Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 9, 2012, Pages 3299-3304

  Lee, Sang Chul ^a   Park, Keunwan ^a   Han, Jieun ^a   Lee, Joong Jae ^a   Kim, Hyun Jung ^b,c   Hong, Seungpyo ^a   Heu, Woosung ^a   Kim, Yu Jung ^d   Ha, Jae Seok ^d   Lee, Seung Goo ^d   Cheong, Hae Kap ^b   Jeon, Young Ho ^b   Kim, Dongsup ^a   Kim, Hak Sung ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Korea Basic Science Institute (KBSI)   (South Korea)

^c Chungbuk National University   (South Korea)

^d Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

Modular architecture; Molecular binder; Non antibody scaffold; Repeat protein

Indexed keywords

ANTIBODY; INTERLEUKIN 6; LYMPHOCYTE RECEPTOR; MOLECULAR SCAFFOLD; MYELOID DIFFERENTIATION PROTEIN 2; PROTEIN; REPEBODY; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ANTIBODY ENGINEERING; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONSENSUS SEQUENCE; CRYSTAL STRUCTURE; FEMALE; JAWLESS VERTEBRATE; NONHUMAN; PH; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN STABILITY; THERMODYNAMICS; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; CIRCULAR DICHROISM; CONSENSUS SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HAGFISHES; HYDROGEN-ION CONCENTRATION; LAMPREYS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STABILITY; RECEPTORS, IMMUNOLOGIC; RECOMBINANT FUSION PROTEINS; SUBSTRATE SPECIFICITY; TEMPERATURE;

VERTEBRATA;

EID: 84863229636     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1113193109     Document Type: Article

References (36)

1. Andrade MA, Perez-Iratxeta C, Ponting CP (2001) Protein repeats: Structures, functions, and evolution. J Struct Biol 134:117-131.
2. Binz HK, Stumpp MT, Forrer P, Amstutz P, Pluckthun A (2003) Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332:489-503. (Pubitemid 37020959)
3. Binz H, et al. (2004) High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 22:575-582. (Pubitemid 38590636)
4. Main ERG, et al. (2005) A recent theme in protein engineering: The design, stability and folding of repeat proteins. Curr Opin Struct Biol 15:464-471. (Pubitemid 41073839)
5. Skerra A (2007) Alternative non-antibody scaffolds for molecular recognition. Curr Opin Biotechol 18:295-304.
6. Werner RG (2004) Economic aspects of commercial manufacture of biopharmaceuticals. J Biotechnol 113:171-182.
7. Gebauer M, Skerra A (2009) Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol 13:245-255.
8. Binz HK, Amstutz P, Pluckthun A (2005) Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23:1257-1268. (Pubitemid 41486853)
9. Pancer Z, et al. (2004) Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430:174-180.
10. Alder MN, et al. (2005) Diversity and function of adaptive immune receptors in a jawless vertebrate. Science 310:1970-1973. (Pubitemid 43005993)
11. Saha NR, Smith J, Amemiya CT (2010) Evolution of adaptive immune recognition in jawless vertebrates. Semin Immunol 22:25-33.
12. Enkhbayar P, Kamiya M, Osaki M, Matsumoto T, Matsushima N (2004) Structural principles of leucine-rich repeat (LRR) proteins. Proteins 54:394-403. (Pubitemid 38197354)
13. Alder MN, et al. (2008) Antibody responses of variable lymphocyte receptors in the lamprey. Nat Immunol 9:319-327. (Pubitemid 351267329)
14. Herrin BR, et al. (2008) Structure and specificity of lamprey monoclonal antibodies. Proc Natl Acad Sci USA 105:2040-2045. (Pubitemid 351439461)
15. Tasumi S, et al. (2009) High-affinity lamprey VLRA and VLRB monoclonal antibodies. Proc Natl Acad Sci USA 106:12891-12896.
16. Han BW, Herrin BR, Cooper MD, Wilson IA (2008) Antigen recognition by variable lymphocyte receptors. Science 321:1834-1837.
17. Velikovsky CA, et al. (2009) Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Nat Struct Biol 16:725-744.
18. Deng L, et al. (2010) A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey. Proc Natl Acad Sci USA 107:13408-13413.
19. Kajander T, Cortajarena AL, Regan L (2006) Consensus design as a tool for engineering repeat proteins. Methods Mol Biol 340:151-170.
20. Main ERG, Xiong Y, Cocco MJ, D'Andrea L, Regan L (2003) Design of stable alpha-helical arrays from an idealized TPR motif. Structure 11:497-508. (Pubitemid 36579128)
21. Mosavi LK, Minor DL, Peng ZY (2002) Consensus-derived structural determinants of the ankyrin repeat motif. Proc Natl Acad Sci USA 99:16029-16034. (Pubitemid 35462743)
22. Stumpp MT, Forrer P, Binz HK, Pluckthun A (2003) Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J Mol Biol 332:471-487. (Pubitemid 37020958)
23. Apweiler R, et al. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38:D142-D148.
24. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61-D65. (Pubitemid 46056171)
25. Courtemanche N, Barrick D (2008) The leucine-rich repeat domain of internalin B folds along a polarized N-terminal pathway. Structure 16:705-714. (Pubitemid 351615016)
26. MarinoM, Braun L, Cossart P, Ghosh P (1999) Structure of the InlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L-monocytogenes. Mol Cell 4:1063-1072. (Pubitemid 30054911)
27. Liu Y, Kuhlman B (2006) RosettaDesign server for protein design. Nucleic Acids Res 34: W235-W238. (Pubitemid 44529770)
28. Medzhitov R (2001) Toll-like receptors and innate immunity. Nat Rev Immunol 1:135-145.
29. Kumar H, Kawai T, Akira S (2009) Toll-like receptors and innate immunity. Biochem Biophys Res Commun 388:621-625.
30. Jung K, et al. (2009) Toll-like receptor 4 decoy, TOY, attenuates gram-negative bacterial sepsis. PLoS One 4:e7403.
31. Kim HM, et al. (2007) Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist eritoran. Cell 130:906-917. (Pubitemid 47332573)
32. Fiser A, Do RKG, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773.
33. Nishimoto N, Kishimoto T (2006) Interleukin 6: From bench to bedside. Nat Clin Pract Rheumatol 2:619-626. (Pubitemid 44650950)
34. Kobe B, Kajava AV (2000) When protein folding is simplified to protein coiling: The continuum of solenoid protein structures. Trends Biochem Sci 25:509-515.
35. Wetzel SK, Settanni G, Kenig M, Binz HK, Pluckthun A (2008) Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. J Mol Biol 376:241-257.
36. Lee CMY, Iorno N, Sierro F, Christ D (2007) Selection of human antibody fragments by phage display. Nat Protoc 2:3001-3008.