Synthetic fusion protein design and applications

Biotechnology Advances

Volumn 33, Issue 1, 2015, Pages 155-164

  Yu, Kai ^a   Liu, Chengcheng ^b   Kim, Byung Gee ^c   Lee, Dong Yup ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b AGENCY FOR SCIENCE   (Singapore)

^c Seoul National University   (South Korea)

Author keywords

Domain insertion; Fusion protein; Linker design; Protein therapeutics; Synthetic protein engineering

Indexed keywords

BIOTECHNOLOGY;

DESIGN STRATEGIES; DOMAIN INSERTION; FUSION PROTEINS; PHARMACEUTICAL APPLICATIONS; PROTEIN SWITCHES; PROTEIN THERAPEUTICS; SYNTHETIC PROTEIN; SYSTEMATIC DESIGNS;

PROTEINS;

BIOENGINEERING; BIOTECHNOLOGY; EXPERIMENTAL DESIGN; LITERATURE REVIEW; PROTEIN;

HYBRID PROTEIN;

BIOTECHNOLOGY; CHEMISTRY; GENETICS; HUMAN; PROTEIN CONFORMATION; PROTEIN ENGINEERING;

BIOTECHNOLOGY; HUMANS; PROTEIN CONFORMATION; PROTEIN ENGINEERING; RECOMBINANT FUSION PROTEINS;

EID: 84922832412     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2014.11.005     Document Type: Review

References (101)

1. Amaro F., Turkewitz A.P., Martín-González A., Gutiérrez J.C. Functional GFP-metallothionein fusion protein from Tetrahymena thermophila: a potential whole-cell biosensor for monitoring heavy metal pollution and a cell model to study metallothionein overproduction effects. Biometals 2014, 27:195-205.
2. Andersen J.T., Dalhus B., Viuff D., Ravn B.T., Gunnarsen K.S., Plumridge A., et al. Extending serum half-life of albumin by engineering neonatal Fc receptor (FcRn) binding. J Biol Chem 2014, 289:13492-13502.
3. Arai R., Ueda H., Kitayama A., Kamiya N., Nagamune T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Eng 2001, 14:529-532.
4. Arnold U. Incorporation of non-natural modules into proteins: structural features beyond the genetic code. Biotechnol Lett 2009, 31:1129-1139.
5. Aroul-Selvam R., Hubbard T., Sasidharan R. Domain insertions in protein structures. J Mol Biol 2004, 338:633-641.
6. Ashworth J., Baker D. Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Res 2009, 37:e73.
7. Baslé E., Joubert N., Pucheault M. Protein chemical modification on endogenous amino acids. Chem Biol 2010, 17:213-227.
8. Beck A., Reichert J.M. Therapeutic Fc-fusion proteins and peptides as successful alternatives to antibodies. MAbs 2011, 3:415-416.
9. Béguin P. Hybrid enzymes. Curr Opin Biotechnol 1999, 10:336-340.
10. Bell M.R., Engleka M.J., Malik A., Strickler J.E. To fuse or not to fuse: what is your purpose?. Protein Sci 2013, 22:1466-1477.
11. Berrondo M., Ostermeier M., Gray J.J. Structure prediction of domain insertion proteins from structures of individual domains. Structure 2008, 16:513-527.
12. Betton J.-M., Jacob J.P., Hofnung M., Broome-Smith J.K. Creating a bifunctional protein by insertion of b-lactamase into the maltodextrin-binding protein. Nat Biotechnol 1997, 15:1276-1279.
13. Bundy B.C., Swartz J.R. Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation. Bioconjug Chem 2010, 21:255-263.
14. Castillo J., Gaspar S., Leth S., Niculescu M., Mortari A., Bontidean I., et al. Biosensors for life quality: design, development and applications. Sensors Actuators B Chem 2004, 102:179-194.
15. Chen X., Bai Y., Zaro J.L., Shen W.-C. Design of an in vivo cleavable disulfide linker in recombinant fusion proteins. Biotechniques 2010, 49:513-518.
16. Chen X., Zaro J.L., Shen W.-C. Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev 2013, 65:1357-1369.
17. Chen X., Liu H., Zhang T., Liu Y., Xie X., Wang Z., et al. A vaccine of L2 epitope repeats fused with a modified IgG1 Fc induced cross-neutralizing antibodies and protective immunity against divergent human papillomavirus types. PLoS One 2014, 9:e95448.
18. Cheng T., Blundell T., Fernandez-Recio J. Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinformatics 2008, 9:441.
19. Chiang J., Li I., Pham E., Truong K. FPMOD: a modeling tool for sampling the conformational space of fusion proteins. EMBS '06 28th Annual International Conference of the IEEE2006 2006, 4111-4114.
20. Choi K.-Y., Jung E.-O., Jung D.-H., Pandey B.P., Lee N., Yun H., et al. Novel iron-sulfur containing NADPH-reductase from Nocardia farcinica IFM10152 and fusion construction with CYP51 lanosterol demethylase. Biotechnol Bioeng 2012, 109:630-636.
21. Choudhury R., Tsai Y.S., Dominguez D., Wang Y., Wang Z. Engineering RNA endonucleases with customized sequence specificities. Nat Commun 2012, 3:1147.
22. Chung B.K.S., Lee D.-Y. Computational codon optimization of synthetic gene for protein expression. BMC Syst Biol 2012, 6:134.
23. Collinet B., Hervé M., Pecorari F., Minard P., Eder O., Desmadril M. Functionally accepted insertions of proteins within protein domains. J Biol Chem 2000, 275:17428-17433.
24. Cortez-Retamozo V., Backmann N., Senter P.D., Wernery U., De Baetselier P., Muyldermans S., et al. Efficient cancer therapy with a nanobody-based conjugate. Cancer Res 2004, 64:2853-2857.
25. Crasto C.J., Feng J. LINKER: a program to generate linker sequences for fusion proteins. Protein Eng 2000, 13:309-312.
26. Czajkowsky D.M., Hu J., Shao Z., Pleass R.J. Fc-fusion proteins: new developments and future perspectives. EMBO Mol Med 2012, 4:1015-1028.
27. de Graaf A.J., Kooijman M., Hennink W.E., Mastrobattista E. Nonnatural amino acids for site-specific protein conjugation. Bioconjug Chem 2009, 20:1281-1295.
28. Dueber J.E., Wu G.C., Malmirchegini G.R., Moon T.S., Petzold C.J., Ullal A.V., et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 2009, 27:753-759.
29. Evenäs J., Tugarinov V., Skrynnikov N.R., Goto N.K., Muhandiram R., Kay L.E. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J Mol Biol 2001, 309:961-974.
30. Frommer W.B., Davidson M.W., Campbell R.E. Genetically encoded biosensors based on engineered fluorescent proteins. Chem Soc Rev 2009, 38:2833-2841.
31. George R.A., Heringa J. An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng 2002, 15:871-879.
32. Govardhan C.P. Crosslinking of enzymes for improved stability and performance. Curr Opin Biotechnol 1999, 10:331-335.
33. Grünberg R., Serrano L. Strategies for protein synthetic biology. Nucleic Acids Res 2010, 38:2663-2675.
34. Guntas G., Ostermeier M. Creation of an allosteric enzyme by domain insertion. J Mol Biol 2004, 336:263-273.
35. Haga T., Hirakawa H., Nagamune T. Fine tuning of spatial arrangement of enzymes in a PCNA-mediated multienzyme complex using a rigid poly-l-proline linker. PLoS One 2013, 8:e75114.
36. Halin C., Gafner V., Villani M.E., Borsi L., Berndt A., Kosmehl H., et al. Synergistic therapeutic effects of a tumor targeting antibody fragment, fused to interleukin 12 and to tumor necrosis factor α. Cancer Res 2003, 63:3202-3210.
37. Hatzakis N.S., Engelkamp H., Velonia K., Hofkens J., Christianen P.C.M., Svendsen A., et al. Synthesis and single enzyme activity of a clicked lipase-BSA hetero-dimer. Chem Commun 2006, 2012-2014.
38. Heck T., Faccio G., Richter M., Thöny-Meyer L. Enzyme-catalyzed protein crosslinking. Appl Microbiol Biotechnol 2013, 97:461-475.
39. Hirakawa H., Nagamune T. Molecular assembly of P450 with ferredoxin and ferredoxin reductase by fusion to PCNA. ChemBioChem 2010, 11:1517-1520.
40. Hirakawa H., Kamiya N., Tanaka T., Nagamune T. Intramolecular electron transfer in a cytochrome P450cam system with a site-specific branched structure. Protein Eng Des Sel 2007, 20:453-459.
41. Ho M.L., Adler B.A., Torre M.L., Silberg J.J., Suh J. SCHEMA computational design of virus capsid chimeras: calibrating how genome packaging, protection, and transduction correlate with calculated structural disruption. ACS Synth Biol 2013, 2:724-733.
42. Höcker B. Design of proteins from smaller fragments - learning from evolution. Curr Opin Struct Biol 2014, 27:56-62.
43. Huston J.S., Levinson D., Mudgett-Hunter M., Tai M.S., Novotný J., Margolies M.N., et al. Protein engineering of antibody binding sites: recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli. Proc Natl Acad Sci 1988, 85:5879-5883.
44. Iturrate L., Sánchez-Moreno I., Oroz-Guinea I., Pérez-Gil J., García-Junceda E. Preparation and characterization of a bifunctional aldolase/kinase enzyme: a more efficient biocatalyst for C-C bond formation. Chem Eur J 2010, 16:4018-4030.
45. Jana S., Deb J.K. Strategies for efficient production of heterologous proteins in Escherichia coli. Appl Microbiol Biotechnol 2005, 67:289-298.
46. Jiang L., Althoff E.A., Clemente F.R., Doyle L., Röthlisberger D., Zanghellini A., et al. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
47. Kanwar M., Wright R.C., Date A., Tullman J., Ostermeier M. Chapter seventeen - protein switch engineering by domain insertion. Methods enzymol 2013, 369-388. Academic Press. E.K. Amy (Ed.).
48. Kavoosi M., Creagh A.L., Kilburn D.G., Haynes C.A. Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed in Escherichia coli. Biotechnol Bioeng 2007, 98:599-610.
49. King N.P., Bale J.B., Sheffler W., McNamara D.E., Gonen S., Gonen T., et al. Accurate design of co-assembling multi-component protein nanomaterials. Nature 2014, 510:103-108.
50. Koga N., Tatsumi-Koga R., Liu G., Xiao R., Acton T.B., Montelione G.T., et al. Principles for designing ideal protein structures. Nature 2012, 491:222-227.
51. Krauss U., Lee J., Benkovic S.J., Jaeger K.-E. LOVely enzymes - towards engineering light-controllable biocatalysts. Microb Biotechnol 2010, 3:15-23.
52. Kufner K., Lipps G. Construction of a chimeric thermoacidophilic beta-endoglucanase. BMC Biochem 2013, 14:11.
53. Lanci C.J., MacDermaid C.M., Kang S.-g., Acharya R., North B., Yang X., et al. Computational design of a protein crystal. Proc Natl Acad Sci 2012, 109:7304-7309.
54. Lee J., Natarajan M., Nashine V.C., Socolich M., Vo T., Russ W.P., et al. Surface sites for engineering allosteric control in proteins. Science 2008, 322:438-442.
55. Levary D.A., Parthasarathy R., Boder E.T., Ackerman M.E. Protein-protein fusion catalyzed by sortase A. PLoS One 2011, 6:e18342.
56. Lindbladh C., Persson M., BÜLow L., Mosbach K. Characterization of a recombinant bifunctional enzyme, galactose dehydrogenase/bacterial luciferase, displaying an improved bioluminescence in a three-enzyme system. Eur J Biochem 1992, 204:241-247.
57. Liu W., Wang P. Cofactor regeneration for sustainable enzymatic biosynthesis. Biotechnol Adv 2007, 25:369-384.
58. Long M. A new function evolved from gene fusion. Genome Res 2000, 10:1655-1657.
59. Losi A. Flavin-based blue-light photosensors: a photobiophysics update. Photochem Photobiol 2007, 83:1283-1300.
60. Lungu Oana I., Hallett Ryan A., Choi Eun J., Aiken Mary J., Hahn Klaus M., Kuhlman B. Designing photoswitchable peptides using the AsLOV2 domain. Chem Biol 2012, 19:926.
61. Meister G.E., Joshi N.S. An engineered calmodulin-based allosteric switch for peptide biosensing. ChemBioChem 2013, 14:1460-1467.
62. Mekhaiel D.N.A., Czajkowsky D.M., Andersen J.T., Shi J., El-Faham M., Doenhoff M., et al. Polymeric human Fc-fusion proteins with modified effector functions. Sci Rep 2011, 1:124.
63. Melo J.V. The diversity of BCR-ABL fusion proteins and their relationship to leukemia phenotype. Blood 1996, 88:2375-2384.
64. Mills J.H., Khare S.D., Bolduc J.M., Forouhar F., Mulligan V.K., Lew S., et al. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc 2013, 135:13393-13399.
65. Minamihata K., Goto M., Kamiya N. Protein heteroconjugation by the peroxidase-catalyzed tyrosine coupling reaction. Bioconjug Chem 2011, 22:2332-2338.
66. Miyawaki A., Tsien R.Y. Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein. Methods Enzymol 2000, 327:472-500.
67. Mizoue L.S., Chazin W.J. Engineering and design of ligand-induced conformational change in proteins. Curr Opin Struct Biol 2002, 12:459-463.
68. Morris A.L., MacArthur M.W., Hutchinson E.G., Thornton J.M. Stereochemical quality of protein structure coordinates. Proteins Struct Funct Bioinf 1992, 12:345-364.
69. Pack P., Müller K., Zahn R., Plückthun A. Tetravalent miniantibodies with high avidity assembling in Escherichia coli. J Mol Biol 1995, 246:28-34.
70. Pedelacq J.-D., Cabantous S., Tran T., Terwilliger T.C., Waldo G.S. Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 2006, 24:79-88.
71. Pérez-Arellano I., Carmona-Álvarez F., Martínez A.I., Rodríguez-Díaz J., Cervera J. Pyrroline-5-carboxylate synthase and proline biosynthesis: from osmotolerance to rare metabolic disease. Protein Sci 2010, 19:372-382.
72. Pham E., Chiang J., Li I., Shum W., Truong K. A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space. Structure 2007, 15:515-523.
73. Rapin N., Porse B.T. Oncogenic fusion proteins expressed in immature hematopoietic cells fail to recapitulate the transcriptional changes observed in human AML. Oncogenesis 2014, 3:e106.
74. Rawlings N.D., Barrett A.J., Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2012, 40:D343-D350.
75. Rheinnecker M., Hardt C., Ilag L.L., Kufer P., Gruber R., Hoess A., et al. Multivalent antibody fragments with high functional affinity for a tumor-associated carbohydrate antigen. J Immunol 1996, 157:2989-2997.
76. Rizk M., Antranikian G., Elleuche S. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes. Biochem Biophys Res Commun 2012, 428:1-5.
77. Rothlisberger D., Khersonsky O., Wollacott A.M., Jiang L., DeChancie J., Betker J., et al. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
78. Sabourin M., Tuzon C.T., Fisher T.S., Zakian V.A. A flexible protein linker improves the function of epitope-tagged proteins in Saccharomyces cerevisiae. Yeast 2007, 24:39-45.
79. Sachdev D., Chirgwin J.M. Order of fusions between bacterial and mammalian proteins can determine solubility in Escherichia coli. Biochem Biophys Res Commun 1998, 244:933-937.
80. Schmidt S.R. Fusion protein technologies for biopharmaceuticals: applications and challenges 2013, John Wiley & Sons, Inc., Hoboken, New Jersey. 1st ed.
81. Schulte S. Half-life extension through albumin fusion technologies. Thromb Res 2009, 124:S6-S8.
82. Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., Lambert A.R., St.Clair J.L., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
83. Snapp E. Design and use of fluorescent fusion proteins in cell biology. Current protocols in cell biology 2001, John Wiley and Sons, Inc.
84. Sokolowska-Wedzina A., Borek A., Chudzian J., Jakimowicz P., Zakrzewska M., Otlewski J. Efficient production and purification of extracellular domain of human FGFR-Fc fusion proteins from Chinese hamster ovary cells. Protein Expr Purif 2014, 99:50-57.
85. Strickland D., Moffat K., Sosnick T.R. Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci 2008, 105:10709-10714.
86. Terpe K. Overview of tag protein fusions: From molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 2003, 60:523-533.
87. Tinberg C.E., Khare S.D., Dou J., Doyle L., Nelson J.W., Schena A., et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature 2013, 501:212-216.
88. Tong L. Acetyl-coenzyme A, carboxylase: crucial metabolic enzyme and attractive target for drug discovery. Cell Mol Life Sci 2005, 62:1784-1803.
89. 3 linker sequence results in enhanced protein expression. Mol Immunol 2004, 40:717-722.
90. 2+ imaging by a new calmodulin-GFP fusion molecule. Nat Struct Mol Biol 2001, 8:1069-1073.
91. Tsien R.Y. The green fluorescent protein. Annu Rev Biochem 1998, 67:509-544.
92. Voigt C.A., Martinez C., Wang Z.-G., Mayo S.L., Arnold F.H. Protein building blocks preserved by recombination. Nat Struct Mol Biol 2002, 9:553-558.
93. Volzing K., Biliouris K., Kaznessis Y.N. ProTeOn and ProTeOff, new protein devices that inducibly activate bacterial gene expression. ACS Chem Biol 2011, 6:1107-1116.
94. Wang R., Xue Y., Wu X., Song X., Peng J. Enhancement of engineered trifunctional enzyme by optimizing linker peptides for degradation of agricultural by-products. Enzyme Microb Technol 2010, 47:194-199.
95. Wollacott A.M., Zanghellini A., Murphy P., Baker D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci 2007, 16:165-175.
96. Wu C., Ying H., Grinnell C., Bryant S., Miller R., Clabbers A., et al. Simultaneous targeting of multiple disease mediators by a dual-variable-domain immunoglobulin. Nat Biotechnol 2007, 25:1290-1297.
97. Xiao J., Tolbert T.J. Synthesis of N-terminally linked protein dimers and trimers by a combined native chemical ligation-CuAAC click chemistry strategy. Org Lett 2009, 11:4144-4147.
98. Xue F., Gu Z., Feng J.-a. LINKER: A web server to generate peptide sequences with extended conformation. Nucleic Acids Res 2004, 32(Suppl. 2):W562-W565.
99. Yamamura Y., Hirakawa H., Yamaguchi S., Nagamune T. Enhancement of sortase A-mediated protein ligation by inducing a b-hairpin structure around the ligation site. Chem Commun 2011, 47:4742-4744.
100. Yin T., Wu Y.I. Guiding lights: recent developments in optogenetic control of biochemical signals. Pflügers Arch - Eur J Physiol 2013, 465:397-408.
101. Yu Y., Lutz S. Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnol 2011, 29:18-25.