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References

  • 1
    Dwyer MA, Looger LL, Hellinga HW ( 2003) Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc Natl Acad Sci USA 100: 1125511260.
  • 2
    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: 79077912.
  • 3
    Kaplan J, DeGrado WF ( 2004) De novo design of catalytic proteins. Proc Natl Acad Sci USA 101: 1156611570.
  • 4
    Korkegian A, Black ME, Baker D, Stoddard BL ( 2005) Computational thermostabilization of an enzyme. Science 308: 857860.
  • 5
    Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Rothlisberger D, Baker D ( 2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 27852794.
  • 6
    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: 582588.
  • 7
    Fazelinia H, Cirino PC, Maranas CD ( 2007) Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. Biophys J 92: 21202130.
  • 8
    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: 3065830666.
  • 9
    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: 16.
  • 10
    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: 4853.
  • 11
    Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D ( 2008) De novo computational design of retro-aldol enzymes. Science 319: 13871391.
  • 12
    Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D ( 2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190195.
  • 13
    Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Jr., Stoddard BL, Baker D ( 2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441: 656659.
  • 14
    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: 763785.
  • 15
    Clarke ND, Yuan SM ( 1995) Metal search: a computer program that helps design tetrahedral metal-binding sites. Proteins 23: 256263.
  • 16
    Dahiyat BI, Mayo SL ( 1997) De novo protein design: fully automated sequence selection. Science 278: 8287.
  • 17
    Cesaro-Tadic S, Lagos D, Honegger A, Rickard JH, Partridge LJ, Blackburn GM, Pluckthun A ( 2003) Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library. Nat Biotechnol 21: 679685.
  • 18
    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: 68556860.
  • 19
    Seelig B, Szostak JW ( 2007) Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448: 828831.
  • 20
    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: 787803.
  • 21
    Klemba M, Gardner KH, Marino S, Clarke ND, Regan L ( 1995) Novel metal-binding proteins by design. Nat Struct Biol 2: 368373.
  • 22
    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: 82698277.
  • 23
    Benson DE, Wisz MS, Hellinga HW ( 2000) Rational design of nascent metalloenzymes. Proc Natl Acad Sci USA 97: 62926297.
  • 24
    Yang W, Lee HW, Hellinga H, Yang JJ ( 2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47: 344356.
  • 25
    Roberts VA, Iverson BL, Iverson SA, Benkovic SJ, Lerner RA, Getzoff ED, Tainer JA ( 1990) Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket. Proc Natl Acad Sci USA 87: 66546658.
  • 26
    Looger LL, Dwyer MA, Smith JJ, Hellinga HW ( 2003) Computational design of receptor and sensor proteins with novel functions. Nature 423: 185190.
  • 27
    Benson DE, Haddy AE, Hellinga HW ( 2002) Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry 41: 32623269.
  • 28
    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: 10711095.
  • 29
    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): 628636.
  • 30
    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: 1056010567.
  • 31
    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: 232239.
  • 32
    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: 571574.
  • 33
    Yang W, Jones LM, Isley L, Ye Y, Lee HW, Wilkins A, Liu ZR, Hellinga HW, Malchow R, Ghazi M, Yang JJ ( 2003) Rational design of a calcium-binding protein. J Am Chem Soc 125: 61656171.
  • 34
    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: 429434.
  • 35
    Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ ( 2005) Design of a calcium-binding protein with desired structure in a cell adhesion molecule. J Am Chem Soc 127: 20852093.
  • 36
    Yang W, Lee HW, Hellinga H, Yang JJ ( 2002) Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 47: 344356.
  • 37
    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: 42454255.
  • 38
    Aravind P, Chandra K, Reddy PP, Jeromin A, Chary KV, Sharma Y ( 2008) Regulatory and structural EF-hand motifs of neuronal calcium sensor-1: Mg 2+ modulates Ca 2+ binding, Ca 2+-induced conformational changes, and equilibrium unfolding transitions. J Mol Biol 376: 11001115.
  • 39
    Teplyakov AV, Kuranova IP, Harutyunyan EH, Vainshtein BK, Frommel C, Hohne WE, Wilson KS ( 1990) Crystal structure of thermitase at 1.4 A resolution. J Mol Biol 214: 261279.
  • 40
    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: 29532961.
  • 41
    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: 135144.
  • 42
    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: 96749680.
  • 43
    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: 73057314.
  • 44
    Horrocks WD,Jr ( 1993) Luminescence spectroscopy. Methods Enzymol 226: 495538.
  • 45
    ILOG ( 2006) ILOG CPLEX 10.1 User's Manual. Sunnyvale, CA, USA: ILOG S.A. and ILOG, Inc.
  • 46
    Floudas CA ( 2000) Deterministic global optimization: theory, methods, and applications. Dordrecht: Kluwer Academic Publishers, p. xvii.
  • 47
    Saraf MC, Moore GL, Goodey NM, Cao VY, Benkovic SJ, Maranas CD ( 2006) IPRO: an iterative computational protein library redesign and optimization procedure. Biophys J 90: 41674180.
  • 48
    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: SchleyerR, editor. The encyclopedia of computational chemistry. Chichester, West Sussex, England: Wiley, pp. 271277.
  • 49
    Jiang X, Farid H, Pistor E, Farid RS ( 2000) A new approach to the design of uniquely folded thermally stable proteins. Protein Sci 9: 403416.
  • 50
    Arnold FH, Georgiou G ( 2003) Directed evolution library craetion. New York, NY, USA: Humana Press.
  • 51
    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: 232234.
  • 52
    Amersham-Biosciences ( 2002) GST gene fusion system handbook. Piscataway, NJ, USA: Amersham-Biosciences.
  • 53
    Barela TD, Sherry AD ( 1976) A simple, one-step fluorometric method for determination of nanomolar concentrations of terbium. Anal Biochem 71: 351357.
  • 54
    Falke JJ, Snyder EE, Thatcher KC, Voertler CS ( 1991) Quantitating and engineering the ion specificity of an EF-hand-like Ca2+ binding. Biochemistry 30: 86908697.
  • 55
    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: 66976705.