self- Sufficient, Highly Active Alkane
Hydroxylase. Nature Biotechnology. 20: 1135–1139.
Wang, Q., Buckle, A. M., Foster, N. M., Johnson, C. M. and Fersht, A.
R. 1999. Design of Highly Stable Functional GroEL Minichaperones.
Protein Science. 8: 2186–2193.
Yan, Z. X., Hui, R., Lin, M., Qing, H. G., Jun, T. X. and He, C. Q.
Enhancement of the Thermostability of β- 1,3-1,4-glucanase by
Directed Evolution. Journal of Zhejiang Universiti SCIENCE A. 7(11):
–1955.
Parsiegla, G., Schmidt, A. K. and Schulz, G. E. 1998. Substrate
Binding to a Cyclodextrin Glycosyltransferase and Mutations
Increasing the γ-cyclodextrin Production. European Journal of
Biochemistry. 255: 710–717.
Brange, J., Ribel, U., Hansen, J. F., Dodson, G., Hansen, M. T.,
Havelund, S., Melberg, S. G., Norris, F., Norris, K., Snel, L., Sorensen,
A. R. and Voigt, H. O. 1988. Monomeric insulins obtained by protein
engineering and their medical implications. Nature, 333:679–682.
Chow, J. Y., Xue, B., Lee, K. H., Tung, A., Wu, L., Robinson, R. C.,
and Yew, W. S. 2010. Directed Evolution of a Thermostable QuorumQuenching Lactonase from the Amidohydrolase Superfamily. Journal
of Biological Chemistry. 285(52): 40911–40920.
Zhou, M., Xu, H., Wei, X., Ye, Z., Wei, Y., Gong, W., Wang, Y. and
Zhu, Z. 2006. Identification of a Glyphosate-Resistant Mutant of Rice
-Enolpyruvylshikimate-3-Phosphate Synthase Using a Directed
Evolution Strategy. Plant Physiology. 140: 184–195.
Castle, L. A., Siehl, D. L., Gorton, R., Patten, P. A., Chen, Y. H.,
Bertain, S., Choe, H. J., Duck, N., Wong, J., Liu, D., and Lassner, M.
W. 2004. Discovery and Directed Evolution of a Glyphosate Tolerance
Gene. Science. 304: 1151–1154.
Handa, P. and Varshney, U. 1998. Rapid and Reliable Site Directed
Mutagenesis Using Kunkel's Approach. Indian Journal of Biochemistry
and Biophysics. 25(2): 63–66.
Kammann, M., Laufs, J., Schell, J. and Gronenbom, B. 1989. Rapid
Insertional Mutagenesis of DNA by Polymerase Chain Reaction
(PCR). Nucleic Acids Research. 17: 5404.
Ke, S. H. and Madison, E. L. 1997. Rapid and Efficient Site-directed
Mutagenesis by Single-tube ‘Megaprimer’ PCR Method. Nucleic Acids
Research. 25(16): 3371–3372.
McPherson, M. and Moller, S. 2006. PCR. 2
nd ed. United Kingdom:
Taylor & Francis Group.
Howorka, S. and Bayley, H. 2002. High-Throughput Scanning
Mutagenesis by recombinant Polymerase Chain Reaction. In Braman,
J. (Ed.) Methods in Molecular Biology: In Vitro Mutagenesis
Protocols). New Jersey: Humana Press Inc. 139–147
Khemakhem, B., Ali, M. B., Aghajari, N., Juy, M., Haser, R., and
Bejar, S. 2009. The Importance of an Extra Loop in the B-Domain of
an Α-Amylase from B. stearothermophilus US100. Biochemical and
Biophysical Research Communications. 385(1): 78–83.
Witkowski, W. A., and Hardy, J. A. 2009. L2′ Loop is Critical for
Caspase-7 Active Site Formation. Protein Science. 18(7): 1459–1468.
Rezaie, A. R., and Yang, L. 2005. Deletion of the 60-loop Provides
New Insights into the Substrate and Inhibitor Specificity of Thrombin.
Thrombosis and Haemostasis. 93: 1047–1054.
Santini, S., and Derreumaux, P. 2004. Helix H1 of the Prion Protein is
Rather Stable Against Environmental Perturbations: Molecular
Dynamics of Mutation and Deletion Variants of PrP(90–231). Cellular
and Molecular Life Sciences. 61(7): 951–960.
Babu, K. S., Antony, A., Muthukumaran, T., and Meenakshisundaram,
S. 2008. Construction of Intein-Mediated Hgmcsf Expression Vector
and its Purification in Pichia Pastoris. Protein Expression and
Purification. 57(2): 201–205.
Gruber, K., Klintschar, G., Hayn, M., Schlacher, A., Steiner, W. and
Kratky, C. 1998. Thermophilic xylanase from Thermomyces
lanuginosus: High Resolution X-ray Structure and Modelling Study.
Biochemistry. 37: 13475–13485.
Brakmann, S. and Schwienhorst, A. 2004. Evolutionary Methods in
Biotechnology. Wiley-VCH, Weinheim.
Volkov, A. A. and Arnold, F. H. 2000. Methods for in vitro DNA
Recombination and Random Chimeragenesis. Methods in Enzymology.
: 447–456
Eswar, N., Marti-Renom, M. A., Webb, B., Madhusudhan, M. S.,
Eramian, D., Shen, M., Pieper, U. and Sali, A. 2006. Comparative
Protein Structure Modeling with MODELLER. Current Protocols in
Bioinformatics. (15:5.6.1–5.6.30.). California: John Wiley & Sons, Inc.
Zhang, Y. 2008. I-TASSER Server for Protein 3D Structure Prediction.
BMC Bioinformatics. 38(3): 95–109.
Brown, C., George, G., Jasaroska, S., Kidolezi, Y. and Ochoa, J.
http://www.kellogg.northwestern.edu/Departments/International/Intern
ationalFocus/Article/2011_Southeast%20Asian%20Biotech.aspx.
Goh, K. M., Mahadi, N. M., Hassan, O., Rahman, R. N. Z. R. A., and
Illias, R. M. 2009. A Predominant β-CGTase G1 Engineered to
Elucidate the Relationship between Protein Structure and Product
specificity. Journal of Molecular Catalysis B: Enzymatic. 57(1-4):
–277.
Low, K. O., Mahadi, N. M., Rahim, R. A., Rabu, A., Bakar, F. D. A.,
Murad, A. M. A. and Illias, R. M. 2010. Enhanced Secretory
Production of Hemolysin-mediated Cyclodextrin Glucanotransferase in
Escherichia Coli by Random Mutagenesis of the ABC Transporter
System. Journal of Biotechnology. 150: 453–459.
Abdullah, M. A. F., and Dean, D. H. 2004. Enhancement of Cry19Aa
Mosquitocidal Activity Against Aedes Aegypti by Mutations in the Putative Loop Regions of Domain II. Applied Environmental
Microbiology. 70(6): 3769–3771.
Nyon, M. P., Rice, D. W., Berrisford, J. M., Hounslow, A. M., Moir,
A. J. G., Huang, H., Nathan, S., Mahadi, N. M., Bakar, F. D., and
Craven, C. J. 2009. Catalysis by Glomerella cingulata Cutinase
Requires Conformational Cycling Between the Active and Inactive
States of its Catalytic Triad. Journal of Molecular Biology. 385(1):
–235.
Zhang, H., Lountos, G., Ching, C., and Jiang, R. 2010. Engineering of
Glycerol Dehydrogenase for Improved Activity Towards 1, 3-
butanediol. Applied Microbiology and Biotechnology. 88(1): 117–124.
Wongsantichon, J., Robinson, Robert,C., and Ketterman, and Albert,J.
Structural Contributions of Delta Class Glutathione Transferase
Active-site Residues to Catalysis. Biochemical Journal. 428: 25–32.
Chua, C. S., Biermann, D., Goo, K. S., and Sim, T. S. 2008.
Elucidation of Active Site Residues of Arabidopsis Thaliana Flavonol
Synthase Provides a Molecular Platform for Engineering Flavonols.
Phytochemistry. 69(1): 66–75.
Tan, C. L., Yeo, C. C., Khoo, H. E., and Poh, C. L. 2005. Replacement
of Tyrosine 181 by Phenylalanine in Gentisate 1,2-Dioxygenase I from
Pseudomonas alcaligenes NCIMB 9867 Enhances Catalytic Activities.
Journal of Bacteriology. 187(21): 7543–7545.
Spadiut, O., Pisanelli, I., Maischberger, T., Peterbauer, C., Gorton, L.,
Chaiyen, P., and Haltrich, D. 2009. Engineering of pyranose 2-oxidase:
Improvement for Biofuel Cell and Food Applications through SemiRational Protein Design. Journal of Biotechnology. 139(3): 250–257.
Katane, M., Saitoh, Y., Maeda, K., Hanai, T., Sekine, M., Furuchi, T.,
and Homma, H. 2011. Role of the Active Site Residues Arginine-216
And Arginine-237 in the Substrate Specificity of Mammalian DAspartate Oxidase. Amino Acids. 40(2): 467–476.
Kataoka, K., Hirota, S., Maeda, Y., Kogi, H., Shinohara, N., Sekimoto,
M., and Sakurai, T. 2011. Enhancement of Laccase Activity through
the Construction and Breakdown of a Hydrogen Bond at The Type I
Copper Center in Escherichia coli CueO and the Deletion Mutant Δα5-
CueO. Biochemistry. 50(4): 558–565.
Menach, E., Yasukawa, K., and Inouye, K. 2010. Effects of SiteDirected Mutagenesis of the Loop Residue of the N-Terminal Domain
Gly117 of Thermolysin on its Catalytic Activity. Bioscience,
Biotechnology, and Biochemistry. 74: 2457–2462.
Yasukawa, K., Mizuno, M., Konishi, A., and Inouye, K. 2010. Increase
in Thermal Stability of Moloney Murine Leukaemia Virus Reverse
Transcriptase by Site-directed Mutagenesis. Journal of Biotechnology.
(3): 299–306.
Suzuki, Y., Asada, K., Miyazaki, J., Tomita, T., Kuzuyama, T., and
Nishiyama, M. 2010. Enhancement of the Latent 3-isopropylmalate
Dehydrogenase Activity of Promiscuous Homoisocitrate
Dehydrogenase by Directed Evolution. Biochemical Journal. 431:
–410.
Kawata, T., and Ogino, H. 2010. Amino Acid Residues Involved in
Organic Solvent-stability of the LST-03 Lipase. Biochemical and
Biophysical Research Communications. 400(3): 384–388.
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