Computational design of four-helix bundle proteins that bind nonbiological cofactors

Biotechnology Progress

Volumn 24, Issue 1, 2008, Pages 74-79

  Lehmann, Andreas ^a   Saven, Jeffery G ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOACTIVITY; COMPLEXATION; COMPUTER AIDED ANALYSIS;

FOUR-HELIX BUNDLE PROTEINS; NONBIOLOGICAL COFACTORS;

PROTEINS;

HEME; PROTEIN;

BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFERENCE PAPER; METABOLISM; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE;

BINDING SITES; COMPUTER SIMULATION; HEME; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 39049157863     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp070178q     Document Type: Conference Paper

References (77)

1. Ratner, B. D.; Bryant, S. J. Biomaterials: where we have been and where we are going. Annu. Rev. Biomed. Eng. 2004, 6, 41-75.
2. Kopecek, J. Smart and genetically engineered biomaterials and drug delivery systems. Eur. J. Pharm. Sci. 2003, 20 (1), 1-16.
3. Mart, R. J.; Osborne, R. D.; Stevens, M. M.; Ulijn, R. V. Peptide-based stimuli-responsive biomaterials. Soft Matter 2006, 2 (10), 822-835.
4. Woolfson, D. N.; Ryadnov, M. G. Peptide-based fibrous biomaterials: some things old, new and borrowed. Curr. Opin. Chem. Biol. 2006, 10 (6), 559-567.
5. Zhang, S. G. Fabrication of novel biomaterials through molecular self-assembly. Nat. Biotechnol. 2003, 21 (10), 1171-1178.
6. Langer, R.; Tirrell, D. A. Designing materials for biology and medicine. Nature 2004, 428 (6982), 487-492.
7. Maskarinec, S. A.; Tirrell, D. A. Protein engineering approaches to biomaterials design. Curr. Opin. Biotechnol. 2005, 16 (4), 422-426.
8. Fairman, R.; Akerfeldt, K. S. Peptides as novel smart materials. Curr. Opin. Struct. Biol. 2005, 15 (4), 453-463.
9. Anfinsen, C. B. Principles that govern the folding of protein chains. Science 1973, 181 (4096), 223-230.
10. Izarzugaza, J. M. G.; Grana, O.; Tress, M. L.; Valencia, A.; Clarke, N. D. Assessment of intramolecular contact predictions for CASP7. Proteins: Struct., Funct., Bioinf. 2007, 69 (Suppl. 8), 152-158.
11. Vincent, J. J.; Tai, C. H.; Sathyanarayana, B. K.; Lee, B. Assessment of CASP6 predictions for new and nearly new fold targets. Proteins: Struct., Funct., Bioinf. 2005, 61 (Suppl. 7), 67-83.
12. Wang, L.; Schultz, P. G. Expanding the genetic code. Angew. Chem., Int. Ed. 2005, 44 (1), 34-66.
13. Budisa, N. Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire. Angew. Chem., Int. Ed. 2004, 43 (47), 6426-6463.
14. Link, A. J.; Mock, M. L.; Tirrell, D. A. Non-canonical amino acids in protein engineering. Curr. Opin. Biotechnol. 2003, 14 (6), 603-609.
15. Sarikaya, M.; Tamerler, C.; Jen, A. K. Y.; Schulten, K.; Baneyx, F. Molecular biomimetics: nanotechnology through biology. Nat. Mater. 2003, 2 (9), 577-585.
16. Gibney, B. R. Heme Protein Database, http://heme.chem.columbia.edu/heme. php (accessed January 8, 2008).
17. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28 (1), 235-242.
18. Lombardi, A.; Nastri, F.; Pavone, V. Peptide-based heme-protein models. Chem. Rev. 2001, 101 (10), 3165-3189.
19. Paoli, M.; Marles-Wright, J.; Smith, A. Structure-function relationships in heme-proteins. DNA Cell Biol. 2002, 21 (4), 271-280.
20. Reedy, C. J.; Gibney, B. R. Heme protein assemblies. Chem. Rev. 2004, 104 (2), 617-649.
21. Dolphin, D. The Porphyrins; Academic Press, Inc.: New York, 1978/79; Vols. 1-7.
22. Battersby, A. R.; Leeper, F. J. Biosynthesis of the pigments of life - Mechanistic studies on the conversion of porphobilinogen to uroporphyrinogen- III. Chem. Rev. 1990, 90 (7), 1261-1274.
23. Battersby, A. R. How nature builds the pigments of life - the conquest of vitamin B-12. Science 1994, 264 (5165), 1551-1557.
24. Battersby, A. R. Natures pathways to the pigments of life. Nat. Prod. Rep. 1987, 4 (1), 77-87.
25. Leeper, F. J. The biosynthesis of porphyrins, chlorophylls, and vitamin-B12. Nat. Prod. Rep. 1989, 6 (2), 171-203.
26. Izadi, N.; Henry, Y.; Haladjian, J.; Goldberg, M. E.; Wandersman, C.; Delepierre, M.; Lecroisey, A. Purification and characterization of an extracellular heme-binding protein, HasA, involved in heme iron acquisition. Biochemistry 1997, 36 (23), 7050-7057.
27. Horton, P.; Whitmarsh, J.; Cramer, W. A. On the specific site of action of 3-(3,4-dichlorophenyl)-1,1-dimethylurea in chloroplasts - Inhibition of a dark acid-induced decrease in midpoint potential of cytochrome B-559. Arch. Biochem. Biophys. 1976, 176 (2), 519-524.
28. Iwata, S.; Lee, J. W.; Okada, K.; Lee, J. K.; Iwata, M.; Rasmussen, B.; Link, T. A.; Ramaswamy, S.; Jap, B. K. Complete structure of the 11-subunit bovine mitochondrial cytochrome bc(1) complex. Science 1998, 281 (5373), 64-71.
29. Brandt, U.; Trumpower, B. L. The protonmotive Q-cycle in mitochondria and bacteria. Crit. Rev. Biochem. Mol. Biol. 1994, 29 (3), 165-197.
30. Hunte, C.; Palsdottir, H.; Trumpower, B. L. Protonmotive pathways and mechanisms in the cytochrome bc(1) complex. FEBS Lett. 2003, 545 (1), 39-46.
31. Discher, B. M.; Koder, R. L.; Moser, C. C.; Dutton, P. L. Hydrophillic to amphiphilic design in redox protein maquettes. Curr. Opin. Chem. Biol. 2003, 7 (6), 741-748.
32. Robertson, D. E.; Farid, R. S.; Moser, C. C.; Urbauer, J. L.; Mulholland, S. E.; Pidikiti, R.; Lear, J. D.; Wand, A. J.; DeGrado, W. F.; Dutton, P. L. Design and synthesis of multi-heme proteins. Nature 1994, 368 (6470), 425-431.
33. Ho, S. P.; DeGrado, W. F. Design of a 4-helix bundle protein-Synthesis of peptides which self-associate into a helical protein. J. Am. Chem. Soc. 1987, 109 (22), 6751-6758.
34. Handel, T.; DeGrado, W. F. De novo design of a Zn-2+-binding protein. J. Am. Chem. Soc. 1990, 112 (18), 6710-6711.
35. Handel, T. M.; Williams, S. A.; DeGrado, W. F. Metal-ion dependent modulation of the dynamics of a designed protein. Science 1993, 261 (5123), 879-885.
36. Choma, C. T.; Lear, J. D.; Nelson, M. J.; Dutton, P. L.; Robertson, D. E.; DeGrado, W. F. Design of a heme-binding 4-helix bundle. J. Am. Chem. Soc. 1994, 116 (3), 856-865.
37. Gibney, B. R.; Rabanal, F.; Reddy, K. S.; Dutton, P. L. Effect of four helix bundle topology on heme binding and redox properties. Biochemistry 1998, 37 (13), 4635-4643.
38. Gibney, B. R.; Rabanal, F.; Skalicky, J. J.; Wand, A. J.; Dutton, P. L. Iterative protein redesign. J. Am. Chem. Soc. 1999, 121 (21), 4952-4960.
39. Huang, S. S.; Koder, R. L.; Lewis, M.; Wand, A. J.; Dutton, P. L. The HP-1 maquette: From an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (15), 5536-5541.
40. Ghirlanda, G.; Osyczka, A.; Liu, W. X.; Antolovich, M.; Smith, K. M.; Dutton, P. L.; Wand, A. J.; DeGrado, W. F. De novo design of a D-2-symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc(1). J. Am. Chem. Soc. 2004, 126 (26), 8141-8147.
41. Rau, H. K.; Haehnel, W. Design, synthesis, and properties of a novel cytochrome b model. J. Am. Chem. Soc. 1998, 120 (3), 468-476.
42. Mutter, M.; Vuilleumier, S. A chemical approach to protein design-Template-assembled synthetic proteins (TASP). Angew. Chem., Int. Ed. Engl. 1989, 28 (5), 535-554.
43. Kamtekar, S.; Schiffer, J. M.; Xiong, H. Y.; Babik, J. M.; Hecht, M. H. Protein design by binary patterning of polar and nonpolar amino-acids. Science 1993, 262 (5140), 1680-1685.
44. Rojas, N. R. L.; Kamtekar, S.; Simons, C. T.; McLean, J. E.; Vogel, K. M.; Spiro, T. G.; Farid, R. S.; Hecht, M. H. De novo heme proteins from designed combinatorial libraries. Protein Sci. 1997, 6 (12), 2512-2524.
45. Wei, Y. N.; Liu, T.; Sazinsky, S. L.; Moffet, D. A.; Pelczer, I.; Hecht, M. H. Stably folded de novo proteins from a designed combinatorial library. Protein Sci. 2003, 12 (1), 92-102.
46. Wei, Y.; Kim, S.; Fela, D.; Baum, J.; Hecht, M. H. Solution structure of a de novo protein from a designed combinatorial library. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (23), 13270-13273.
47. Marder, S. R.; Kippelen, B.; Jen, A. K. Y.; Peyghambarian, N. Design and synthesis of chromophores and polymers for electrooptic and photorefractive applications. Nature 1997, 388 (6645), 845-851.
48. Prasad, P. N.; Williams, D. J. Introduction to Nonlinear Optical Effects in Molecules and Polymers; John Wiley & Sons: New York, 1991.
49. Sutherland, R. L. Handbook of Nonlinear Optics; Marcel Dekker: New York, 1996.
50. Wolff, J. J.; Wortmann, R. Organic materials for second-order non-linear optics. In Adv. Phys. Org. Chem. 1999, 32, 121-217.
51. Dalton, L. Nonlinear optical polymeric materials: From chromophore design to commercial applications. In Polymers for Photonics Applications I 2002, 158, 1-86.
52. Dalton, L. R.; Steier, W. H.; Robinson, B. H.; Zhang, C.; Ren, A.; Garner, S.; Chen, A. T.; Londergan, T.; Irwin, L.; Carlson, B.; Fifield, L.; Phelan, G.; Kincaid, C.; Amend, J.; Jen, A. From molecules to opto-chips; organic electro-optic materials. J. Mater. Chem. 1999, 9 (9), 1905-1920.
53. Verbiest, T.; Houbrechts, S.; Kauranen, M.; Clays, K.; Persoons, A. Second-order nonlinear optical materials: recent advances in chromophore design. J. Mater. Chem. 1997, 7 (11), 2175-2189.
54. Maiman, T. H. Stimulated optical radiation in ruby. Nature 1960, 187 (4736), 493-494.
55. Davydov, B. L.; Derkacheva, L. D.; Dunina, V. V.; Zhabotin, M. E.; Zolin, V. F.; Koreneva, L. G.; Samokhin, M. A. Connection between charge transfer and laser second harmonic generation. JETP Lett.-USSR 1970, 12 (1), 16.
56. Nalwa, H. S.; Watanabe, T.; Miyata, S. Organic materials for second-order nonlinear optics. In Nonlinear Optics of Organic Molecules and Polymers; Nalwa, H. S., Miyata, S., Eds.; CRC Press: Boca Raton 1997; pp 89-350.
57. Uyeda, H. T.; Zhao, Y. X.; Wostyn, K.; Asselberghs, I.; Clays, K.; Persoons, A.; Therien, M. J. Unusual frequency dispersion effects of the nonlinear optical response in highly conjugated (polypyridyl)-metal-(porphinato) zinc(II) chromophores. J. Am. Chem. Soc. 2002, 124 (46), 13806-13813.
58. Shi, Y. Q.; Zhang, C.; Zhang, H.; Bechtel, J. H.; Dalton, L. R.; Robinson, B. H.; Steier, W. H. Low (sub-1-volt) halfwave voltage polymeric electro-optic modulators achieved by controlling chromophore shape. Science 2000, 288 (5463), 119-122.
59. MacPhee, C. E.; Woolfson, D. N. Engineered and designed peptide-based fibrous biomaterials. Curr. Opin. Solid State Mater. Sci. 2004, 8 (2), 141-149.
60. Woolfson, D. N. The design of coiled-coil structures and assemblies. In Fibrous Proteins: Coiled-Coils Collagen and Elastomers; Academic Press: New York, 2005; Advances in Protein Chemistry Vol. 70; p 79.
61. Kono, H.; Saven, J. G. Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure. J. Mol. Biol. 2001, 306 (3), 607-628.
62. Calhoun, J. R.; Kono, H.; Lahr, S.; Wang, W.; DeGrado, W. F.; Saven, J. G. Computational design and characterization of a monomelic helical dinuclear metalloprotein. J. Mol. Biol. 2003, 334 (5), 1101-1115.
63. Cochran, F. V.; Wu, S. P.; Wang, W.; Nanda, V.; Saven, J. G.; Therien, M. J.; DeGrado, W. F. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. J. Am. Chem. Soc. 2005, 127 (5), 1346-1347.
64. Swift, J.; Wehbi, W. A.; Kelly, B. D.; Stowell, X. F.; Saven, J. G.; Dmochowski, I. J. Design of functional ferritin-like proteins with hydrophobic cavities. J. Am. Chem. Soc. 2006, 128 (20), 6611-6619.
65. North, B.; Cristian, L.; Stowell, X. F.; Lear, J. D.; Saven, J. G.; DeGrado, W. F. Characterization of a membrane protein folding motif the ser zipper, using designed peptides. J. Mol. Biol. 2006, 359 (4), 930-939.
66. Nanda, V.; Rosenblatt, M. M.; Osyczka, A.; Kono, H.; Getahun, Z.; Dutton, P. L.; Saven, J. G.; DeGrado, W. F. De novo design of a redox-active minimal rubredoxin mimic. J. Am. Chem. Soc. 2005, 127 (16), 5804-5805.
67. Shifman, J. M.; Mayo, S. L. Modulating calmodulin binding specificity through computational protein design. J. Mol. Biol. 2002, 323 (3), 417-423.
68. Shiamoka, M.; Shifman, J. M.; Jing, H.; Tagaki, J.; Mayo, S. L.; Springer, T. A. Computational design of an integrin I domain stabilized in the open high affinity conformation. Nat. Struct. Biol. 2000, 7 (8), 674-678.
69. Dahiyat, B. I.; Mayo, S. L. De novo protein design: Fully automated sequence selection. Science 1997, 278 (5335), 82-87.
70. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003, 302 (5649), 1364-1368.
71. Korkegian, A.; Black, M. E.; Baker, D.; Stoddard, B. L. Computational thermostabilization of an enzyme. Science 2005, 308 (5723), 857-860.
72. Marvin, J. S.; Hellinga, H. W. Conversion of a maltose receptor into a zinc biosensor by computational design. Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (9), 4955-4960.
73. Looger, L. L.; Dwyer, M. A.; Smith, J. J.; Hellinga, H. W. Computational design of receptor and sensor proteins with novel functions. Nature 2003, 423 (6936), 185-190.
74. Dwyer, M. A.; Looger, L. L.; Hellinga, H. W. Computational design of a biologically active enzyme. Science 2004, 304 (5679), 1967-1971.
75. North, B.; Summa, C. M.; Ghirlanda, G.; DeGrado, W. F. D-n-Symmetrical tertiary templates for the design of tubular proteins. J. Mol. Biol. 2001, 311 (5), 1081-1090.
76. Betz, S. F.; DeGrado, W. F. Controlling topology and native-like behavior of de novo-designed peptides: Design and characterization of antiparallel four-stranded coiled coils. Biochemistry 1996, 35 (21), 6955-6962.
77. Bender, G. M.; Lehmann, A.; Zou, H.; Cheng, H.; Fry, H. C.; Engel, D.; Therien, M. J.; Blasie, J. K.; Roder, H.; Saven, J. G.; DeGrado, W. F. De novo design of a single-chain diphenylporphyrin metalloprotein. J. Am. Chem. Soc. 2007, 129 (35), 10732-10740.