Self-assembling Symmetric Protein Materials
Jennifer E. Padilla
- [email protected]
- +1-310-825-8901 | Fax: +1-310-206-3914
University of California, Los Angeles, Department of Chemistry and Biochemistry, 212 Boyer Hall, 611 Charles E. Young Dr. South, Los Angeles, CA, USA, 90095-1569
Search for more papers by this authorTianwei Yu
- [email protected]
- +1-310-825-8901 | Fax: +1-310-206-3914
University of California, Los Angeles, Department of Chemistry and Biochemistry, 212 Boyer Hall, 611 Charles E. Young Dr. South, Los Angeles, CA, USA, 90095-1569
Search for more papers by this authorJennifer E. Padilla
- [email protected]
- +1-310-825-8901 | Fax: +1-310-206-3914
University of California, Los Angeles, Department of Chemistry and Biochemistry, 212 Boyer Hall, 611 Charles E. Young Dr. South, Los Angeles, CA, USA, 90095-1569
Search for more papers by this authorTianwei Yu
- [email protected]
- +1-310-825-8901 | Fax: +1-310-206-3914
University of California, Los Angeles, Department of Chemistry and Biochemistry, 212 Boyer Hall, 611 Charles E. Young Dr. South, Los Angeles, CA, USA, 90095-1569
Search for more papers by this authorAbstract
- Introduction to Self-assembly
- Protein Properties that Promote Self-assembly
- Historical Outline
- Chemical Structures
- Symmetry
- Symmetry Elements
- Symmetric Contacts in Proteins
- Multiple Symmetry Elements
- Naturally Occurring Symmetric Complexes
- Protein Oligomers
- Icosahedral Viral Capsids
- Clathrin
- Filaments
- S-layers
- Protein Crystals
- Designed Self-assembling Protein Complexes
- Coiled-coil Extensions
- Domain Swapping
- Symmetric Construction
- Polyvalency
- Observing Protein Assemblies
- Transmission Electron Microscopy
- Cryoelectron Microscopy
- Atomic Force Microscopy
- X-ray and Electron Diffraction
- Applications
- Patents
- Outlook and Perspectives
References
- Adams, M. J., Blundell, T. L., Dodson, E. J., Dodson, G. G., Yijayan, M., Baker, E. N., Harding, M. M., Hodgkin, D. C., Rimmer, B., Sheat, S. (1969) Structure of rhombohedral 2 zinc insulin crystals, Nature 224, 491–495.
- Amos, L. A., Klug, A. (1974) Arrangement of subunits in flagellar microtubules, J. Cell Sci. 14, 523–549.
- Anderson, W. F., Ohlendorf, D. H., Takeda, Y., Matthews, B. W. (1981) Structure of the cro repressor from bacteriophage lambda and its interaction with DNA, Nature 290, 754– 758.
- Bennett, M. J., Choe, S., Eisenberg, D. (1994) Domain swapping – entangling alliances between proteins, Proc. Natl. Acad. Sci. USA 91, 3127–3131.
- Boisen, M. B., Gibbs, G. V. (1985) Mathematical crystallography: an introduction to the mathematical foundations of crystallography, Washington, DC: Mineralogical Society of America.
- Boisvert, D. C., Wang, J. M., Otwinowski, Z., Horwich, A. L., Sigler, P. B. (1996) The 2.4 angstrom crystal structure of the bacterial chaperonin GroEL complexed with ATP gamma S, Nature Struct. Biol. 3, 170–177.
- Caspar, D. L. D., Klug, A. (1962) Physical principles in the construction of regular viruses, Cold Spring Harbor Symp. Quant. Biol. 27, 1–24.
- Creighton, T. E. (1993) Proteins: structures and molecular properties, New York: W. H. Freeman.
- Crick, F. H. C., Watson, J. D. (1956) Structure of small viruses, Nature 177, 473–476.
- Crowfoot, D. (1935) X-ray single crystal photographs of insulin, Nature 135, 591–592.
-
Dotan, N.,
Arad, D.,
Frolow, F.,
Freeman, A.
(1999)
Self-assembly of a tetrahedral lectin into predesigned diamondlike protein crystals,
Angew. Chemie Int. Ed. 38,
2363–2366.
10.1002/(SICI)1521-3773(19990816)38:16<2363::AID-ANIE2363>3.0.CO;2-D CAS Web of Science® Google Scholar
- Douglas, T., et al. (2002) Self-assembling Protein Cage-Systems and Applications in Nanotechnology, in: Biopolymers ( A. Steinbüchel, Ed.), Weinheim, Germany: Wiley-VCH, Vol. 8.
- Douglas, T., Young, M. (1998) Host-guest encapsulation of materials by assembled virus protein cages, Nature 393, 152–155.
- Downing, K. H. (2000) Structural basis for the interaction of tubulin with proteins and drugs that affect microtubule dynamics, Annu. Rev. Cell Dev. Biol. 16, 89–111.
- Eakins, F., Al-Khayat, H. A., Kensler, R. W., Morris, E. P., Squire, J. M. (2002) 3D structure of fish muscle myosin filaments, J. Struct. Biol. 137, 154–163.
- Engel, A., Lyubchenko, Y., Muller, D. (1999) Atomic force microscopy: a powerful tool to observe biomolecules at work, Trends Cell Biol. 9, 77–80.
- Fernandez-Lopez, S., Kim, H. S., Choi, E. C., Delgado, M., Granja, J. R., Khasanov, A., Kraehenbuehl, K., Long, G., Weinberger, D. A., Wilcoxen, K. M., Ghadiri, M. R. (2001) Antibacterial agents based on the cyclic d,l-alpha-peptide architecture, Nature 412, 452–455.
- Franklin, R. E. (1955) Structure of tobacco mosaic virus, Nature 175, 379–381.
- Geeves, M. A., Holmes, K. C. (1999) Structural mechanism of muscle contraction, Annu. Rev. Biochem. 68, 687–728.
- Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E., Khazanovich, N. (1993) Self-assembling organic nanotubes based on a cyclic peptide architecture, Nature 366, 324–327.
- Goodsell, D. S., Olson, A. J. (2000) Structural symmetry and protein function, Annu. Rev. Biophys. Biomol. Struct. 29, 105–153.
- Hanson, J., Huxley, H. E. (1953) Structural basis of the cross-striations in muscle, Nature 172, 530–532.
- Hanson, J., Lowy, J. (1963) The structure of F-actin and of actin filaments isolated from muscle, J. Mol. Biol. 6, 46–60.
- Harris, R. E. (1991) Electron Microscopy in Biology, a Practical Approach, Oxford University Press, New York.
- Hartgerink, J. D., Beniash, E., Stupp, S. I. (2001) Self-assembly and mineralization of peptide-amphiphile nanofibers, Science 294, 1684–1688.
- Hecht, H. J., Sobek, H., Haag, T., Pfeifer, O., Vanpee, K. H. (1994) The metal-ion free oxidoreductase from Streptomyces aureofaciens has an alpha/beta hydrolase fold, Nature Struct. Biol. 1, 532–537.
- Holmes, T. C. (2002) Novel peptide-based biomaterial scaffolds for tissue engineering, Trends Biotechnol. 20, 16–21.
- Holmes, T. C., de Lacalle, S., Su, X., Liu, G., Rich, A., Zhang, S. (2000) Extensive neurite outgrowth and active synapse formation on self-assembling peptide scaffolds, Proc. Natl. Acad. Sci. USA 97, 6728–6733.
- Hornung, C. P. (1959) Handbook of Designs and Devices, New York: Dover Publications, Inc..
- Houwink, A. L. (1953) A macromolecular mono-layer in the cell wall of Spirillum spec., Biochim. Biophys. Acta 10, 360–366.
- Kanaseki, T., Kadota, K. (1969) The “Vesicle in a basket”, J. Cell Biol. 42, 202–220.
- Kim, C. A., Phillips, M. L., Kim, W., Gingery, M., Tran, H. H., Robinson, M. A., Faham, S., Bowie, J. U. (2001) Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression, EMBO J. 20, 4173–4182.
- Kim, C. A., Gingery, M., Pilpa, R. M., Bowie, J. U. (2002) The SAM domain of polyhomeotic forms a helical polymer, Nature Struct. Biol. 9, 453–457.
- Kim, K. K., Kim, R., Kim, S. H. (1998) Crystal structure of a small heat-shock protein, Nature 394, 595–599.
- Klug, A. (1999) The tobacco mosaic virus particle: structure and assembly, Philos. Trans. R. Soc. Lond. B Biol. Sci. 354, 531–535.
- Klug, A., Caspar, D. L. D. (1960) The structure of small viruses, in: Advances in Virus Research, Volume 7 (Smith, K. M., Lauffer, M. A., Eds.), New York, London: Academic Press Inc., 225.
- Kraulis, P. J. (1991) Molscript – a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946–950.
- Liu, Y., Eisenberg, D. (2002) 3D domain swapping: as domains continue to swap, Protein Sci. 11, 1285–1299.
- Merritt, E. A., Bacon, D. J. (1997) Raster3D: photorealistic molecular graphics, Macromol. Crystallogr. Pt B 277, 505–524.
- Ogihara, N. L., Ghirlanda, G., Bryson, J. W., Gingery, M., DeGrado, W. F., Eisenberg, D. (2001) Design of three-dimensional domain-swapped dimers and fibrous oligomers, Proc. Natl. Acad. Sci. USA 98, 1404–1409.
- Orlova, A., Galkin, V. E., VanLoock, M. S., Kim, E., Shvetsov, A., Reisler, E., Egelman, E. H. (2001) Probing the structure of F-actin: cross-links constrain atomic models and modify actin dynamics, J. Mol. Biol. 312, 95–106.
- Padilla, J. E., Colovos, C., Yeates, T. O. (2001) Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments, Proc. Natl. Acad. Sci. USA 98, 2217–2221.
- Pandya, M. J., Spooner, G. M., Sunde, M., Thorpe, J. R., Rodger, A., Woolfson, D. N. (2000) Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis, Biochemistry 39, 8728–8734.
- Parry, D. A., Steinert, P. M. (1999) Intermediate filaments: molecular architecture, assembly, dynamics and polymorphism, Q. Rev. Biophys. 32, 99–187.
- Potekhin, S. A., Melnik, T. N., Popov, V., Lanina, N. F., Vazina, A. A., Rigler, P., Verdini, A. S., Corradin, G., Kajava, A. V. (2001) De novo design of fibrils made of short alpha-helical coiled coil peptides, Chem. Biol. 8, 1025–1032.
- Rossmann, M. G., Arnold, E., International Union of Crystallography (2001) International tables for crystallography, Volume F. Crystallography of biological macromolecules, Dordrecht, London: Kluwer Academic, published for the International Union of Crystallography.
- Scheuring, S., Stahlberg, H., Chami, M., Houssin, C., Rigaud, J. L., Engel, A. (2002) Charting and unzipping the surface layer of Corynebacterium glutamicum with the atomic force microscope, Mol. Microbiol. 44, 675–684.
- Slautterback, D. B. (1963) Cytoplasmic microtubules, J. Cell Biol. 18, 367–388.
- Sleytr, U.B. (2002) Self-assembly Protein Systems: Microbial S-layers, in: Biopolymers, Vol. 7 (Steinbüchel, A., Ed.) Weinheim: Wiley-VCH, pp. 285–338.
- Sleytr, U. B. (1978) Regular arrays of macromolecules on bacterial cell walls: structure, chemistry, assembly, and function, Int. Rev. Cytol. 53, 1–64.
- Sleytr, U. B., Beveridge, T. J. (1999) Bacterial S-layers, Trends Microbiol. 7, 253–260.
- Sleytr, U. B., Sara, M., Pum, D., Schuster, B. (2001) Characterization and use of crystalline bacterial cell surface layers, Prog. Surface Sci. 68, 231–278.
- Smith, C. J., Grigorieff, N., Pearse, B. M. (1998) Clathrin coats at 21 Å resolution: a cellular assembly designed to recycle multiple membrane receptors, EMBO J. 17, 4943–4953.
- Squire, J. M. (1971) General model for the structure of all myosin-containing filaments, Nature 233, 457–462.
-
Stewart, P. L.,
Cary, R. B.,
Peterson, S. R.,
Chiu, C. Y.
(2000)
Digitally collected cryo-electron micrographs for single particle reconstruction,
Microsc. Res. Technique 49,
224–232.
10.1002/(SICI)1097-0029(20000501)49:3<224::AID-JEMT2>3.0.CO;2-0 CAS PubMed Web of Science® Google Scholar
- Strauss, J. H., Strauss, E. G. (2002) Viruses and Human Disease, San Diego: Academic Press.
- van Heel, M., Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M., Patwardhan, A. (2000) Single-particle electron cryo-microscopy: towards atomic resolution, Q. Rev. Biophys. 33, 307–369.
- Villeret, V., Clantin, B., Tricot, C., Legrain, C., Roovers, M., Stalon, V., Glansdorff, N., VanBeeumen, J. (1998) The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures, Proc. Natl. Acad. Sci. USA 95, 2801–2806.
- Wade, R. H., Meurer-Grob, P., Metoz, F., Arnal, I. (1998) Organisation and structure of microtubules and microtubule-motor protein complexes, Eur. Biophys. J. 27, 446–454.
- Watt, J. M. (1985) The Principles and Practice of Electron Microscopy, Cambridge: Cambridge University Press.
- Wilson, H. R. (1966) Diffraction of X-rays by Proteins, Nucleic Acids and Viruses, New York: St. Martin's Press.
- Wukovitz, S. W., Yeates, T. O. (1995) Why protein crystals favour some space-groups over others, Nature Struct. Biol. 2, 1062–1067.
- Xu, Z. H., Horwich, A. L., Sigler, P. B. (1997) The crystal structure of the asymmetric GroEL-GroES-(ADP)(7) chaperonin complex, Nature 388, 741–750.
- Yeates, T. O., Padilla, J. E. (2002) Designing supramolecular protein assemblies, Curr. Opin. Struct. Biol. 12, 464–470.
Biopolymers Online: Biology • Chemistry • Biotechnology • Applications
Browse other articles of this reference work: