Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules

Current Opinion in Biotechnology

Volumn 20, Issue 4, 2009, Pages 398-404

  Koide, Shohei ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIRECTED EVOLUTION; ENZYME ENGINEERING; NATURAL ARCHITECTURE; NOVEL PROTEINS; PROTEIN ARCHITECTURES; PROTEIN ENGINEERING; PROTEIN FUNCTIONS; PROTEIN STRUCTURES;

BIOCHEMICAL ENGINEERING; GENETIC ENGINEERING; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION;

ENGINEERING EXHIBITIONS;

BCR ABL PROTEIN; DIHYDROFOLATE REDUCTASE; PDZ PROTEIN; PHYTOCHROME B; PROTEIN CDC42; PROTEIN SH2; WISKOTT ALDRICH SYNDROME PROTEIN; ZINC FINGER PROTEIN;

ALLOSTERISM; BINDING AFFINITY; BIOSENSOR; BIOTECHNOLOGY; CONFORMATIONAL TRANSITION; DIRECTED MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW;

PROTEIN FOLDING; PROTEINS;

EID: 70349770900     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2009.07.007     Document Type: Review

References (49)

1. Pluckthun A., and Mayo S.L. The design of evolution and the evolution of design. Curr Opin Struct Biol 17 (2007) 451-453
2. Kortemme T., and Baker D. Computational design of protein-protein interactions. Curr Opin Chem Biol 8 (2004) 91-97
3. Winter G., Griffiths A.D., Hawkins R.E., and Hoogenboom H.R. Making antibodies by phage display technology. Annu Rev Immunol 12 (1994) 433-455
4. Binz H.K., Amstutz P., and Pluckthun A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23 (2005) 1257-1268
5. Looger L.L., Dwyer M.A., Smith J.J., and Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 423 (2003) 185-190
6. Yoshikuni Y., Ferrin T.E., and Keasling J.D. Designed divergent evolution of enzyme function. Nature 440 (2006) 1078-1082
7. Sidhu S.S., and Fellouse F.A. Synthetic therapeutic antibodies. Nat Chem Biol 2 (2006) 682-688
8. Bershtein S., and Tawfik D.S. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 12 (2008) 151-158
9. Persson H., Lantto J., and Ohlin M. A focused antibody library for improved hapten recognition. J Mol Biol 357 (2006) 607-620
10. Bashton M., and Chothia C. The generation of new protein functions by the combination of domains. Structure 15 (2007) 85-99
11. Rossmann M.G., Moras D., and Olsen K.W. Chemical and biological evolution of nucleotide-binding protein. Nature 250 (1974) 194-199
12. Gilbert W. Why genes in pieces?. Nature 271 (1978) 501
13. Blake C.C.F. Do genes-in-pieces imply proteins-in-pieces?. Nature 273 (1978) 267
14. Todd A.E., Orengo C.A., and Thornton J.M. Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10 (2002) 1435-1451
15. Bogarad L.D., and Deem M.W. A hierarchical approach to protein molecular evolution. Proc Natl Acad Sci U S A 96 (1999) 2591-2595
16. Pawson T., and Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 300 (2003) 445-452
17. Fellouse F.A., Esaki K., Birtalan S., Raptis D., Cancasci V.J., Koide A., Jhurani P., Vasser M., Wiesmann C., Kossiakoff A.A., et al. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol 373 (2007) 924-940
18. Sidhu S.S., and Koide S. Phage display for engineering and analyzing protein interaction interfaces. Curr Opin Struct Biol 17 (2007) 481-487
19. Bromley S.K., Burack W.R., Johnson K.G., Somersalo K., Sims T.N., Sumen C., Davis M.M., Shaw A.S., Allen P.M., and Dustin M.L. The immunological synapse. Annu Rev Immunol 19 (2001) 375-396
20. Duan J., Wu J., Valencia C.A., and Liu R. Fibronectin type III domain based monobody with high avidity. Biochemistry 46 (2007) 12656-12664
21. Choo Y., and Klug A. Designing DNA-binding proteins on the surface of filamentous phage. Curr Opin Biotechnol 6 (1995) 431-436
22. Blancafort P., Segal D.J., and Barbas III C.F. Designing transcription factor architectures for drug discovery. Mol Pharmacol 66 (2004) 1361-1371
23. Silverman J., Liu Q., Bakker A., To W., Duguay A., Alba B.M., Smith R., Rivas A., Li P., Le H., et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol 23 (2005) 1556-1561. This paper describes the design principle of avimers, generating very high-affinity molecules to multiple targets, and in vivo efficacy of an anti-interleukin 6 avimer.
24. Vogel C., Bashton M., Kerrison N.D., Chothia C., and Teichmann S.A. Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 14 (2004) 208-216
25. Burroughs A.M., Allen K.N., Dunaway-Mariano D., and Aravind L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 361 (2006) 1003-1034. A particularly comprehensive comparison of structures of an enzyme superfamily that supports nonhomologous recombination (in this case insertion) as a dominant driving force for functional diversification.
26. Huang J., Koide A., Makabe K., and Koide S. Design of protein function leaps by directed domain interface evolution. Proc Natl Acad Sci U S A 105 (2008) 6578-6583. This work establishes the affinity clamp concept, generates high-affinity affinity peptide-binding proteins, and shows their utility as antibody alternatives. A high-resolution crystal structure of a clamp-peptide complex validates the design.
27. Ferrer M., Maiolo J., Kratz P., Jackowski J., Murphy D., Delagrave S., and Inglese J. Directed evolution of PDZ variants to generate high-affinity detection reagents. Protein Eng Des Sel 18 (2005) 165-173
28. Huang J, Makabe K, Biancalana M, Koide A, Koide S: Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. J Mol Biol 2009, doi:10.1016/j.jmb.2009.07.067.
29. Huse M., and Kuriyan J. The conformational plasticity of protein kinases. Cell 109 (2002) 275-282
30. Hantschel O., and Superti-Furga G. Regulation of the c-Abl and Bcr-Abl tyrosine kinases. Nat Rev Mol Cell Biol 5 (2004) 33-44
31. Dueber J.E., Yeh B.J., Bhattacharyya R.P., and Lim W.A. Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 14 (2004) 690-699
32. Bhattacharyya R.P., Remenyi A., Yeh B.J., and Lim W.A. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 75 (2006) 655-680
33. Howard P.L., Chia M.C., Del Rizzo S., Liu F.F., and Pawson T. Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins. Proc Natl Acad Sci U S A 100 (2003) 11267-11272
34. Antunes M.S., Morey K.J., Tewari-Singh N., Bowen T.A., Smith J.J., Webb C.T., Hellinga H.W., and Medford J.I. Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5 (2009) 270
35. Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J Mol Biol 12 (1965) 88-118
36. Dueber J.E., Yeh B.J., Chak K., and Lim W.A. Reprogramming control of an allosteric signaling switch through modular recombination. Science 301 (2003) 1904-1908
37. Dueber J.E., Mirsky E.A., and Lim W.A. Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat Biotechnol 25 (2007) 660-662. This work demonstrates the capacity of modular combination to create switches with nonlinear, highly cooperative responses.
38. Wright C.M., Heins R.A., and Ostermeier M. As easy as flipping a switch?. Curr Opin Chem Biol 11 (2007) 342-346
39. Ostermeier M. Designing switchable enzymes. Curr Opin Struct Biol (2009) 10.1016/j.sbi.2009.04.007. A recent review on the design of protein switches.
40. Edwards W.R., Busse K., Allemann R.K., and Jones D.D. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Res 36 (2008) e78
41. Radley T.L., Markowska A.I., Bettinger B.T., Ha J.H., and Loh S.N. Allosteric switching by mutually exclusive folding of protein domains. J Mol Biol 332 (2003) 529-536
42. Cutler T.A., Mills B.M., Lubin D.J., Chong L.T., and Loh S.N. Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains. J Mol Biol 386 (2009) 854-868
43. Moglich A., Ayers R.A., and Moffat K. Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 385 (2009) 1433-1444
44. Strickland D., Moffat K., and Sosnick T.R. Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci U S A 105 (2008) 10709-10714. Design of mutual exclusivity by designing an overlap of a helix between two modules. A light-switchable transcription factor was successfully produced.
45. Lee J., Natarajan M., Nashine V.C., Socolich M., Vo T., Russ W.P., Benkovic S.J., and Ranganathan R. Surface sites for engineering allosteric control in proteins. Science 322 (2008) 438-442
46. •,40], the photoswitch of this work is based on modular design using light-dependent protein-protein interaction. In addition, this switch can be turned on and off using light of different wavelengths.
47. Sallee N.A., Yeh B.J., and Lim W.A. Engineering modular protein interaction switches by sequence overlap. J Am Chem Soc 129 (2007) 4606-4611. This describes the generation of modular switches by designing a segmental overlap between two modules that creates steric mutual exclusivity. Both modular domains and short peptides were used as building blocks.
48. 2+-sensing molecular switch based on alternate frame protein folding. ACS Chem Biol 3 (2008) 723-732. This describes a new strategy to engineer fluorescence sensors using a ligand-binding module that does not exhibit a large conformational change.
49. Liang J., Kim J.R., Boock J.T., Mansell T.J., and Ostermeier M. Ligand binding and allostery can emerge simultaneously. Protein Sci 16 (2007) 929-937. The authors find a hybrid molecule between β-lactamase and MBP has acquired new binding function to zinc and also heterotropic allostery, demonstrating domain/module recombination as a route to new molecular recognition and regulation.