Computational design of co-assembling protein-DNA nanowires

Nature

Volumn 525, Issue 7568, 2015, Pages 230-233

  Mou, Yun ^a   Yu, Jiun Yann ^b   Wannier, Timothy M ^b   Guo, Chin Lin ^c   Mayo, Stephen L ^a,b  

^a California Institute of Technology   (United States)

^b California Institute of Technology HHMI   (United States)

^c California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA A; DNA HYBRID; DOUBLE STRANDED DNA; EPITOPE; HOMODIMER; NANOMATERIAL; NANOWIRE; RNA; ENGRAIL PROTEIN, DROSOPHILA; HOMEODOMAIN PROTEIN; TRANSCRIPTION FACTOR;

CHEMICAL ANALYSIS; DESIGN METHOD; DNA; FLY; NANOPARTICLE; NANOTECHNOLOGY; NUCLEIC ACID; PEPTIDE; PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; BINDING SITE; BIOCOMPATIBILITY; CONJUGATION; CRYSTAL STRUCTURE; DATA BASE; DNA BINDING; DNA PROTEIN COMPLEX; DNA STRUCTURE; DROSOPHILA; DROSOPHILA MELANOGASTER; DRUG DELIVERY SYSTEM; FLUORESCENCE MICROSCOPY; FOURIER TRANSFORMATION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE MOTIF; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; STATIC ELECTRICITY; WILD TYPE; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CRYSTALLIZATION; DRUG DESIGN; GENETICS; METABOLISM; NANOTECHNOLOGY; PROTEIN MULTIMERIZATION;

BINDING SITES; COMPUTER SIMULATION; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA; DRUG DESIGN; HOMEODOMAIN PROTEINS; MICROSCOPY, ATOMIC FORCE; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; NANOTECHNOLOGY; NANOWIRES; PROTEIN MULTIMERIZATION; TRANSCRIPTION FACTORS;

EID: 84941243015     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14874     Document Type: Article

References (30)

1. Sarikaya, M., Tamerler, C., Jen, A. K. Y., Schulten, K., Baneyx, F. Molecular biomimetics: nanotechnology through biology. Nature Mater. 2, 577-585 (2003).
2. Chen, J.H.Seeman, N. C. Synthesis fromDNAof amoleculewiththe connectivity of a cube. Nature 350, 631-633 (1991).
3. Seeman, N. C. DNA in a material world. Nature 421, 427-431 (2003).
4. Rothemund, P.W.K. FoldingDNAto create nanoscale shapes and patterns. Nature 440, 297-302 (2006).
5. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414-418 (2009).
6. Zhang, S., Holmes, T., Lockshin, C., Rich, A. Spontaneous assembly of a selfcomplementary oligopeptide to forma stable macroscopic membrane. Proc. Natl Acad. Sci. USA 90, 3334-3338 (1993).
7. Zhang, S. Fabrication of novel biomaterials through molecular self-assembly. Nature Biotechnol. 21, 1171-1178 (2003).
8. Fletcher, J. M. et al. Self-assembling cages from coiled-coil peptide modules. Science 340, 595-599 (2013).
9. Brodin, J. D. et al. Metal-directed, chemically tunable assembly of one-, two-and three-dimensional crystalline protein arrays. Nature Chem. 4, 375-382 (2012).
10. Lai, Y. T., Cascio, D., Yeates, T. O. Structure of a 16-nm cage designed by using protein oligomers. Science 336, 1129 (2012).
11. King, N. P. et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171-1174 (2012).
12. Lanci, C. J. et al. Computational design of a protein crystal. Proc. Natl Acad. Sci. USA 109, 7304-7309 (2012).
13. King, N. P. et al. Accurate design of co-assembling multi-component protein nanomaterials. Nature 510, 103-108 (2014).
14. Huang, P. S. et al. High thermodynamic stability of parametrically designed helical bundles. Science 346, 481-485 (2014).
15. Thomson, A. R. et al. Computational design of water-soluble a-helical barrels. Science 346, 485-488 (2014).
16. Chang, M., Yang, C. S., Huang, D. M. Aptamer-conjugated DNA icosahedral nanoparticles as a carrier of doxorubicin for cancer therapy. ACS Nano 5, 6156-6163 (2011).
17. Amir, Y. et al. Universal computing byDNAorigami robots in a living animal. Nature Nanotechnol. 9, 353-357 (2014).
18. Sanchez, C., Julian, B., Belleville, P., Popall, M. Applications of hybrid organic-inorganic nanocomposites. J. Mater. Chem. 15, 3559-3592 (2005).
19. Grigoryan, G. et al. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 332, 1071-1076 (2011).
20. Niemeyer, C. M., Koehler, J., Wuerdemann, C. DNA-directed assembly of bienzymic complexes fromin vivo biotinylatedNAD(P)H:FMNoxidoreductase and luciferase. ChemBioChem 3, 242-245 (2002).
21. Sano, T.,Smith, C. L., Cantor, C. R. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 258, 120-122 (1992).
22. Wilner, O. I., Shimron, S., Weizmann, Y., Wang, Z. G., Willner, I. Self-assembly of enzymes on DNA scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires. Nano Lett. 9, 2040-2043 (2009).
23. Delebecque, C. J., Lindner, A. B., Silver, P. A., Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470-474 (2011).
24. Draganescu, A., Tullius, T. D. The DNA binding specificity of engrailed homeodomain. J. Mol. Biol. 276, 529-536 (1998).
25. Guerrero, L., Smart, O. S., Woolley, G. A., Allemann, R. K. Photocontrol of DNA binding specificity of a miniature engrailed homeodomain. J.Am. Chem. Soc. 127, 15624-15629 (2005).
26. Marshall, S. A., Morgan, C. S., Mayo, S. L. Electrostatics significantly affect the stability of designed homeodomain variants. J. Mol. Biol. 316, 189-199 (2002).
27. Shah, P. S. et al. Full-sequence computational design and solution structure of a thermostable protein variant. J. Mol. Biol. 372, 1-6 (2007).
28. Mou, Y., Huang, P.-S., Hsu, F.-C., Huang, S.-J., Mayo, S. L. Computational design and experimental verification of a symmetric protein homodimer. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1505072112 (2015).
29. Mou, Y., Huang, P.-S., Thomas, L. M., Mayo, S. L. Using molecular dynamics simulations as an aid in the prediction of domain swapping of computationally designed protein variants. J. Mol. Biol, 427, 2697-2706 (2015).
30. Whaley, S. R., English, D. S., Hu, E. L., Barbara, P. F., Belcher, A. M. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405, 665-668 (2000).