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Volumn 9, Issue 4, 2017, Pages 353-360

Computational design of self-assembling cyclic protein homo-oligomers

Author keywords

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Indexed keywords

PROTEIN;

EID: 85016278795     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.2673     Document Type: Article
Times cited : (106)

References (35)
  • 1
    • 22944475303 scopus 로고    scopus 로고
    • Protein oligomerization: How and why
    • Ali, M. H. & Imperiali, B. Protein oligomerization: how and why. Bioorg. Med. Chem. 13, 5013-5020 (2005).
    • (2005) Bioorg. Med. Chem , vol.13 , pp. 5013-5020
    • Ali, M.H.1    Imperiali, B.2
  • 3
    • 84896733458 scopus 로고    scopus 로고
    • Evolutionary physicochemical, and functional mechanisms of protein homooligomerization
    • Nishi, H., Hashimoto, K., Madej, T. & Panchenko, A. R. Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. Prog. Mol. Biol. Transl. 117, 3-24 (2013).
    • (2013) Prog. Mol. Biol. Transl , vol.117 , pp. 3-24
    • Nishi, H.1    Hashimoto, K.2    Madej, T.3    Panchenko, A.R.4
  • 4
    • 84866511067 scopus 로고    scopus 로고
    • A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology
    • Fletcher, J. M. et al. A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology. ACS Synth. Biol. 1, 240-250 (2012).
    • (2012) ACS Synth. Biol , vol.1 , pp. 240-250
    • Fletcher, J.M.1
  • 5
    • 84955562942 scopus 로고    scopus 로고
    • De novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
    • Smock, R. G., Yadid, I., Dym, O., Clarke, J. & Tawfik, D. S. De novo evolutionary emergence of a symmetrical protein is shaped by folding constraints. Cell 164, 476-486 (2016).
    • (2016) Cell , vol.164 , pp. 476-486
    • Smock, R.G.1    Yadid, I.2    Dym, O.3    Clarke, J.4    Tawfik, D.S.5
  • 6
    • 84908072118 scopus 로고    scopus 로고
    • Computational design of a self-assembling symmetrical β-propeller protein
    • Voet, A. R. D. et al. Computational design of a self-assembling symmetrical β-propeller protein. Proc. Natl Acad. Sci. USA 111, 15102-15107 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 15102-15107
    • Voet, A.R.D.1
  • 8
    • 84855685292 scopus 로고    scopus 로고
    • Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer
    • Der, B. S. et al. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J. Am. Chem. Soc. 134, 375-385 (2012).
    • (2012) J. Am. Chem. Soc , vol.134 , pp. 375-385
    • Der, B.S.1
  • 9
    • 84940548990 scopus 로고    scopus 로고
    • Computational design and experimental verification of a symmetric protein homodimer
    • 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 112, 10714-10719 (2015).
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. 10714-10719
    • Mou, Y.1    Huang, P.S.2    Hsu, F.C.3    Huang, S.J.4    Mayo, S.L.5
  • 10
    • 85016316759 scopus 로고    scopus 로고
    • De novo design of an ideal TIM-barrel scaffold
    • Huang, P. S. et al. De novo design of an ideal TIM-barrel scaffold. Protein Sci. 24, 186-186 (2015).
    • (2015) Protein Sci , vol.24 , pp. 186
    • Huang, P.S.1
  • 11
    • 84943415110 scopus 로고    scopus 로고
    • Control over overall shape and size in de novo designed proteins
    • Lin, Y. -R. et al. Control over overall shape and size in de novo designed proteins. Proc. Natl Acad. Sci. USA 112, E5478-E5485 (2015).
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. E5478-E5485
    • Lin, Y.-R.1
  • 12
    • 84868611622 scopus 로고    scopus 로고
    • Principles for designing ideal protein structures
    • Koga, N. et al. Principles for designing ideal protein structures. Nature 491, 222-227 (2012).
    • (2012) Nature , vol.491 , pp. 222-227
    • Koga, N.1
  • 13
    • 84920768290 scopus 로고    scopus 로고
    • A general computational approach for repeat protein design
    • Parmeggiani, F. et al. A general computational approach for repeat protein design. J. Mol. Biol. 427, 563-575 (2015).
    • (2015) J. Mol. Biol , vol.427 , pp. 563-575
    • Parmeggiani, F.1
  • 14
    • 84908235298 scopus 로고    scopus 로고
    • High thermodynamic stability of parametrically designed helical bundles
    • Huang, P. -S. et al. High thermodynamic stability of parametrically designed helical bundles. Science 346, 481-485 (2014).
    • (2014) Science , vol.346 , pp. 481-485
    • Huang, P.-S.1
  • 15
    • 84951320596 scopus 로고    scopus 로고
    • Exploring the repeat protein universe through computational protein design
    • Brunette, T. J. et al. Exploring the repeat protein universe through computational protein design. Nature 528 580-584 (2015).
    • (2015) Nature , vol.528 , pp. 580-584
    • Brunette, T.J.1
  • 16
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • Main, E. R. G., Xiong, Y., Cocco, M. J., D'Andrea, L. & Regan, L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 11, 497-508 (2003).
    • (2003) Structure , vol.11 , pp. 497-508
    • Main, E.R.G.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5
  • 17
    • 67649852558 scopus 로고    scopus 로고
    • Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins
    • Pechmann, S., Levy, E. D., Tartaglia, G. G. & Vendruscolo, M. Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins. Proc. Natl Acad. Sci. USA 106, 10159-10164 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 10159-10164
    • Pechmann, S.1    Levy, E.D.2    Tartaglia, G.G.3    Vendruscolo, M.4
  • 18
    • 84896689230 scopus 로고    scopus 로고
    • Structural evolutionary, and assembly principles of protein oligomerization
    • Levy, E. D. & Teichmann, S. Structural, evolutionary, and assembly principles of protein oligomerization. Prog. Mol. Biol. Transl. 117, 25-51 (2013).
    • (2013) Prog. Mol. Biol. Transl , vol.117 , pp. 25-51
    • Levy, E.D.1    Teichmann, S.2
  • 19
    • 0242299201 scopus 로고    scopus 로고
    • Dissecting subunit interfaces in homodimeric proteins
    • Bahadur, R. P., Chakrabarti, P., Rodier, F. & Janin, J. Dissecting subunit interfaces in homodimeric proteins. Proteins 53, 708-719 (2003).
    • (2003) Proteins , vol.53 , pp. 708-719
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 20
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur, R.P., Chakrabarti, P., Rodier, F. & Janin, J. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol. 336, 943-955 (2004).
    • (2004) J. Mol. Biol , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 21
    • 52649130704 scopus 로고    scopus 로고
    • Protein-protein interaction and quaternary structure
    • Janin, J., Bahadur, R. P. & Chakrabarti, P. Protein-protein interaction and quaternary structure. Q. Rev. Biophys. 41, 133-180 (2008).
    • (2008) Q. Rev. Biophys , vol.41 , pp. 133-180
    • Janin, J.1    Bahadur, R.P.2    Chakrabarti, P.3
  • 22
    • 78650905964 scopus 로고    scopus 로고
    • (eds Johnson, M. L. & Brand, L.),Elsevier
    • Leaver-Fay, A. et al. in Computer Methods, Part C Vol. 487 (eds Johnson, M. L. & Brand, L.) 545-574 (Elsevier, 2011).
    • (2011) Computer Methods, Part C , vol.487 , pp. 545-574
    • Leaver-Fay, A.1
  • 23
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen, R. & Weng, Z. P. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47, 281-294 (2002).
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.P.2
  • 24
    • 17444385658 scopus 로고    scopus 로고
    • M-ZDOCK: A grid-based approach for Cn symmetric multimer docking
    • Pierce, B., Tong, W.W. &Weng, Z. P. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics 21, 1472-1478 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 1472-1478
    • Pierce, B.1    Tong, W.W.2    Weng, Z.P.3
  • 26
    • 85016273507 scopus 로고    scopus 로고
    • Protein-protein docking predictions with RosettaDock
    • Gray, J. J. & Baker, D. Protein-protein docking predictions with RosettaDock. Biophys. J. 86, 306A-306A (2004).
    • (2004) Biophys. J , vol.86 , pp. 306A-306A
    • Gray, J.J.1    Baker, D.2
  • 27
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray, J. J. et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331, 281-299 (2003).
    • (2003) J. Mol. Biol , vol.331 , pp. 281-299
    • Gray, J.J.1
  • 28
    • 77952816540 scopus 로고    scopus 로고
    • Lysozyme-stabilized gold fluorescent cluster: Synthesis and application as Hg2+ sensor
    • Wei, H. et al. Lysozyme-stabilized gold fluorescent cluster: synthesis and application as Hg2+ sensor. Analyst 135, 1406-1410 (2010).
    • (2010) Analyst , vol.135 , pp. 1406-1410
    • Wei, H.1
  • 29
    • 38049051121 scopus 로고    scopus 로고
    • OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
    • Lu, M., Dousis, A. D. & Ma, J. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J. Mol. Biol. 376, 288-301 (2008).
    • (2008) J. Mol. Biol , vol.376 , pp. 288-301
    • Lu, M.1    Dousis, A.D.2    Ma, J.3
  • 31
    • 84864577143 scopus 로고    scopus 로고
    • Predictive Bcl-2 family binding models rooted in experiment or structure
    • DeBartolo, J., Dutta, S., Reich, L. & Keating, A. E. Predictive Bcl-2 family binding models rooted in experiment or structure. J. Mol. Biol. 422, 124-144 (2012).
    • (2012) J. Mol. Biol , vol.422 , pp. 124-144
    • DeBartolo, J.1    Dutta, S.2    Reich, L.3    Keating, A.E.4
  • 32
    • 79959615159 scopus 로고    scopus 로고
    • RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite
    • Fleishman, S. J. et al. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One 6, e20161 (2011).
    • (2011) PLoS One , vol.6 , pp. e20161
    • Fleishman, S.J.1
  • 33
    • 77954280480 scopus 로고    scopus 로고
    • FoXS: A web server for rapid computation and fitting of SAXS profiles
    • Schneidman-Duhovny, D., Hammel, M. & Sali, A. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 38, W540-W544 (2010).
    • (2010) Nucleic Acids Res , vol.38 , pp. W540-W544
    • Schneidman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 34
    • 84966333727 scopus 로고    scopus 로고
    • De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
    • Boyken, S. E. et al. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 352, 680-687 (2016).
    • (2016) Science , vol.352 , pp. 680-687
    • Boyken, S.E.1
  • 35
    • 84926289262 scopus 로고    scopus 로고
    • Control of repeat-protein curvature by computational protein design
    • Park, K. et al. Control of repeat-protein curvature by computational protein design. Nat. Struct. Mol. Biol. 22, 167-174 (2015).
    • (2015) Nat. Struct. Mol. Biol , vol.22 , pp. 167-174
    • Park, K.1


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