Principles for designing ordered protein assemblies

Trends in Cell Biology

Volumn 22, Issue 12, 2012, Pages 653-661

  Lai, Yen Ting ^a   King, Neil P ^b   Yeates, Todd O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Assembly; Biomaterials; Cages; Nanomaterials; Protein design; Symmetry

Indexed keywords

GOLD NANOPARTICLE; SINGLE WALLED NANOTUBE;

ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; OLIGOMERIZATION; PARTICLE SIZE; PH; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STABILITY; REVIEW; SYNTHETIC BIOLOGY;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; NANOTECHNOLOGY; NANOTUBES, PEPTIDE; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN MULTIMERIZATION; PROTEINS; SYNTHETIC BIOLOGY;

EID: 84869861857     PISSN: 09628924     EISSN: 18793088     Source Type: Journal    
DOI: 10.1016/j.tcb.2012.08.004     Document Type: Review

References (55)

1. Schwille P. Bottom-up synthetic biology: engineering in a tinkerer's world. Science 2011, 333:1252-1254.
2. Tan C., et al. Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 2009, 5:842-848.
3. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
4. Zhang S.G., et al. Design of nanostructured biological materials through self-assembly of peptides and proteins. Curr. Opin. Chem. Biol. 2002, 6:865-871.
5. Yeates T.O., Padilla J.E. Designing supramolecular protein assemblies. Curr. Opin. Struct. Biol. 2002, 12:464-470.
6. Zhang S.G. Fabrication of novel biomaterials through molecular self-assembly. Nat. Biotechnol. 2003, 21:1171-1178.
7. Petka W.A., et al. Reversible hydrogels from self-assembling artificial proteins. Science 1998, 281:389-392.
8. Ogihara N.L., et al. Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:1404-1409.
9. Woolfson D.N. Building fibrous biomaterials from alpha-helical and collagen-like coiled-coil peptides. Biopolymers 2010, 94:118-127.
10. Ghadiri M.R., et al. Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 1993, 366:324-327.
11. Ryadnov M.G., Woolfson D.N. Introducing branches into a self-assembling peptide fiber. Angew. Chem. Int. Ed. Engl. 2003, 42:3021-3023.
12. Levy E.D., et al. Assembly reflects evolution of protein complexes. Nature 2008, 453:U1262-U1266.
13. Goodsell D.S., Olson A.J. Structural symmetry and protein function. Annu. Rev. Biophys. Biomol. Struct. 2000, 29:105-153.
14. Crick F.H.C., Watson J.D. Structure of small viruses. Nature 1956, 177:473-475.
15. Wukovitz S.W., Yeates T.O. why protein crystals favor some space-groups over others. Nat. Struct. Biol. 1995, 2:1062-1067.
16. Padilla J.E., et al. Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:2217-2221.
17. Plevka P., et al. Crystal structure of human enterovirus 71. Science 2012, 336:1274.
18. Lai Y.T., et al. Structure of a 16-nm cage designed by using protein oligomers. Science 2012, 336:1129.
19. Ringler P., Schulz G.E. Self-assembly of proteins into designed networks. Science 2003, 302:106-109.
20. Usui K., et al. Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks. Protein Sci. 2009, 18:960-969.
21. Raman S., et al. Structure-based design of peptides that self-assemble into regular polyhedral nanoparticles. Nanomedicine 2006, 2:95-102.
22. Sinclair J.C., et al. Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat. Nanotechnol. 2011, 6:558-562.
23. Leaver-Fay A., et al. Rosetta3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011, 487:545-574.
24. Fleishman S.J., et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 2011, 332:816-821.
25. Huang P.S., et al. A de novo designed protein-protein interface. Protein Sci. 2007, 16:2770-2774.
26. Grueninger D., et al. Designed protein-protein association. Science 2008, 319:206-209.
27. Radford R.J., Tezcan F.A. A superprotein triangle driven by nickel(II) coordination: exploiting non-natural metal ligands in protein self-assembly. J. Am. Chem. Soc. 2009, 131:9136-9137.
28. Salgado E.N., et al. Metal templated design of protein interfaces. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:1827-1832.
29. Der B.S., et al. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J. Am. Chem. Soc. 2012, 134:375-385.
30. Salgado E.N., et al. Metal-directed protein self-assembly. Acc. Chem. Res. 2010, 43:661-672.
31. Stranges P.B., et al. Computational design of a symmetric homodimer using beta-strand assembly. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:20562-20567.
32. Zaccai N.R., et al. A de novo peptide hexamer with a mutable channel. Nat. Chem. Biol. 2011, 7:935-941.
33. Korendovych I.V., et al. De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex. J. Am. Chem. Soc. 2010, 132:15516-15518.
34. King N.P., et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 2012, 336:1171-1174.
35. Brodin J.D., et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat. Chem. 2012, 4:375-382.
36. Lanci C.J., et al. Computational design of a protein crystal. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:7304-7309.
37. Andre I., et al. Prediction of the structure of symmetrical protein assemblies. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:17656-17661.
38. Wang C., et al. Protein-protein docking with backbone flexibility. J. Mol. Biol. 2007, 373:503-519.
39. Carlson J.C.T., et al. Chemically controlled self-assembly of protein nanorings. J. Am. Chem. Soc. 2006, 128:7630-7638.
40. Fegan A., et al. Chemically controlled protein assembly: techniques and applications. Chem. Rev. 2010, 110:3315-3336.
41. Grigoryan G., et al. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 2011, 332:1071-1076.
42. Tsai C.J., et al. Principles of nanostructure design with protein building blocks. Proteins 2007, 68:1-12.
43. Worsdorfer B., et al. Directed evolution of a protein container. Science 2011, 331:589-592.
44. Woolfson D.N., Mahmoud Z.N. More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials. Chem. Soc. Rev. 2010, 39:3464-3479.
45. Howorka S. Rationally engineering natural protein assemblies in nanobiotechnology. Curr. Opin. Biotechnol. 2011, 22:485-491.
46. Tschiggerl H., et al. Exploitation of the S-layer self-assembly system for site directed immobilization of enzymes demonstrated for an extremophilic laminarinase from Pyrococcus furiosus. J. Biotechnol. 2008, 133:403-411.
47. Minten I.J., et al. Controlled encapsulation of multiple proteins in virus capsids. J. Am. Chem. Soc. 2009, 131:17771-17773.
48. Tong G.J., et al. Viral capsid dna aptamer conjugates as multivalent cell-targeting vehicles. J. Am. Chem. Soc. 2009, 131:11174-11178.
49. Han M., et al. Targeted vault nanoparticles engineered with an endosomolytic peptide deliver biomolecules to the cytoplasm. ACS Nano 2011, 5:6128-6137.
50. Smith M.L., et al. Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications. Virology 2006, 348:475-488.
51. Ilk N., et al. S-layer fusion proteins - construction principles and applications. Curr. Opin. Biotechnol. 2011, 22:824-831.
52. Delebecque C.J., et al. Organization of intracellular reactions with rationally designed RNA assemblies. Science 2011, 333:470-474.
53. Dueber J.E., et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 2009, 27:753-759.
54. de la Rica R., Matsui H. Applications of peptide and protein-based materials in bionanotechnology. Chem. Soc. Rev. 2010, 39:3499-3509.
55. Yeates T.O. Nanobiotechnology: protein arrays made to order. Nat. Nanotechnol. 2011, 6:541-542.