Highly stable binding proteins derived from the hyperthermophilic Sso7d scaffold

Journal of Molecular Biology

Volumn 409, Issue 4, 2011, Pages 601-616

  Gera, Nimish ^a   Hussain, Mahmud ^a   Wright, Robert C ^a   Rao, Balaji M ^a  

^a North Carolina State University   (United States)

Author keywords

alternate scaffold; hyperthermophilic protein scaffolds; protein engineering; stability; yeast surface display

Indexed keywords

BACTERIAL PROTEIN; BETA CATENIN; CYSTEINE; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; FLUORESCEIN; GUANIDINE; IMMUNOGLOBULIN; LYSOZYME; MUTANT PROTEIN; PROTEIN SSO7D; RIBONUCLEASE; STREPTAVIDIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CYTOPLASM; DENATURATION; DIFFERENTIAL SCANNING CALORIMETRY; DISSOCIATION CONSTANT; DNA SEQUENCE; EGG; ENZYME ACTIVITY; ESCHERICHIA COLI; FEMALE; FLUORESCENCE ACTIVATED CELL SORTING; HEN; HYPERTHERMOPHILIC ARCHAEON; MELTING POINT; MOLECULAR LIBRARY; MOUSE; MUTAGENESIS; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN ISOLATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN TARGETING; SACCHAROMYCES CEREVISIAE; SULFOLOBUS SOLFATARICUS;

ARCHAEA; ESCHERICHIA COLI; SULFOLOBUS SOLFATARICUS;

EID: 79957773363     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.04.020     Document Type: Article

References (56)

1. Binz H.K., Amstutz P., and Pluckthun A. Engineering novel binding proteins from nonimmunoglobulin domains Nat. Biotechnol. 23 2005 1257 1268 (Pubitemid 41486853)
2. Skerra A. Alternative non-antibody scaffolds for molecular recognition Curr. Opin. Biotechnol. 18 2007 295 304 (Pubitemid 47385180)
3. Gebauer M., and Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics Curr. Opin. Chem. Biol. 13 2009 245 255
4. Koide A., and Koide S. Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain Methods Mol. Biol. 352 2007 95 109
5. Hackel B.J., Kapila A., and Wittrup K.D. Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuffling J. Mol. Biol. 381 2008 1238 1252
6. Lipovsek D., Lippow S.M., Hackel B.J., Gregson M.W., Cheng P., Kapila A., and Wittrup K.D. Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies J. Mol. Biol. 368 2007 1024 1041 (Pubitemid 46584683)
7. Stumpp M.T., Binz H.K., and Amstutz P. DARPins: a new generation of protein therapeutics Drug Discov. Today 13 2008 695 701
8. Zahnd C., Wyler E., Schwenk J.M., Steiner D., Lawrence M.C., and McKern N.M. A designed ankyrin repeat protein evolved to picomolar affinity to Her2 J. Mol. Biol. 369 2007 1015 1028 (Pubitemid 46754059)
9. Nygren P.A. Alternative binding proteins: affibody binding proteins developed from a small three-helix bundle scaffold FEBS J. 275 2008 2668 2676
10. Lofblom J., Feldwisch J., Tolmachev V., Carlsson J., Stahl S., and Frejd F.Y. Affibody molecules: engineered proteins for therapeutic, diagnostic and biotechnological applications FEBS Lett. 584 2010 2670 2680
11. Bloom J.D., Labthavikul S.T., Otey C.R., and Arnold F.H. Protein stability promotes evolvability Proc. Natl Acad. Sci. USA 103 2006 5869 5874
12. Karshikoff A., and Ladenstein R. Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads Trends Biochem. Sci. 26 2001 550 556 (Pubitemid 32823440)
13. Ladenstein R., and Antranikian G. Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water Adv. Biochem. Eng. Biotechnol. 61 1998 37 85
14. Baumann H., Knapp S., Lundback T., Ladenstein R., and Hard T. Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus Nat. Struct. Biol. 1 1994 808 819
15. Edmondson S.P., and Shriver J.W. DNA binding proteins Sac7d and Sso7d from Sulfolobus Methods Enzymol. 334 2001 129 145 (Pubitemid 32507268)
16. Knapp S., Mattson P.T., Christova P., Berndt K.D., Karshikoff A., and Vihinen M. Thermal unfolding of small proteins with SH3 domain folding pattern Proteins: Struct. Funct. Bioinformatics 31 1998 309 319 (Pubitemid 28217818)
17. Baumann H., Knapp S., Karshikoff A., Ladenstein R., and Hard T. DNA-binding surface of the Sso7d protein from Sulfolobus solfataricus J. Mol. Biol. 247 1995 840 846
18. Knapp S., Karshikoff A., Berndt K.D., Christova P., Atanasov B., and Ladenstein R. Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus J. Mol. Biol. 264 1996 1132 1144 (Pubitemid 27019497)
19. Boder E.T., and Wittrup K.D. Yeast surface display for screening combinatorial polypeptide libraries Nat. Biotechnol. 15 1997 553 557 (Pubitemid 27251573)
20. Gai S.A., and Wittrup K.D. Yeast surface display for protein engineering and characterization Curr. Opin. Struct. Biol. 17 2007 467 473 (Pubitemid 47454774)
21. Mouratou B., Schaeffer F., Guilvout I., Tello-Manigne D., Pugsley A.P., Alzari P.M., and Pecorari F. Remodeling a DNA-binding protein as a specific in vivo inhibitor of bacterial secretin PulD Proc. Natl Acad. Sci. USA 104 2007 17983 17988 (Pubitemid 350210807)
22. Shehi E., Serina S., Fumagalli G., Vanoni M., Consonni R., and Zetta L. The Sso7d DNA-binding protein from Sulfolobus solfataricus has ribonuclease activity FEBS Lett. 497 2001 131 136 (Pubitemid 32476891)
23. Swers J.S., Kellogg B.A., and Wittrup K.D. Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display Nucleic Acids Res. 32 2004 e36
24. Shusta E.V., Kieke M.C., Parke E., Kranz D.M., and Wittrup K.D. Yeast polypeptide fusion surface display levels predict thermal stability and soluble secretion efficiency J. Mol. Biol. 292 1999 949 956 (Pubitemid 29481708)
25. Kieke M.C., Cho B.K., Boder E.T., Kranz D.M., and Wittrup K.D. Isolation of anti-T cell receptor scFv mutants by yeast surface display Protein Eng. 10 1997 1303 1310 (Pubitemid 28077683)
26. Park S., Xu Y., Stowell X.F., Gai F., Saven J.G., and Boder E.T. Limitations of yeast surface display in engineering proteins of high thermostability Protein Eng. Des. Sel. 19 2006 211 217
27. Ackerman M., Levary D., Tobon G., Hackel B., Orcutt K.D., and Wittrup K.D. Highly avid magnetic bead capture: an efficient selection method for de novo protein engineering utilizing yeast surface display Biotechnol. Prog. 25 2009 774 783
28. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
29. Chao G., Lau W.L., Hackel B.J., Sazinsky S.L., Lippow S.M., and Wittrup K.D. Isolating and engineering human antibodies using yeast surface display Nat. Protoc. 1 2006 755 768
30. Hackel B.J., and Wittrup K.D. The full amino acid repertoire is superior to serine/tyrosine for selection of high affinity immunoglobulin G binders from the fibronectin scaffold Protein Eng. Des. Sel. 23 2010 211 219
31. Catanzano F., Graziano G., Fusi P., Tortora P., and Barone G. Differential scanning calorimetry study of the thermodynamic stability of some mutants of Sso7d from Sulfolobus solfataricus Biochemistry 37 1998 10493 10498 (Pubitemid 28357573)
32. Worn A., and Pluckthun A. Different equilibrium stability behavior of ScFv fragments: identification, classification, and improvement by protein engineering Biochemistry 38 1999 8739 8750
33. Agrawal V., and Kishan R.K. Functional evolution of two subtly different (similar) folds BMC Struct. Biol. 1 2001 5
34. Kishan K.V., and Agrawal V. SH3-like fold proteins are structurally conserved and functionally divergent Curr. Protein Pept. Sci. 6 2005 143 150 (Pubitemid 40614138)
35. Arcus V. OB-fold domains: a snapshot of the evolution of sequence, structure and function Curr. Opin. Struct. Biol. 12 2002 794 801 (Pubitemid 36009497)
36. Granata V., Vecchio P.D., Barone G., Shehi E., Fusi P., Tortora P., and Graziano G. Guanidine-induced unfolding of the Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus Int. J. Biol. Macromol. 34 2004 195 201 (Pubitemid 38844650)
37. Pavoor T.V., Cho Y.K., and Shusta E.V. Development of GFP-based biosensors possessing the binding properties of antibodies Proc. Natl Acad. Sci. USA 106 2009 11895 11900
38. Hackel B.J., Ackerman M., Howland S.W., and Wittrup K.D. Stability and CDR composition biases enrich binder functionality landscapes J. Mol. Biol. 401 2010 84 96
39. Silverman A.P., Levin A.M., Lahti J.L., and Cochran J.R. Engineered cystine-knot peptides that bind alpha(v)beta(3) integrin with antibody-like affinities J. Mol. Biol. 385 2009 1064 1075
40. Feldhaus M.J., Siegel R.W., Opresko L.K., Coleman J.R., Feldhaus J.M., and Yeung Y.A. Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library Nat. Biotechnol. 21 2003 163 170 (Pubitemid 36188215)
41. Cinier M., Petit M., Williams M.N., Fabre R.M., Pecorari F., and Talham D.R. Bisphosphonate adaptors for specific protein binding on zirconium phosphonate-based microarrays Bioconjug. Chem. 20 2009 2270 2277
42. Feldwisch J., Tolmachev V., Lendel C., Herne N., Sjoberg A., and Larsson B. Design of an optimized scaffold for affibody molecules J. Mol. Biol. 398 2010 232 247
43. Shehi E., Granata V., Del Vecchio P., Barone G., Fusi P., Tortora P., and Graziano G. Thermal stability and DNA binding activity of a variant form of the Sso7d protein from the archeon Sulfolobus solfataricus truncated at leucine 54 Biochemistry 42 2003 8362 8368 (Pubitemid 36858997)
44. Consonni R., Arosio I., Recca T., Fusi P., and Zetta L. Structural determinants responsible for the thermostability of Sso7d and its single point mutants Proteins: Struct. Funct. Bioinformatics 67 2007 766 775 (Pubitemid 46625591)
45. Consonni R., Santomo L., Fusi P., Tortora P., and Zetta L. A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from Sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core Biochemistry 38 1999 12709 12717
46. Bertschinger J., Grabulovski D., and Neri D. Selection of single domain binding proteins by covalent DNA display Protein Eng. Des. Sel. 20 2007 57 68 (Pubitemid 46410870)
47. Renzone G., Vitale R.M., Scaloni A., Rossi M., Amodeo P., and Guagliardi A. Structural characterization of the functional regions in the archaeal protein Sso7d Proteins: Struct. Funct. Bioinformatics 67 2007 189 197 (Pubitemid 46340138)
48. VanAntwerp J.J., and Wittrup K.D. Fine affinity discrimination by yeast surface display and flow cytometry Biotechnol. Prog. 16 2000 31 37 (Pubitemid 30097647)
49. Boder E.T., and Wittrup K.D. Optimal screening of surface-displayed polypeptide libraries Biotechnol. Prog. 14 1998 55 62 (Pubitemid 28118264)
50. Rao B.M., Girvin A.T., Ciardelli T., Lauffenburger D.A., and Wittrup K.D. Interleukin-2 mutants with enhanced alpha-receptor subunit binding affinity Protein Eng. 16 2003 1081 1087 (Pubitemid 38281759)
51. Rasband W.S. ImageJ 1997-2009 U. S. National Institutes of Health Bethesda, Maryland, USA http://rsb.info.nih.gov/ij/
52. Bloom L., and Calabro V. FN3: a new protein scaffold reaches the clinic Drug Discov. Today 14 2009 949 955
53. Parker M.H., Chen Y., Danehy F., Dufu K., Ekstrom J., and Getmanova E. Antibody mimics based on human fibronectin type three domain engineered for thermostability and high-affinity binding to vascular endothelial growth factor receptor two Protein Eng. Des. Sel. 18 2005 435 444 (Pubitemid 41219890)
54. Wetzel S.K., Settanni G., Kenig M., Binz H.K., and Pluckthun A. Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins J. Mol Biol. 376 2008 241 257
55. Skerra A. Alternative binding proteins: anticalins - harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities FEBS J. 275 2008 2677 2683 (Pubitemid 351678679)
56. Schlehuber S., and Skerra A. Tuning ligand affinity, specificity, and folding stability of an engineered lipocalin variant - a so-called 'anticalin' - using a molecular random approach Biophys. Chem. 96 2002 213 228 (Pubitemid 34548234)