Abstract
Proteins are one of the most important and resourceful biomolecules that find applications in health, industry, medicine, research, and biotechnology. Given its tremendous relevance, protein engineering has emerged as significant biotechnological intervention in this area. Strategic utilization of protein engineering methods and approaches has enabled better enzymatic properties, better stability, increased catalytic activity and most importantly, interesting and wide range applicability of proteins. In fact, the commercialization of engineered proteins have manifested in economically beneficial and viable solutions for industry and healthcare sector. Protein engineering has also evolved to become a powerful tool contributing significantly to the developments in both synthetic biology and metabolic engineering. The present review revisits the current trends in protein engineering approaches such as rational design, directed evolution, de novo design, computational approaches etc. and encompasses the recent progresses made in this field over the last few years. The review also throws light on advanced or futuristic protein engineering aspects, which are being explored for design and development of novel proteins with improved properties or advanced applications.
Keywords: Protein engineering, rational design, directed evolution, de novo design, computational methods, semi-rational approach.
Graphical Abstract
[1]
Singh, R.K.; Lee, J.K.; Selvaraj, C.; Singh, R.; Li, J.; Kim, S.Y.; Kalia, V.C. Protein engineering approaches in the post-genomic era. Curr. Protein Pept. Sci., 2018, 19, 5-15.
[2]
Shukla, P. Futuristic protein engineering: Developments and avenues. Curr. Protein Pept. Sci., 2018, 19, 3-4.
[3]
Grand View Research. Market Research Report on Protein Engineering
Market Analysis By Technology (Rational Protein Design,
Directed Evolution, Hybrid Approach), By Protein Type (Insulin,
Monoclonal Antibodies), By Product, By End-use, And Segment
Forecasts, 2018-2025. Available at:; https://www.grandviewre-search.com/press-release/global-protein-engineering-market(Accessed
September 10, 2018)..
[4]
Baweja, M.; Nain, L.; Kawarabayasi, Y.; Shukla, P. Current technological improvements in enzymes toward their biotechnological applications. Front. Microbiol., 2016, 7, 965.
[5]
Kumar, V.; Baweja, M.; Liu, H.; Shukla, P. Microbial enzyme engineering: Applications and perspectives. In: Recent Advances in Applied Microbiology; Shukla, P., Ed.; Springer: Singapore, 2017; pp. 259-273.
[6]
Chiu, M.L.; Gilliland, G.L. Engineering antibody therapeutics. Curr. Opin. Struct. Biol., 2016, 38, 163-173.
[7]
Jemli, S.; Ayadi-Zouari, D.; Hlima, H.B.; Bejar, S. Biocatalysts: Application and engineering for industrial purposes. Crit. Rev. Biotechnol., 2016, 36, 246-258.
[8]
Manas, N.H.A.; Jonet, M.A.; Murad, A.M.A.; Mahadi, N.M.; Illias, R.M. Modulation of transglycosylation and improved malto-oligosaccharide synthesis by protein engineering of maltogenic amylase from Bacillus lehensis G1. Process Biochem., 2015, 50, 1572-1580.
[9]
Basu, M.; Kumar, V.; Shukla, P. Recombinant approaches for microbial xylanases: Recent advances and perspectives. Curr. Protein Pept. Sci., 2018, 19, 87-99.
[10]
Zorn, K.; Oroz-Guinea, I.; Brundiek, H.; Bornscheuer, U.T. Engineering and application of enzymes for lipid modification, an update. Prog. Lipid Res., 2016, 63, 153-164.
[11]
Nisha, M.; Satyanarayana, T. Characteristics, protein engineering and applications of microbial thermostable pullulanases and pullulan hydrolases. Appl. Microbiol. Biotechnol., 2016, 100, 5661-5679.
[12]
Martinez, A.T.; Ruiz-Dueñas, F.J.; Camarero, S.; Serrano, A.; Linde, D.; Lund, H.; Vind, J.; Tovborg, M.; Herold-Majumdar, O.M.; Hofrichter, M.; Liers, C. Oxidoreductases on their way to industrial biotransformations. Biotechnol. Adv., 2017, 35, 815-831.
[13]
Kumar, V.; Dangi, A.K.; Shukla, P. Engineering thermostable microbial xylanases toward its industrial applications. Mol. Biotechnol., 2018, 60, 226-235.
[14]
Foo, J.L.; Ching, C.B.; Chang, M.W.; Leong, S.S.J. The imminent role of protein engineering in synthetic biology. Biotechnol. Adv., 2012, 30, 541-549.
[15]
Glasscock, C.J.; Lucks, J.B.; De Lisa, M.P. Engineered protein machines: Emergent tools for synthetic biology. Cell Chem. Biol., 2016, 23, 45-56.
[16]
Erb, T.J.; Jones, P.R.; Bar-Even, A. Synthetic metabolism: Metabolic engineering meets enzyme design. Curr. Opin. Chem. Biol., 2017, 37, 56-62.
[17]
Irfan, M.; Gonzalez, C.F.; Raza, S.; Rafiq, M.; Hasan, F.; Khan, S.; Shah, A.A. Improvement in thermostability of xylanase from Geobacillus thermodenitrificans C5 by site directed mutagenesis. Enzyme Microb. Technol., 2018, 111, 38-47.
[18]
Wang, X.; Du, J.; Zhang, Z.Y.; Fu, Y.J.; Wang, W.M.; Liang, A.H. A rational design to enhance the resistance of Escherichia coli phytase appA to trypsin. Appl. Microbiol. Biotechnol., 2018, 102(22), 9647-9656.
[19]
Courtois, F.; Agrawal, N.J.; Lauer, T.M.; Trout, B.L. Rational design of therapeutic mAbs against aggregation through protein engineering and incorporation of glycosylation motifs applied to bevacizumab. MAbs, 2016, 8, 99-112.
[20]
Kim, D.S.; Choi, J.R.; Ko, J.; Kim, K. Re-engineering of bacterial luciferase; For new aspects of bioluminescence. Curr. Protein Pept. Sci., 2018, 19, 16-21.
[21]
El Khatib, M.; Martins, A.; Bourgeois, D.; Colletier, J.P.; Adam, V. Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm. Sci. Rep., 2016, 6, 18459.
[22]
Gaw, S.L.; Sakala, G.; Nir, S.; Saha, A.; Xu, Z.J.; Lee, P.S.; Reches, M. Rational design of amphiphilic peptides and its effect on antifouling performance. Biomacromolecules, 2018, 19, 3620-3627.
[23]
Viña‐Gonzalez, J.; Elbl, K.; Ponte, X.; Valero, F.; Alcalde, M. Functional expression of aryl‐alcohol oxidase in Saccharomyces cerevisiae and Pichia pastoris by directed evolution. Biotechnol. Bioeng., 2018, 115, 1666-1674.
[24]
Tang, Z.; Jin, W.; Sun, R.; Liao, Y.; Zhen, T.; Chen, H.; Wu, Q.; Gou, L.; Li, C. Improved thermostability and enzyme activity of a recombinant phyA mutant phytase from Aspergillus niger N25 by directed evolution and site-directed mutagenesis. Enzyme Microb. Technol., 2018, 108, 74-81.
[25]
Li, G.; Maria-Solano, M.A.; Romero-Rivera, A.; Osuna, S.; Reetz, M.T. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem. Commun., 2017, 53, 9454-9457.
[26]
Liu, Z.Q.; Wu, L.; Zhang, X.J.; Xue, Y.P.; Zheng, Y.G. Directed evolution of carbonyl reductase from Rhodosporidium toruloides and its application in stereoselective synthesis of tert-butyl (3 R, 5 S)-6-chloro-3, 5-dihydroxyhexanoate. J. Agric. Food Chem., 2017, 65, 3721-3729.
[27]
Larue, K.; Melgar, M.; Martin, V.J. Directed evolution of a fungal β-glucosidase in Saccharomyces cerevisiae. Biotechnol. Biofuels, 2016, 9, 52.
[28]
Axarli, I.; Muleta, A.W.; Chronopoulou, E.G.; Papageorgiou, A.C.; Labrou, N.E. Directed evolution of glutathione transferases towards a selective glutathione-binding site and improved oxidative stability. Biochim. Biophys. Acta-General Subjects, 2017, 1861, 3416-3428.
[29]
Tian, K.; Tai, K.; Chua, B.J.W.; Li, Z. Directed evolution of Thermomyces lanuginosus lipase to enhance methanol tolerance for efficient production of biodiesel from waste grease. Bioresour. Technol., 2017, 245, 1491-1497.
[30]
Sirois, A.R.; Deny, D.A.; Baierl, S.R.; George, K.S.; Moore, S.J. Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding. PLoS One, 2018, 13, e0197029.
[31]
Valetti, F.; Gilardi, G. Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules, 2013, 3, 778-811.
[32]
Shen, J.W.; Qi, J.M.; Zhang, X.J.; Liu, Z.Q.; Zheng, Y.G. Significantly increased catalytic activity of Candida antarctica lipase B for the resolution of cis-(±)-dimethyl 1-acetylpiperidine-2, 3-dicarboxylate. Catal. Sci. Technol., 2018, 8, 4718-4725.
[33]
Chen, K.C.; Zheng, M.M.; Pan, J.; Li, C.X.; Xu, J.H. Protein engineering and homologous expression of Serratia marcescens lipase for efficient synthesis of a pharmaceutically relevant chiral epoxyester. Appl. Biochem. Biotechnol., 2017, 183, 543-554.
[34]
Engström, K.; Nyhlén, J.; Sandström, A.G.; Bäckvall, J.E. Directed evolution of an enantioselective lipase with broad substrate scope for hydrolysis of α-substituted esters. J. Am. Chem. Soc., 2010, 132, 7038-7042.
[35]
Zhou, C.; Ye, J.; Xue, Y.; Ma, Y. Directed evolution and structural analysis of alkaline pectate lyase from alkaliphilic Bacillus sp. N16-5 for improvement of thermostability for efficient ramie degumming. Appl. Environ. Microbiol., 2015, 81, 5714-5723.
[36]
Zhao, H.Y.; Feng, H. Engineering Bacillus pumilus alkaline serine protease to increase its low-temperature proteolytic activity by directed evolution. BMC Biotechnol., 2018, 18, 34.
[37]
Chen, H.; Li, M.; Liu, C.; Zhang, H.; Xian, M.; Liu, H. Enhancement of the catalytic activity of Isopentenyldiphosphateisomerase (IDI) from Saccharomyces cerevisiae through random and site-directed mutagenesis. Microb. Cell Fact., 2018, 17, 65.
[38]
Gregor, C.; Sidenstein, S.C.; Andresen, M.; Sahl, S.J.; Danzl, J.G.; Hell, S.W. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Sci. Rep., 2018, 8, 2724.
[39]
Jung, E.; Park, B.G.; Yoo, H.W.; Kim, J.; Choi, K.Y.; Kim, B.G. Semi-rational engineering of CYP153A35 to enhance ω-hydroxylation activity toward palmitic acid. Appl. Microbiol. Biotechnol., 2018, 102, 269-277.
[40]
Arkadash, V.; Yosef, G.; Shirian, J.; Cohen, I.; Horev, Y.; Grossman, M.; Sagi, I.; Radisky, E.S.; Shifman, J.M.; Papo, N. Development of high-affinity and high-specificity inhibitors of metalloproteinase 14 through computational design and directed evolution. J. Biol. Chem., 2017, 292, 3481-3495.
[41]
Gulati, K.; Poluri, K.M. An overview of computational and experimental methods for designing novel proteins. Recent Pat. Biotechnol., 2016, 10, 235-263.
[42]
Burton, A.J.; Thomson, A.R.; Dawson, W.M.; Brady, R.L.; Woolfson, D.N. Installing hydrolytic activity into a completely de novo protein framework. Nat. Chem., 2016, 8, 837-844.
[43]
Thomas, F.; Dawson, W.M.; Lang, E.J.; Burton, A.J.; Bartlett, G.J.; Rhys, G.G.; Mulholland, A.J.; Woolfson, D.N. De novo-designed α-helical barrels as receptors for small molecules. ACS Synth. Biol., 2018, 7, 1808-1816.
[44]
Shen, C.; Iskenderian, A.; Lundberg, D.; He, T.; Palmieri, K.; Crooker, R.; Deng, Q.; Traylor, M.; Gu, S.; Rong, H.; Ehmann, D. Protein engineering on human recombinant follistatin: Enhancing pharmacokinetic characteristics for therapeutic application. J. Pharmacol. Exp. Ther., 2018, 366, 291-302.
[45]
Pandelieva, A.T.; Baran, M.J.; Calderini, G.F.; McCann, J.L.; Tremblay, V.; Sarvan, S.; Davey, J.A.; Couture, J.F.; Chica, R.A. Brighter red fluorescent proteins by rational design of triple-decker motif. ACS Chem. Biol., 2016, 11, 508-517.
[46]
Gu, H.; Liao, Y.; Zhang, J.; Wang, Y.; Liu, Z.; Cheng, P.; Wang, X.; Zou, Q.; Gu, J. Rational design and evaluation of an artificial Escherichia coli K1 protein vaccine candidate based on the structure of OmpA. Front. Cell. Infect. Microbiol., 2018, 8, 172.
[47]
Wu, X.; Tian, Z.; Jiang, X.; Zhang, Q.; Wang, L. Enhancement in catalytic activity of Aspergillus niger XynB by selective site-directed mutagenesis of active site amino acids. Appl. Microbiol. Biotechnol., 2018, 102, 249-260.
[48]
Chen, X.; Li, W.; Ji, P.; Zhao, Y.; Hua, C.; Han, C. Engineering the conserved and noncatalytic residues of a thermostable β-1, 4-endoglucanase to improve specific activity and thermostability. Sci. Rep., 2018, 8, 2954.
[49]
Molina‐Espeja, P.; Cañellas, M.; Plou, F.J.; Hofrichter, M.; Lucas, F.; Guallar, V.; Alcalde, M. Synthesis of 1‐naphthol by a natural peroxygenase engineered by directed evolution. ChemBioChem, 2016, 17, 341-349.
[50]
Li, Y.X.; Yi, P.; Yan, Q.J.; Qin, Z.; Liu, X.Q.; Jiang, Z.Q. Directed evolution of a β-mannanase from Rhizomucor miehei to improve catalytic activity in acidic and thermophilic conditions. Biotechnol. Biofuels, 2017, 10, 143.
[51]
Kan, S.J.; Lewis, R.D.; Chen, K.; Arnold, F.H. Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life. Science, 2016, 354, 1048-1051.
[52]
Chen, Z.; Geng, F.; Zeng, A.P. Protein design and engineering of a de novo pathway for microbial production of 1, 3‐propanediol from glucose. Biotechnol. J., 2015, 10, 284-289.
[53]
Donnelly, A.E.; Murphy, G.S.; Digianantonio, K.M.; Hecht, M.H. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat. Chem. Biol., 2018, 14, 253-255.
[54]
Zheng, T.; Martínez, F.P.; Storm, I.M.; Rombouts, W.; Sprakel, J.; de Vries, R.; Schirhagl, R. De novo designed proteins for colloidal stabilization and improvement of cellular uptake. Biophys. J., 2018, 114, 362.
[55]
Xia, Y.; Cui, W.; Cheng, Z.; Peplowski, L.; Liu, Z.; Kobayashi, M.; Zhou, Z. Improving the thermostability and catalytic efficiency of the subunit‐fused nitrile hydratase by semi‐rational engineering. ChemCatChem, 2018, 10, 1370-1375.
[56]
Fladischer, P.; Weingartner, A.; Blamauer, J.; Darnhofer, B.; Birner‐Gruenberger, R.; Kardashliev, T.; Ruff, A.J.; Schwaneberg, U.; Wiltschi, B. A semi‐rationally engineered bacterial pyrrolysyl‐tRNAsynthetase genetically encodes phenyl azide chemistry. Biotechnol. J., 2018. 10.1002/biot.201800125
[Epub ahead of print].
[57]
Zhang, W.H.; Otting, G.; Jackson, C.J. Protein engineering with unnatural amino acids. Curr. Opin. Struct. Biol., 2013, 23, 581-587.
[58]
Ravikumar, Y.; Nadarajan, S.P.; Yoo, T.H.; Lee, C.S.; Yun, H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol., 2015, 33, 462-470.
[59]
Neumann-Staubitz, P.; Neumann, H. The use of unnatural amino acids to study and engineer protein function. Curr. Opin. Struct. Biol., 2016, 38, 119-128.
[60]
van Eldijk, M.B.; van Hest, J.C. Residue-specific incorporation of noncanonical amino acids for protein engineering.Noncanonical Amino Acids; Lemke, E.A., Ed.; Humana Press: New York, 2018, pp. 137-145.
[61]
Grinstead, K.M.; Rowe, L.; Ensor, C.M.; Joel, S.; Daftarian, P.; Dikici, E.; Zingg, J.M.; Daunert, S. Red-shifted aequorin variants incorporating non-canonical amino acids: Applications in in vivo imaging. PLoS One, 2016, 11, e0158579.
[62]
Damborsky, J.; Brezovsky, J. Computational tools for designing and engineering enzymes. Curr. Opin. Chem. Biol., 2014, 19, 8-16.
[63]
Verma, R.; Schwaneberg, U.; Roccatano, D. Computer-aided protein directed evolution: A review of web servers, databases and other computational tools for protein engineering. Comput. Struct. Biotechnol. J., 2012, 2, e201209008.
[64]
Ebert, M.C.; Pelletier, J.N. Computational tools for enzyme improvement: why everyone can–and should–use them. Curr. Opin. Chem. Biol., 2017, 37, 89-96.
[65]
Dvorak, P.; Bednar, D.; Vanacek, P.; Balek, L.; Eiselleova, L.; Stepankova, V.; Sebestova, E. KunovaBosakova, M.; Konecna, Z.; Mazurenko, S.; Kunka, A. Computer‐assisted engineering of hyperstable fibroblast growth factor 2. Biotechnol. Bioeng., 2018, 115, 850-862.
[66]
Mills, J.H.; Sheffler, W.; Ener, M.E.; Almhjell, P.J.; Oberdorfer, G.; Pereira, J.H.; Parmeggiani, F.; Sankaran, B.; Zwart, P.H.; Baker, D. Computational design of a homotrimericmetalloprotein with a trisbipyridyl core. Proc. Natl. Acad. Sci. USA, 2016, 113, 15012-15017.
[67]
Li, R.; Wijma, H.J.; Song, L.; Cui, Y.; Otzen, M.; Tian, Y.E.; Du, J.; Li, T.; Niu, D.; Chen, Y.; Feng, J. Computational redesign of enzymes for regio-and enantioselectivehydroamination. Nat. Chem. Biol., 2018, 14, 664-670.
[68]
Sammond, D.W.; Kastelowitz, N.; Donohoe, B.S.; Alahuhta, M.; Lunin, V.V.; Chung, D.; Sarai, N.S.; Yin, H.; Mittal, A.; Himmel, M.E.; Guss, A.M. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. Biotechnol. Biofuels, 2018, 11, 189.
[69]
Wu, B.; Wijma, H.J.; Song, L.; Rozeboom, H.J.; Poloni, C.; Tian, Y.; Arif, M.I.; Nuijens, T.; Quaedflieg, P.J.; Szymanski, W.; Feringa, B.L. Versatile peptide C-terminal functionalization via a computationally engineered peptide amidase. ACS Catal., 2016, 6, 5405-5414.
[70]
Choi, Y.H.; Kim, J.H.; Park, B.S.; Kim, B.G. Solubilization and iterative saturation mutagenesis of α1, 3‐fucosyltransferase from Helicobacter pylori to enhance its catalytic efficiency. Biotechnol. Bioeng., 2016, 113, 1666-1675.
[71]
Dangi, A.K.; Sinha, R.; Dwivedi, S.; Gupta, S.K.; Shukla, P.S. Cell line techniques and gene editing tools for antibody production: A Review. Front. Pharmacol., 2018, 9, 630.
[72]
Gupta, S.K.; Shukla, P. Gene editing for cell engineering: trends and applications. Crit. Rev. Biotechnol., 2017, 37, 672-684.
[73]
Garst, A.D.; Bassalo, M.C.; Pines, G.; Lynch, S.A.; Halweg-Edwards, A.L.; Liu, R.; Liang, L.; Wang, Z.; Zeitoun, R.; Alexander, W.G.; Gill, R.T. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat. Biotechnol., 2017, 35, 48-55.
[74]
Brödel, A.K.; Isalan, M.; Jaramillo, A. Engineering of biomolecules by bacteriophage directed evolution. Curr. Opin. Biotechnol., 2018, 51, 32-38.
[75]
Hu, J.H.; Miller, S.M.; Geurts, M.H.; Tang, W.; Chen, L.; Sun, N.; Zeina, C.M.; Gao, X.; Rees, H.A.; Lin, Z.; Liu, D.R. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 2018, 556, 57-63.
[76]
Hubbard, B.P.; Badran, A.H.; Zuris, J.A.; Guilinger, J.P.; Davis, K.M.; Chen, L.; Tsai, S.Q.; Sander, J.D.; Joung, J.K.; Liu, D.R. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat. Methods, 2015, 12, 939-942.
[77]
Wang, T.; Badran, A.H.; Huang, T.P.; Liu, D.R. Continuous directed evolution of proteins with improved soluble expression. Nat. Chem. Biol., 2018, 14, 972-980.
[78]
Filipovič, J.; Vávra, O.; Plhák, J.; Bednář, D.; Marques, S.M.; Brezovský, J.; Matyska, L.; Damborský, J. CaverDock: A novel method for the fast analysis of ligand transport. 2018. Available at:
https://arxiv.org/abs/1809.03453
(Accessed 15 September, 2018).
[79]
Mazurenko, S.; Stourac, J.; Kunka, A.; Nedeljković, S.; Bednar, D.; Prokop, Z. Damborsky, J. CalFitter: A web server for analysis of protein thermal denaturation data. Nucleic Acids Res., 2018, 46, W344-W349.
[80]
Sumbalova, L.; Stourac, J.; Martinek, T.; Bednar, D.; Damborsky, J. HotSpot Wizard 3.0: Web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Res., 2018, 46, W356-W362.
[81]
Wrenbeck, E.E.; Faber, M.S.; Whitehead, T.A. Deep sequencing methods for protein engineering and design. Curr. Opin. Struct. Biol., 2017, 45, 36-44.
[82]
Kumar, V.; Kumar, A.; Chhabra, D.; Shukla, P. Improved biobleaching of mixed hardwood pulp and process optimization using novel GA-ANN and GA-ANFIS hybrid statistical tools. Bioresour. Technol., 2019. 10.1016/j.biortech.2018.09.115
Epub 2018 Sep 22.
[83]
Singh, P.K.; Shukla, P. Systems biology as an approach for deciphering microbial interactions. Brief. Funct. Genomics, 2015, 14, 166-168.
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