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Volumn 22, Issue 2, 2015, Pages 167-174

Control of repeat-protein curvature by computational protein design

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE RICH REPEAT PROTEIN; MOLECULAR SCAFFOLD; PROTEIN; REPEAT PROTEIN SCAFFOLD; UNCLASSIFIED DRUG; LEUCINE-RICH REPEAT PROTEINS;

EID: 84926289262     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2938     Document Type: Article
Times cited : (78)

References (46)
  • 1
    • 27144511241 scopus 로고    scopus 로고
    • Engineering novel binding proteins from nonimmunoglobulin domains
    • Binz, H.K., Amstutz, P. & Pluckthun, A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23, 1257-1268 (2005).
    • (2005) Nat. Biotechnol. , vol.23 , pp. 1257-1268
    • Binz, H.K.1    Amstutz, P.2    Pluckthun, A.3
  • 2
    • 34548522063 scopus 로고    scopus 로고
    • Alternative non-antibody scaffolds for molecular recognition
    • Skerra, A. Alternative non-antibody scaffolds for molecular recognition. Curr. Opin. Biotechnol. 18, 295-304 (2007).
    • (2007) Curr. Opin. Biotechnol. , vol.18 , pp. 295-304
    • Skerra, A.1
  • 3
    • 67649872364 scopus 로고    scopus 로고
    • Engineered protein scaffolds as next-generation antibody therapeutics
    • Gebauer, M. & Skerra, A. Engineered protein scaffolds as next-generation antibody therapeutics. Curr. Opin. Chem. Biol. 13, 245-255 (2009).
    • (2009) Curr. Opin. Chem. Biol. , vol.13 , pp. 245-255
    • Gebauer, M.1    Skerra, A.2
  • 4
    • 84881115632 scopus 로고    scopus 로고
    • Tandem-repeat proteins: Regularity plus modularity equals design-ability
    • Javadi, Y. & Itzhaki, L.S. Tandem-repeat proteins: regularity plus modularity equals design-ability. Curr. Opin. Struct. Biol. 23, 622-631 (2013).
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 622-631
    • Javadi, Y.1    Itzhaki, L.S.2
  • 5
    • 84877274659 scopus 로고    scopus 로고
    • Nanostructured functional films from engineered repeat proteins
    • Grove, T.Z., Regan, L. & Cortajarena, A.L. Nanostructured functional films from engineered repeat proteins. J. R. Soc. Interface 10, 20130051 (2013).
    • (2013) J. R. Soc. Interface , vol.10 , pp. 20130051
    • Grove, T.Z.1    Regan, L.2    Cortajarena, A.L.3
  • 6
    • 84871955080 scopus 로고    scopus 로고
    • Fibrous nanostructures from the self-assembly of designed repeat protein modules
    • Phillips, J.J., Millership, C. & Main, E.R. Fibrous nanostructures from the self-assembly of designed repeat protein modules. Angew. Chem. Int. Edn Engl. 51, 13132-13135 (2012).
    • (2012) Angew. Chem. Int. Edn Engl. , vol.51 , pp. 13132-13135
    • Phillips, J.J.1    Millership, C.2    Main, E.R.3
  • 7
    • 84877736928 scopus 로고    scopus 로고
    • Bioinspired self-assembled peptide nanofibers with thermostable multivalent α-helices
    • Han, S.H., Lee, M.K. & Lim, Y.B. Bioinspired self-assembled peptide nanofibers with thermostable multivalent α-helices. Biomacromolecules 14, 1594-1599 (2013).
    • (2013) Biomacromolecules , vol.14 , pp. 1594-1599
    • Han, S.H.1    Lee, M.K.2    Lim, Y.B.3
  • 8
    • 0035692811 scopus 로고    scopus 로고
    • The leucine-rich repeat as a protein recognition motif
    • Kobe, B. & Kajava, A.V. The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct. Biol. 11, 725-732 (2001).
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 725-732
    • Kobe, B.1    Kajava, A.V.2
  • 10
    • 34548222514 scopus 로고    scopus 로고
    • Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran
    • Kim, H.M. et al. Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. Cell 130, 906-917 (2007).
    • (2007) Cell , vol.130 , pp. 906-917
    • Kim, H.M.1
  • 11
    • 84904169024 scopus 로고    scopus 로고
    • Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment
    • Parker, R., Mercedes-Camacho, A. & Grove, T.Z. Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment. Protein Sci. 23, 790-800 (2014).
    • (2014) Protein Sci. , vol.23 , pp. 790-800
    • Parker, R.1    Mercedes-Camacho, A.2    Grove, T.Z.3
  • 12
    • 84863229636 scopus 로고    scopus 로고
    • Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
    • Lee, S.C. et al. Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering. Proc. Natl. Acad. Sci. USA 109, 3299-3304 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 3299-3304
    • Lee, S.C.1
  • 13
    • 2342624119 scopus 로고    scopus 로고
    • High-affinity binders selected from designed ankyrin repeat protein libraries
    • Binz, H.K. et al. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22, 575-582 (2004).
    • (2004) Nat. Biotechnol. , vol.22 , pp. 575-582
    • Binz, H.K.1
  • 14
    • 0037468685 scopus 로고    scopus 로고
    • A novel strategy to design binding molecules harnessing the modular nature of repeat proteins
    • Forrer, P., Stumpp, M.T., Binz, H.K. & Pluckthun, A. A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett. 539, 2-6 (2003).
    • (2003) FEBS Lett. , vol.539 , pp. 2-6
    • Forrer, P.1    Stumpp, M.T.2    Binz, H.K.3    Pluckthun, A.4
  • 16
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • Main, E.R., 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.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5
  • 17
    • 84857198283 scopus 로고    scopus 로고
    • Modular recognition of nucleic acids by PUF, TALE and PPR proteins
    • Filipovska, A. & Rackham, O. Modular recognition of nucleic acids by PUF, TALE and PPR proteins. Mol. Biosyst. 8, 699-708 (2012).
    • (2012) Mol. Biosyst. , vol.8 , pp. 699-708
    • Filipovska, A.1    Rackham, O.2
  • 18
    • 84895035916 scopus 로고    scopus 로고
    • Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins
    • Reichen, C., Hansen, S. & Pluckthun, A. Modular peptide binding: from a comparison of natural binders to designed armadillo repeat proteins. J. Struct. Biol. 185, 147-162 (2014).
    • (2014) J. Struct. Biol. , vol.185 , pp. 147-162
    • Reichen, C.1    Hansen, S.2    Pluckthun, A.3
  • 19
    • 84857029597 scopus 로고    scopus 로고
    • The crystal structure of TAL effector PthXo1 bound to its DNA target
    • Mak, A.N., Bradley, P., Cernadas, R.A., Bogdanove, A.J. & Stoddard, B.L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science 335, 716-719 (2012).
    • (2012) Science , vol.335 , pp. 716-719
    • Mak, A.N.1    Bradley, P.2    Cernadas, R.A.3    Bogdanove, A.J.4    Stoddard, B.L.5
  • 20
    • 84903163054 scopus 로고    scopus 로고
    • Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain
    • Ryou, J.H., Park, K., Lee, J.J., Kim, D. & Kim, H.S. Soluble expression of human glycoprotein Ibα in Escherichia coli through replacement of the N-terminal capping domain. Protein Expr. Purif. 101, 21-27 (2014).
    • (2014) Protein Expr. Purif. , vol.101 , pp. 21-27
    • Ryou, J.H.1    Park, K.2    Lee, J.J.3    Kim, D.4    Kim, H.S.5
  • 21
    • 70350540674 scopus 로고    scopus 로고
    • Toll-like receptor 4 decoy, TOY, attenuates gram-negative bacterial sepsis
    • Jung, K. et al. Toll-like receptor 4 decoy, TOY, attenuates gram-negative bacterial sepsis. PLoS ONE 4, e7403 (2009).
    • (2009) PLoS One , vol.4 , pp. e7403
    • Jung, K.1
  • 22
    • 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. doi:10.1016/j.jmb.2014.11.005.
    • J. Mol. Biol.
    • Parmeggiani, F.1
  • 23
    • 80052334922 scopus 로고    scopus 로고
    • RosettaRemodel: A generalized framework for flexible backbone protein design
    • Huang, P.S. et al. RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS ONE 6, e24109 (2011).
    • (2011) PLoS One , vol.6 , pp. e24109
    • Huang, P.S.1
  • 24
    • 84885431817 scopus 로고    scopus 로고
    • High-resolution comparative modeling with RosettaCM
    • Song, Y. et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735-1742 (2013).
    • (2013) Structure , vol.21 , pp. 1735-1742
    • Song, Y.1
  • 25
    • 78650905964 scopus 로고    scopus 로고
    • ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
    • Leaver-Fay, A. et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545-574 (2011).
    • (2011) Methods Enzymol. , vol.487 , pp. 545-574
    • Leaver-Fay, A.1
  • 26
    • 58149463441 scopus 로고    scopus 로고
    • RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
    • Sheffler, W. & Baker, D. RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci. 18, 229-239 (2009).
    • (2009) Protein Sci. , vol.18 , pp. 229-239
    • Sheffler, W.1    Baker, D.2
  • 27
    • 84896575295 scopus 로고    scopus 로고
    • Recognition of lipopolysaccharide pattern by TLR4 complexes
    • Park, B.S. & Lee, J.O. Recognition of lipopolysaccharide pattern by TLR4 complexes. Exp. Mol. Med. 45, e66 (2013).
    • (2013) Exp. Mol. Med. , vol.45 , pp. e66
    • Park, B.S.1    Lee, J.O.2
  • 28
    • 85016370378 scopus 로고    scopus 로고
    • Leucine-rich repeat (LRR) domains containing intervening motifs in plants
    • Matsushima, N. & Miyashita, H. Leucine-rich repeat (LRR) domains containing intervening motifs in plants. Biomolecules 2, 288-311 (2012).
    • (2012) Biomolecules , vol.2 , pp. 288-311
    • Matsushima, N.1    Miyashita, H.2
  • 29
    • 60849092269 scopus 로고    scopus 로고
    • LRRML: A conformational database and an XML description of leucine-rich repeats (LRRs)
    • Wei, T. et al. LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). BMC Struct. Biol. 8, 47 (2008).
    • (2008) BMC Struct. Biol. , vol.8 , pp. 47
    • Wei, T.1
  • 30
    • 23344431978 scopus 로고    scopus 로고
    • The molecular structure of the Toll-like receptor 3 ligand-binding domain
    • Bell, J.K. et al. The molecular structure of the Toll-like receptor 3 ligand-binding domain. Proc. Natl. Acad. Sci. USA 102, 10976-10980 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 10976-10980
    • Bell, J.K.1
  • 31
    • 67349182481 scopus 로고    scopus 로고
    • The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex
    • Park, B.S. et al. The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature 458, 1191-1195 (2009).
    • (2009) Nature , vol.458 , pp. 1191-1195
    • Park, B.S.1
  • 32
    • 79959563138 scopus 로고    scopus 로고
    • Structural basis of steroid hormone perception by the receptor kinase BRI1
    • Hothorn, M. et al. Structural basis of steroid hormone perception by the receptor kinase BRI1. Nature 474, 467-471 (2011).
    • (2011) Nature , vol.474 , pp. 467-471
    • Hothorn, M.1
  • 33
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen, R. & Weng, Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 51, 397-408 (2003).
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 34
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb, H.A., Jackson, R.M. & Sternberg, M.J. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272, 106-120 (1997).
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 35
    • 0027772959 scopus 로고
    • Shape complementarity at protein/protein interfaces
    • Lawrence, M.C. & Colman, P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950 (1993).
    • (1993) J. Mol. Biol. , vol.234 , pp. 946-950
    • Lawrence, M.C.1    Colman, P.M.2
  • 36
  • 37
    • 79956017135 scopus 로고    scopus 로고
    • Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
    • Fleishman, S.J. et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332, 816-821 (2011).
    • (2011) Science , vol.332 , pp. 816-821
    • Fleishman, S.J.1
  • 38
    • 84883277095 scopus 로고    scopus 로고
    • Computational design of a protein-based enzyme inhibitor
    • Procko, E. et al. Computational design of a protein-based enzyme inhibitor. J. Mol. Biol. 425, 3563-3575 (2013).
    • (2013) J. Mol. Biol. , vol.425 , pp. 3563-3575
    • Procko, E.1
  • 39
    • 84875098026 scopus 로고    scopus 로고
    • Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2
    • Epa, V.C. et al. Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2. PLoS ONE 8, e59163 (2013).
    • (2013) PLoS One , vol.8 , pp. e59163
    • Epa, V.C.1
  • 40
    • 84903763186 scopus 로고    scopus 로고
    • A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer
    • Lee, J.J. et al. A high-affinity protein binder that blocks the IL-6/STAT3 signaling pathway effectively suppresses non-small cell lung cancer. Mol. Ther. 22, 1254-1265 (2014).
    • (2014) Mol. Ther. , vol.22 , pp. 1254-1265
    • Lee, J.J.1
  • 41
    • 84875671926 scopus 로고    scopus 로고
    • Pareto-optimal refinement method for protein design scaffolds
    • Nivón, L.G., Moretti, R. & Baker, D. A Pareto-optimal refinement method for protein design scaffolds. PLoS ONE 8, e59004 (2013).
    • (2013) PLoS One , vol.8 , pp. e59004
    • Nivón, L.G.1    Moretti, R.2    Baker, D.A.3
  • 42
    • 67349270900 scopus 로고    scopus 로고
    • Enzymatic assembly of DNA molecules up to several hundred kilobases
    • Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 343-345
    • Gibson, D.G.1
  • 43
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 44
    • 34447508216 scopus 로고    scopus 로고
    • Phaser crystallographic software
    • McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
    • (2007) J. Appl. Crystallogr. , vol.40 , pp. 658-674
    • McCoy, A.J.1
  • 46
    • 0013461295 scopus 로고    scopus 로고
    • Macromolecular TLS refinement in REFMAC at moderate resolutions
    • Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300-321 (2003).
    • (2003) Methods Enzymol. , vol.374 , pp. 300-321
    • Winn, M.D.1    Murshudov, G.N.2    Papiz, M.Z.3


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