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Volumn 111, Issue 50, 2014, Pages 17875-17880

Computational design of a leucine-rich repeat protein with a predefined geometry

Author keywords

Binding scaffold; Buried cysteines; Computational protein design; Geometrical design; Rosetta

Indexed keywords

ANKYRIN; LEUCIN RICH REPEAT PROTEIN; LEUCINE; PROTEIN; RIBONUCLEASE INHIBITOR; UNCLASSIFIED DRUG; LEUCINE-RICH REPEAT PROTEINS; PROTEIN BINDING;

EID: 84918555133     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1413638111     Document Type: Article
Times cited : (49)

References (37)
  • 1
    • 80054856259 scopus 로고    scopus 로고
    • DARPins and other repeat protein scaffolds: Advances in engineering and applications
    • Boersma YL, Plückthun A (2011) DARPins and other repeat protein scaffolds: Advances in engineering and applications. Curr Opin Biotechnol 22(6):849-857.
    • (2011) Curr Opin Biotechnol , vol.22 , Issue.6 , pp. 849-857
    • Boersma, Y.L.1    Plückthun, A.2
  • 2
    • 0035692811 scopus 로고    scopus 로고
    • The leucine-rich repeat as a protein recognition motif
    • Kobe B, Kajava AV (2001) The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 11(6):725-732.
    • (2001) Curr Opin Struct Biol , vol.11 , Issue.6 , pp. 725-732
    • Kobe, B.1    Kajava, A.V.2
  • 3
    • 0344628648 scopus 로고    scopus 로고
    • TPR proteins: The versatile helix
    • D'Andrea LD, Regan L (2003) TPR proteins: The versatile helix. Trends Biochem Sci 28(12):655-662.
    • (2003) Trends Biochem Sci , vol.28 , Issue.12 , pp. 655-662
    • D'Andrea, L.D.1    Regan, L.2
  • 4
    • 33845934490 scopus 로고    scopus 로고
    • Ankyrin repeat: A unique motif mediating proteinprotein interactions
    • Li J, Mahajan A, Tsai M-D (2006) Ankyrin repeat: A unique motif mediating proteinprotein interactions. Biochemistry 45(51):15168-15178.
    • (2006) Biochemistry , vol.45 , Issue.51 , pp. 15168-15178
    • Li, J.1    Mahajan, A.2    Tsai, M.-D.3
  • 5
    • 77649148783 scopus 로고    scopus 로고
    • Functional diversity of ankyrin repeats in microbial proteins
    • Al-Khodor S, Price CT, Kalia A, Abu Kwaik Y (2010) Functional diversity of ankyrin repeats in microbial proteins. Trends Microbiol 18(3):132-139.
    • (2010) Trends Microbiol , vol.18 , Issue.3 , pp. 132-139
    • Al-Khodor, S.1    Price, C.T.2    Kalia, A.3    Abu Kwaik, Y.4
  • 6
    • 84865174088 scopus 로고    scopus 로고
    • Tandem repeats in proteins: From sequence to structure
    • Kajava AV (2012) Tandem repeats in proteins: From sequence to structure. J Struct Biol 179(3):279-288.
    • (2012) J Struct Biol , vol.179 , Issue.3 , pp. 279-288
    • Kajava, A.V.1
  • 7
    • 84884635701 scopus 로고    scopus 로고
    • Repeat protein engineering: Creating functional nanostructures/biomaterials from modular building blocks
    • Main ERG, Phillips JJ, Millership C (2013) Repeat protein engineering: Creating functional nanostructures/biomaterials from modular building blocks. Biochem Soc Trans 41(5):1152-1158.
    • (2013) Biochem Soc Trans , vol.41 , Issue.5 , pp. 1152-1158
    • Main, E.R.G.1    Phillips, J.J.2    Millership, C.3
  • 8
    • 0037468685 scopus 로고    scopus 로고
    • A novel strategy to design binding molecules harnessing the modular nature of repeat proteins
    • Forrer P, Stumpp MT, Binz HK, Plückthun A (2003) A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett 539(1-3):2-6.
    • (2003) FEBS Lett , vol.539 , Issue.1-3 , pp. 2-6
    • Forrer, P.1    Stumpp, M.T.2    Binz, H.K.3    Plückthun, A.4
  • 9
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable innodataalpha-helical arrays from an idealized TPR motif
    • Main ERG, Xiong Y, Cocco MJ, D'Andrea L, Regan L (2003) Design of stable innodataalpha-helical arrays from an idealized TPR motif. Structure 11(5):497-508.
    • (2003) Structure , vol.11 , Issue.5 , pp. 497-508
    • Main, E.R.G.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5
  • 10
    • 0037452697 scopus 로고    scopus 로고
    • Designed to be stable: Crystal structure of a consensus ankyrin repeat protein
    • Kohl A, et al. (2003) Designed to be stable: Crystal structure of a consensus ankyrin repeat protein. Proc Natl Acad Sci USA 100(4):1700-1705.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.4 , pp. 1700-1705
    • Kohl, A.1
  • 11
    • 0042780350 scopus 로고    scopus 로고
    • Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins
    • Binz HK, Stumpp MT, Forrer P, Amstutz P, Plückthun A (2003) Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J Mol Biol 332(2):489-503.
    • (2003) J Mol Biol , vol.332 , Issue.2 , pp. 489-503
    • Binz, H.K.1    Stumpp, M.T.2    Forrer, P.3    Amstutz, P.4    Plückthun, A.5
  • 12
    • 78349304669 scopus 로고    scopus 로고
    • Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats
    • Urvoas A, et al. (2010) Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats. J Mol Biol 404(2):307-327.
    • (2010) J Mol Biol , vol.404 , Issue.2 , pp. 307-327
    • Urvoas, A.1
  • 14
    • 0032478536 scopus 로고    scopus 로고
    • Structural diversity of leucine-rich repeat proteins
    • Kajava AV (1998) Structural diversity of leucine-rich repeat proteins. J Mol Biol 277(3):519-527.
    • (1998) J Mol Biol , vol.277 , Issue.3 , pp. 519-527
    • Kajava, A.V.1
  • 15
    • 42949142243 scopus 로고    scopus 로고
    • The leucine-rich repeat domain of Internalin B folds along a polarized N-terminal pathway
    • Courtemanche N, Barrick D (2008) The leucine-rich repeat domain of Internalin B folds along a polarized N-terminal pathway. Structure 16(5):705-714.
    • (2008) Structure , vol.16 , Issue.5 , pp. 705-714
    • Courtemanche, N.1    Barrick, D.2
  • 16
    • 84904157089 scopus 로고    scopus 로고
    • Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats
    • Dao TP, Majumdar A, Barrick D (2014) Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats. Protein Sci 23(6):801-11.
    • (2014) Protein Sci , vol.23 , Issue.6 , pp. 801-811
    • Dao, T.P.1    Majumdar, A.2    Barrick, D.3
  • 17
    • 0043281585 scopus 로고    scopus 로고
    • Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family
    • Stumpp MT, Forrer P, Binz HK, Plückthun A (2003) Designing repeat proteins: Modular leucine-rich repeat protein libraries based on the mammalian ribonuclease inhibitor family. J Mol Biol 332(2):471-487.
    • (2003) J Mol Biol , vol.332 , Issue.2 , pp. 471-487
    • Stumpp, M.T.1    Forrer, P.2    Binz, H.K.3    Plückthun, A.4
  • 18
    • 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 TZ (2014) 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(6):790-800.
    • (2014) Protein Sci , vol.23 , Issue.6 , pp. 790-800
    • Parker, R.1    Mercedes-Camacho, A.2    Grove, T.Z.3
  • 19
    • 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. (2012) Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering. Proc Natl Acad Sci USA 109(9):3299-3304.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.9 , pp. 3299-3304
    • Lee, S.-C.1
  • 20
    • 79952478259 scopus 로고    scopus 로고
    • The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding
    • Aksel T, Majumdar A, Barrick D (2011) The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. Structure 19(3): 349-360.
    • (2011) Structure , vol.19 , Issue.3 , pp. 349-360
    • Aksel, T.1    Majumdar, A.2    Barrick, D.3
  • 21
    • 0027718173 scopus 로고
    • Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats
    • Kobe B, Deisenhofer J (1993) Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature 366(6457):751-756.
    • (1993) Nature , vol.366 , Issue.6457 , pp. 751-756
    • Kobe, B.1    Deisenhofer, J.2
  • 22
    • 0030596012 scopus 로고    scopus 로고
    • Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A
    • Kobe B, Deisenhofer J (1996) Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol 264(5):1028-1043.
    • (1996) J Mol Biol , vol.264 , Issue.5 , pp. 1028-1043
    • Kobe, B.1    Deisenhofer, J.2
  • 23
    • 36749048724 scopus 로고    scopus 로고
    • Prediction of the structure of symmetrical protein assemblies
    • André I, Bradley P, Wang C, Baker D (2007) Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci USA 104(45):17656-17661.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.45 , pp. 17656-17661
    • André, I.1    Bradley, P.2    Wang, C.3    Baker, D.4
  • 24
    • 79959458821 scopus 로고    scopus 로고
    • Modeling symmetric macromolecular structures in Rosetta3
    • DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I (2011) Modeling symmetric macromolecular structures in Rosetta3. PLoS ONE 6(6):e20450.
    • (2011) PLoS ONE , vol.6 , Issue.6 , pp. e20450
    • DiMaio, F.1    Leaver-Fay, A.2    Bradley, P.3    Baker, D.4    André, I.5
  • 25
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • Das R, Baker D (2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77:363-382.
    • (2008) Annu Rev Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 26
    • 79959615159 scopus 로고    scopus 로고
    • RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite
    • Fleishman SJ, et al. (2011) RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE 6(6):e20161.
    • (2011) PLoS ONE , vol.6 , Issue.6 , pp. e20161
    • Fleishman, S.J.1
  • 27
    • 80052334922 scopus 로고    scopus 로고
    • RosettaRemodel: A generalized framework for flexible backbone protein design
    • Huang P-S, et al. (2011) RosettaRemodel: A generalized framework for flexible backbone protein design. PLoS ONE 6(8):e24109.
    • (2011) PLoS ONE , vol.6 , Issue.8 , pp. e24109
    • Huang, P.-S.1
  • 28
    • 34548094323 scopus 로고    scopus 로고
    • Fourier transform infrared spectroscopic analysis of protein secondary structures
    • Kong J, Yu S (2007) Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochim Biophys Sin (Shanghai) 39(8):549-559.
    • (2007) Acta Biochim Biophys Sin (Shanghai) , vol.39 , Issue.8 , pp. 549-559
    • Kong, J.1    Yu, S.2
  • 29
    • 34250903564 scopus 로고    scopus 로고
    • Fractional 13C enrichment of isolated carbons using [1-13C]- or [2-13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins
    • Lundström P, et al. (2007) Fractional 13C enrichment of isolated carbons using [1-13C]- or [2-13C]-glucose facilitates the accurate measurement of dynamics at backbone Calpha and side-chain methyl positions in proteins. J Biomol NMR 38(3):199-212.
    • (2007) J Biomol NMR , vol.38 , Issue.3 , pp. 199-212
    • Lundström, P.1
  • 30
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • Han B, Liu Y, Ginzinger SW, Wishart DS (2011) SHIFTX2: Significantly improved protein chemical shift prediction. J Biomol NMR 50(1):43-57.
    • (2011) J Biomol NMR , vol.50 , Issue.1 , pp. 43-57
    • Han, B.1    Liu, Y.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 31
    • 78650615363 scopus 로고    scopus 로고
    • Sequence-specific
    • random coil chemical shifts of intrinsically disordered proteins
    • Tamiola K, Acar B, Mulder FAA (2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J Am Chem Soc 132(51):18000-18003.
    • (2010) J Am Chem Soc , vol.132 , Issue.51 , pp. 18000-18003
    • Tamiola, K.1    Acar, B.2    Mulder, F.A.A.3
  • 32
    • 0029088794 scopus 로고
    • Proteins with leucine-rich repeats
    • Kobe B, Deisenhofer J (1995) Proteins with leucine-rich repeats. Curr Opin Struct Biol 5(3):409-416.
    • (1995) Curr Opin Struct Biol , vol.5 , Issue.3 , pp. 409-416
    • Kobe, B.1    Deisenhofer, J.2
  • 33
    • 0030437795 scopus 로고    scopus 로고
    • Structural and functional diversity in the leucine-rich repeat family of proteins
    • Buchanan SGSC, Gay NJ (1996) Structural and functional diversity in the leucine-rich repeat family of proteins. Prog Biophys Mol Biol 65(1-2):1-44.
    • (1996) Prog Biophys Mol Biol , vol.65 , Issue.1-2 , pp. 1-44
    • Buchanan, S.G.S.C.1    Gay, N.J.2
  • 34
    • 34447628760 scopus 로고    scopus 로고
    • Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB
    • Truhlar SME, Torpey JW, Komives EA (2006) Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB. Proc Natl Acad Sci USA 103(50):18951-18956.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.50 , pp. 18951-18956
    • Truhlar, S.M.E.1    Torpey, J.W.2    Komives, E.A.3
  • 35
    • 3042628330 scopus 로고    scopus 로고
    • Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution
    • Croy CH, Bergqvist S, Huxford T, Ghosh G, Komives EA (2004) Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution. Protein Sci 13(7):1767-1777.
    • (2004) Protein Sci , vol.13 , Issue.7 , pp. 1767-1777
    • Croy, C.H.1    Bergqvist, S.2    Huxford, T.3    Ghosh, G.4    Komives, E.A.5
  • 36
    • 36749050344 scopus 로고    scopus 로고
    • Repeat-protein folding: New insights into origins of cooperativity, stability, and topology
    • Kloss E, Courtemanche N, Barrick D (2008) Repeat-protein folding: New insights into origins of cooperativity, stability, and topology. Arch Biochem Biophys 469(1):83-99.
    • (2008) Arch Biochem Biophys , vol.469 , Issue.1 , pp. 83-99
    • Kloss, E.1    Courtemanche, N.2    Barrick, D.3
  • 37
    • 41149085409 scopus 로고    scopus 로고
    • Crystal structure and standardized geometric analysis of InlJ, a listerial virulence factor and leucine-rich repeat protein with a novel cysteine ladder
    • Bublitz M, et al. (2008) Crystal structure and standardized geometric analysis of InlJ, a listerial virulence factor and leucine-rich repeat protein with a novel cysteine ladder. J Mol Biol 378(1):87-96.
    • (2008) J Mol Biol , vol.378 , Issue.1 , pp. 87-96
    • Bublitz, M.1


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