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Volumn 18, Issue 1, 2009, Pages 180-195

OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold

Author keywords

Binding site transfer; Calcium binding pocket; Cell adhesion protein; Computational protein design

Indexed keywords

CD2 ANTIGEN; COPPER; SCAFFOLD PROTEIN; THERMITASE; THIOREDOXIN;

EID: 58149476770     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2     Document Type: Article
Times cited : (40)

References (55)
  • 1
    • 0141706371 scopus 로고    scopus 로고
    • Computational design of a Zn2+ receptor that controls bacterial gene expression
    • Dwyer MA, Looger LL, Hellinga HW (2003) Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc Natl Acad Sci USA 100:11255-11260.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 11255-11260
    • Dwyer, M.A.1    Looger, L.L.2    Hellinga, H.W.3
  • 2
    • 2542523113 scopus 로고    scopus 로고
    • Computational design of receptors for an organophosphate surrogate of the nerve agent soman
    • Allert M, Rizk SS, Looger LL, Hellinga HW (2004) Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proc Natl Acad Sci USA 101:7907-7912.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7907-7912
    • Allert, M.1    Rizk, S.S.2    Looger, L.L.3    Hellinga, H.W.4
  • 3
    • 4143131151 scopus 로고    scopus 로고
    • De novo design of catalytic proteins
    • Kaplan J, DeGrado WF (2004) De novo design of catalytic proteins. Proc Natl Acad Sci USA 101:11566-11570.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 11566-11570
    • Kaplan, J.1    DeGrado, W.F.2
  • 6
    • 33947733170 scopus 로고    scopus 로고
    • Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications
    • Choi EJ, Mao J, Mayo SL (2007) Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications. Protein Sci 16:582-588.
    • (2007) Protein Sci , vol.16 , pp. 582-588
    • Choi, E.J.1    Mao, J.2    Mayo, S.L.3
  • 7
    • 33947672445 scopus 로고    scopus 로고
    • Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity
    • Fazelinia H, Cirino PC, Maranas CD (2007) Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. Biophys J 92:2120-2130.
    • (2007) Biophys J , vol.92 , pp. 2120-2130
    • Fazelinia, H.1    Cirino, P.C.2    Maranas, C.D.3
  • 8
    • 35648999502 scopus 로고    scopus 로고
    • Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity
    • Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ (2007) Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. J Biol Chem 282:30658-30666.
    • (2007) J Biol Chem , vol.282 , pp. 30658-30666
    • Lengyel, C.S.1    Willis, L.J.2    Mann, P.3    Baker, D.4    Kortemme, T.5    Strong, R.K.6    McFarland, B.J.7
  • 9
    • 34547691430 scopus 로고    scopus 로고
    • Full-sequence computational design and solution structure of a thermostable protein variant
    • Shah PS, Hom GK, Ross SA, Lassila JK, Crowhurst KA, Mayo SL (2007) Full-sequence computational design and solution structure of a thermostable protein variant. J Mol Biol 372:1-6.
    • (2007) J Mol Biol , vol.372 , pp. 1-6
    • Shah, P.S.1    Hom, G.K.2    Ross, S.A.3    Lassila, J.K.4    Crowhurst, K.A.5    Mayo, S.L.6
  • 10
    • 33846102955 scopus 로고    scopus 로고
    • Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
    • Treynor TP, Vizcarra CL, Nedelcu D, Mayo SL (2007) Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci USA 104:48-53.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 48-53
    • Treynor, T.P.1    Vizcarra, C.L.2    Nedelcu, D.3    Mayo, S.L.4
  • 14
    • 0026335211 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with predefined geometry
    • Hellinga HW, Richards FM (1991) Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with predefined geometry. J Mol Biol 222:763-785.
    • (1991) J Mol Biol , vol.222 , pp. 763-785
    • Hellinga, H.W.1    Richards, F.M.2
  • 15
    • 0028818241 scopus 로고
    • Metal search: A computer program that helps design tetrahedral metal-binding sites
    • Clarke ND, Yuan SM (1995) Metal search: a computer program that helps design tetrahedral metal-binding sites. Proteins 23:256-263.
    • (1995) Proteins , vol.23 , pp. 256-263
    • Clarke, N.D.1    Yuan, S.M.2
  • 16
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278:82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 18
    • 18744388856 scopus 로고    scopus 로고
    • Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity
    • Varadarajan N, Gam J, Olsen MJ, Georgiou G, Iverson BL (2005) Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc Natl Acad Sci USA 102:6855-6860.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6855-6860
    • Varadarajan, N.1    Gam, J.2    Olsen, M.J.3    Georgiou, G.4    Iverson, B.L.5
  • 19
    • 34547958191 scopus 로고    scopus 로고
    • Selection and evolution of enzymes from a partially randomized non-catalytic scaffold
    • Seelig B, Szostak JW (2007) Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448:828-831.
    • (2007) Nature , vol.448 , pp. 828-831
    • Seelig, B.1    Szostak, J.W.2
  • 20
    • 0026321752 scopus 로고
    • Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin
    • Hellinga HW, Caradonna JP, Richards FM (1991) Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J Mol Biol 222:787-803.
    • (1991) J Mol Biol , vol.222 , pp. 787-803
    • Hellinga, H.W.1    Caradonna, J.P.2    Richards, F.M.3
  • 22
    • 0032499535 scopus 로고    scopus 로고
    • Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design
    • Wisz MS, Garrett CZ, Hellinga HW (1998) Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry 37:8269-8277.
    • (1998) Biochemistry , vol.37 , pp. 8269-8277
    • Wisz, M.S.1    Garrett, C.Z.2    Hellinga, H.W.3
  • 24
    • 0037093639 scopus 로고    scopus 로고
    • Structural analysis, identification, and design of calcium-binding sites in proteins
    • Yang W, Lee HW, Hellinga H, Yang JJ (2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47:344-356.
    • (2002) Proteins , vol.47 , pp. 344-356
    • Yang, W.1    Lee, H.W.2    Hellinga, H.3    Yang, J.J.4
  • 26
    • 0038752617 scopus 로고    scopus 로고
    • Computational design of receptor and sensor proteins with novel functions
    • Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185-190.
    • (2003) Nature , vol.423 , pp. 185-190
    • Looger, L.L.1    Dwyer, M.A.2    Smith, J.J.3    Hellinga, H.W.4
  • 27
    • 0037022813 scopus 로고    scopus 로고
    • Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design
    • Benson DE, Haddy AE, Hellinga HW (2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41:3262-3269.
    • (2002) Biochemistry , vol.41 , pp. 3262-3269
    • Benson, D.E.1    Haddy, A.E.2    Hellinga, H.W.3
  • 28
    • 0024293340 scopus 로고
    • Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules
    • Baker EN (1988) Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules. J Mol Biol 203:1071-1095.
    • (1988) J Mol Biol , vol.203 , pp. 1071-1095
    • Baker, E.N.1
  • 29
    • 0000454598 scopus 로고
    • Refinement of the structure of pseudoazurin from Alcaligenes faecalis S-6 at 1.55 A resolution
    • Petratos K, Dauter Z, Wilson KS (1988) Refinement of the structure of pseudoazurin from Alcaligenes faecalis S-6 at 1.55 A resolution. Acta crystallographica 44(Pt 6):628-636.
    • (1988) Acta crystallographica , vol.44 , Issue.PART 6 , pp. 628-636
    • Petratos, K.1    Dauter, Z.2    Wilson, K.S.3
  • 30
    • 0027340169 scopus 로고
    • The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii
    • Redinbo MR, Cascio D, Choukair MK, Rice D, Merchant S, Yeates TO (1993) The 1.5-A crystal structure of plastocyanin from the green alga Chlamydomonas reinhardtii. Biochemistry 32:10560-10567.
    • (1993) Biochemistry , vol.32 , pp. 10560-10567
    • Redinbo, M.R.1    Cascio, D.2    Choukair, M.K.3    Rice, D.4    Merchant, S.5    Yeates, T.O.6
  • 31
    • 0026488252 scopus 로고
    • Crystal structure at 2.8 A resolution of a soluble form of the cell adhesion molecule CD2
    • Jones EY, Davis SJ, Williams AF, Harlos K, Stuart DI (1992) Crystal structure at 2.8 A resolution of a soluble form of the cell adhesion molecule CD2. Nature 360:232-239.
    • (1992) Nature , vol.360 , pp. 232-239
    • Jones, E.Y.1    Davis, S.J.2    Williams, A.F.3    Harlos, K.4    Stuart, D.I.5
  • 32
    • 0036656219 scopus 로고    scopus 로고
    • Metal-binding studies for a de novo designed calcium-binding protein
    • Wilkins AL, Ye Y, Yang W, Lee HW, Liu ZR, Yang JJ (2002) Metal-binding studies for a de novo designed calcium-binding protein. Protein Eng 15:571-574.
    • (2002) Protein Eng , vol.15 , pp. 571-574
    • Wilkins, A.L.1    Ye, Y.2    Yang, W.3    Lee, H.W.4    Liu, Z.R.5    Yang, J.J.6
  • 34
    • 0042767564 scopus 로고    scopus 로고
    • A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins
    • Ye Y, Shealy S, Lee HW, Torshin I, Harrison R, Yang JJ (2003) A grafting approach to obtain site-specific metal-binding properties of EF-hand proteins. Protein Eng 16:429-434.
    • (2003) Protein Eng , vol.16 , pp. 429-434
    • Ye, Y.1    Shealy, S.2    Lee, H.W.3    Torshin, I.4    Harrison, R.5    Yang, J.J.6
  • 36
    • 0037093639 scopus 로고    scopus 로고
    • Structural analysis, identification, and design of calcium-binding sites in proteins
    • Yang W, Lee HW, Hellinga H, Yang JJ (2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47:344-356.
    • (2002) Proteins , vol.47 , pp. 344-356
    • Yang, W.1    Lee, H.W.2    Hellinga, H.3    Yang, J.J.4
  • 37
    • 36348968387 scopus 로고    scopus 로고
    • Essential dynamics of helices provide a functional classification of EF-hand proteins
    • Capozzi F, Luchinat C, Micheletti C, Pontiggia F (2007) Essential dynamics of helices provide a functional classification of EF-hand proteins. Journal of proteome research 6:4245-4255.
    • (2007) Journal of proteome research , vol.6 , pp. 4245-4255
    • Capozzi, F.1    Luchinat, C.2    Micheletti, C.3    Pontiggia, F.4
  • 38
    • 39049105983 scopus 로고    scopus 로고
    • Regulatory and structural EF-hand motifs of neuronal calciumsensor-1:Mg 2+ modulates Ca 2+ binding, Ca 2+-induced conformational changes, and equilibrium unfolding transitions
    • Aravind P, Chandra K, Reddy PP, Jeromin A, Chary KV, Sharma Y (2008) Regulatory and structural EF-hand motifs of neuronal calciumsensor-1:Mg 2+ modulates Ca 2+ binding, Ca 2+-induced conformational changes, and equilibrium unfolding transitions. J Mol Biol 376:1100-1115.
    • (2008) J Mol Biol , vol.376 , pp. 1100-1115
    • Aravind, P.1    Chandra, K.2    Reddy, P.P.3    Jeromin, A.4    Chary, K.V.5    Sharma, Y.6
  • 40
    • 0025828307 scopus 로고
    • Calcium binding to thermitase. Crystallographic studies of thermitase at 0, 5, and 100 mM calcium
    • Gros P, Kalk KH, Hol WG (1991) Calcium binding to thermitase. Crystallographic studies of thermitase at 0, 5, and 100 mM calcium. J Biol Chem 266:2953-2961.
    • (1991) J Biol Chem , vol.266 , pp. 2953-2961
    • Gros, P.1    Kalk, K.H.2    Hol, W.G.3
  • 41
    • 0018799126 scopus 로고
    • Lanthanide ion probes of structure in biology. Environmentally sensitive fine structure in laser-induced terbium(III) luminescence
    • Sudnick DR, Horrocks WD, Jr (1979) Lanthanide ion probes of structure in biology. Environmentally sensitive fine structure in laser-induced terbium(III) luminescence. Biochimica et biophysica acta 578:135-144.
    • (1979) Biochimica et biophysica acta , vol.578 , pp. 135-144
    • Sudnick, D.R.1    Horrocks Jr, W.D.2
  • 42
    • 0342506478 scopus 로고    scopus 로고
    • Characterization of lanthanide ion binding to the EF-hand protein S100 beta by luminescence spectroscopy
    • Chaudhuri D, Horrocks WD, Jr., Amburgey JC, Weber DJ (1997) Characterization of lanthanide ion binding to the EF-hand protein S100 beta by luminescence spectroscopy. Biochemistry 36:9674-9680.
    • (1997) Biochemistry , vol.36 , pp. 9674-9680
    • Chaudhuri, D.1    Horrocks Jr., W.D.2    Amburgey, J.C.3    Weber, D.J.4
  • 43
    • 18544381886 scopus 로고    scopus 로고
    • Calcium-binding properties of wild-type and EF-hand mutants of S100B in the presence and absence of a peptide derived from the C-terminal negative regulatory domain of p53
    • Markowitz J, Rustandi RR, Varney KM, Wilder PT, Udan R, Wu SL, Horrocks WD, Weber DJ (2005) Calcium-binding properties of wild-type and EF-hand mutants of S100B in the presence and absence of a peptide derived from the C-terminal negative regulatory domain of p53. Biochemistry 44:7305-7314.
    • (2005) Biochemistry , vol.44 , pp. 7305-7314
    • Markowitz, J.1    Rustandi, R.R.2    Varney, K.M.3    Wilder, P.T.4    Udan, R.5    Wu, S.L.6    Horrocks, W.D.7    Weber, D.J.8
  • 44
    • 0027525244 scopus 로고
    • Luminescence spectroscopy
    • Horrocks WD, Jr (1993) Luminescence spectroscopy. Methods Enzymol 226:495-538.
    • (1993) Methods Enzymol , vol.226 , pp. 495-538
    • Horrocks Jr, W.D.1
  • 45
    • 58149465703 scopus 로고    scopus 로고
    • ILOG (2006) ILOG CPLEX 10.1 User's Manual. Sunnyvale, CA, USA: ILOG S.A. and ILOG, Inc.
    • ILOG (2006) ILOG CPLEX 10.1 User's Manual. Sunnyvale, CA, USA: ILOG S.A. and ILOG, Inc.
  • 47
  • 48
    • 0000224283 scopus 로고    scopus 로고
    • CHARMM: The energy function and its parameterization with an overview of the program
    • Schleyer R, editor, Chichester, West Sussex, England: Wiley, pp
    • MacKerell AD, Brooks B, Brooks CL, Nilsson L, Roux B, Won Y, Karplus M (1998) CHARMM: the energy function and its parameterization with an overview of the program. In: Schleyer R, editor. The encyclopedia of computational chemistry. Chichester, West Sussex, England: Wiley, pp. 271-277.
    • (1998) The encyclopedia of computational chemistry , pp. 271-277
    • MacKerell, A.D.1    Brooks, B.2    Brooks, C.L.3    Nilsson, L.4    Roux, B.5    Won, Y.6    Karplus, M.7
  • 49
    • 0033998280 scopus 로고    scopus 로고
    • A new approach to the design of uniquely folded thermally stable proteins
    • Jiang X, Farid H, Pistor E, Farid RS (2000) A new approach to the design of uniquely folded thermally stable proteins. Protein Sci 9:403-416.
    • (2000) Protein Sci , vol.9 , pp. 403-416
    • Jiang, X.1    Farid, H.2    Pistor, E.3    Farid, R.S.4
  • 51
    • 0034213691 scopus 로고    scopus 로고
    • High-yield expression and purification of recombinant proteins in bacteria: A versatile vector for glutathione S-transferase fusion proteins containing two protease cleavage sites
    • Sehgal BU, Dunn R, Hicke L, Godwin HA (2000) High-yield expression and purification of recombinant proteins in bacteria: a versatile vector for glutathione S-transferase fusion proteins containing two protease cleavage sites. Anal Biochem 281:232-234.
    • (2000) Anal Biochem , vol.281 , pp. 232-234
    • Sehgal, B.U.1    Dunn, R.2    Hicke, L.3    Godwin, H.A.4
  • 53
    • 0017071240 scopus 로고
    • A simple, one-step fluorometric method for determination of nanomolar concentrations of terbium
    • Barela TD, Sherry AD (1976) A simple, one-step fluorometric method for determination of nanomolar concentrations of terbium. Anal Biochem 71:351-357.
    • (1976) Anal Biochem , vol.71 , pp. 351-357
    • Barela, T.D.1    Sherry, A.D.2
  • 54
    • 0025950774 scopus 로고
    • Quantitating and engineering the ion specificity of an EF-hand-like Ca2+ binding
    • Falke JJ, Snyder EE, Thatcher KC, Voertler CS (1991) Quantitating and engineering the ion specificity of an EF-hand-like Ca2+ binding. Biochemistry 30:8690-8697.
    • (1991) Biochemistry , vol.30 , pp. 8690-8697
    • Falke, J.J.1    Snyder, E.E.2    Thatcher, K.C.3    Voertler, C.S.4
  • 55
    • 0029954447 scopus 로고    scopus 로고
    • Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: Substitutions at the gateway position
    • Drake SK, Lee KL, Falke JJ (1996) Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: substitutions at the gateway position. Biochemistry 35:6697-6705.
    • (1996) Biochemistry , vol.35 , pp. 6697-6705
    • Drake, S.K.1    Lee, K.L.2    Falke, J.J.3


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