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Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins†

  1. Shona C. Patel1,‡,
  2. Luke H. Bradley2,§,
  3. Sayuri P. Jinadasa2,¶,
  4. Michael H. Hecht2,*

Article first published online: 29 APR 2009

DOI: 10.1002/pro.147

Issue

Protein Science

Protein Science

Volume 18, Issue 7, pages 1388–1400, July 2009

Additional Information

How to Cite

Patel, S. C., Bradley, L. H., Jinadasa, S. P. and Hecht, M. H. (2009), Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins. Protein Science, 18: 1388–1400. doi: 10.1002/pro.147

Author Information

  1. 1

    Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544

  2. 2

    Department of Chemistry, Princeton University, Princeton, New Jersey 08544

  1. ‡

    Merck & Co., Inc., West Point, PA 19486

  2. §

    Departments of Anatomy & Neurobiology, Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536

  3. Columbia University Medical Center, New York, NY 10032

*Department of Chemistry, Princeton University, Princeton, NJ, 08544

  1. †

    The authors dedicate this article to the memory of Walter Kauzmann, a long time member of the Princeton Department of Chemistry. His early insights into the importance of the hydrophobic effect in protein folding were decades ahead of their time, and laid the foundation for the protein design strategy described in this article.

Publication History

  1. Issue published online: 23 JUN 2009
  2. Article first published online: 29 APR 2009
  3. Accepted manuscript online: 29 APR 2009 12:00AM EST
  4. Manuscript Accepted: 13 APR 2009
  5. Manuscript Revised: 12 APR 2009
  6. Manuscript Received: 1 MAR 2009

Funded by

  • National Science Foundation Graduate Fellowship
  • Princeton University Council on Science and Technology
  • NSF grant. Grant Number: MCB-0817651

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References

  • 1
    Jensen RA ( 1976) Enzyme recruitment in evolution of new function. Ann Rev Microbiol 30: 409–425.
  • 2
    Mandecki W ( 1990) A method for construction of long randomized open reading frames and polypeptides. Protein Eng 3: 221–226.
  • 3
    Davidson AR, Sauer RT ( 1994) Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci USA 91: 2146–2150.
  • 4
    Keefe AD, Szostak JW ( 2001) Functional proteins from a random sequence library. Nature 410: 715–718.
  • 5
    Watters AL, Baker D ( 2004) Searching for folded proteins in vitro and in silico. Eur J Biochem 271: 1615–1622.
  • 6
    Chiarabelli C, Vrijbloed JW, De Lucrezia D, Thomas RM, Stano P, Polticelli F, Ottone T, Papa E, Luisi PL ( 2006) Investigation of de novo totally random biosequences. Part II: On the folding frequency in a totally random library of de novo proteins obtained by phage display. Chem Biodivers 3: 840–859.
  • 7
    Go A, Kim S, Baum J, Hecht MH ( 2008) Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci 17: 821–832.
  • 8
    Bradley LH, Kleiner RE, Wang AF, Hecht MH, Wood DW ( 2005) An intein-based genetic selection enables construction of a high-quality library of binary patterned de novo sequences. Protein Eng Des Sel 18: 201–207.
  • 9
    Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH ( 1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262: 1680–1685.
  • 10
    Hecht MH, Das A, Go A, Bradley LH, Wei Y ( 2004) De novo proteins from designed combinatorial libraries. Protein Sci 13: 1711–1723.
  • 11
    West MW, Wang W, Patterson J, Mancias JD, Beasley JR, Hecht MH ( 1999) De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci USA 96: 11211–11216.
  • 12
    Wei Y, Liu T, Sazinsky SL, Moffet DA, Pelczer I, Hecht MH ( 2003) Stably folded de novo proteins from a designed combinatorial library. Protein Sci 12: 92–102.
  • 13
    Kauzmann W ( 1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14: 1–63.
  • 14
    Johnson BH, Hecht MH ( 1994) Recombinant proteins can be isolated from E. coli cells by repeated cycles of freezing and thawing. Biotechnology 12: 1357–1360.
  • 15
    Wei Y, Kim S, Fela D, Baum J, Hecht MH ( 2003) Solution structure of a de novo protein from a designed combinatorial library. Proc Natl Acad Sci USA 100: 13270–13273.
  • 16
    Roy S, Ratnaswamy G, Boice JA, Fairman R, McLendon G, Hecht MH ( 1997) A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties. J Am Chem Soc 119: 5302–5306.
  • 17
    Roy S, Helmer KJ, Hecht MH ( 1997) Detecting native-like properties in combinatorial libraries of de novo proteins. Fold Des 2: 89–92.
  • 18
    Roy S, Hecht MH ( 2000) Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids. Biochemistry 39: 4603–4607.
  • 19
    Rojas NR, Kamtekar S, Simons CT, McLean JE, Vogel KM, Spiro TG, Farid RS, Hecht MH ( 1997) De novo heme proteins from designed combinatorial libraries. Protein Sci 6: 2512–2524.
  • 20
    Moffet DA, Certain LK, Smith AJ, Kessel AJ, Beckwith KA, Hecht MH ( 2000) Peroxidase activity in heme proteins derived from a designed combinatorial library. J Am Chem Soc 122: 7612–7613.
  • 21
    Wei Y, Hecht MH ( 2004) Enzyme-like proteins from an unselected library of designed amino acid sequences. Protein Eng Des Sel 17: 67–75.
  • 22
    Platt J ( 2007) Senior Thesis. NJ: Princeton University.
  • 23
    Webb EC ( 1992) Recommendations of the nomenclature committee of the International union of biochemistry and molecular biology. Enzyme nomenclature. San Diego: Academic Press, p 23.
  • 24
    Orengo CA, Michie AD, Jones DT, Swindells MB, Thornton JM ( 1997) CATH: a hierarchic classification of protein domain structures. Structure 5: 1093–1108.
  • 25
    Hiner ANP, Hernandez-Ruiz J, Arnao MB, Garcia-Canovas F, Acosta M ( 1996) A comparative study of the purity, enzyme activity and inactivation by hydrogen peroxide of commercially available horseradish peroxidase isoenyzmes A and C. Biotechnol Bioeng 50: 655–662.
  • 26
    Wan L, Twitchett MB, Eltis LD, Mauk AG, Smith M ( 1998) In vitro evolution of horse heart myoglobin to increase peroxidase activity. Proc Natl Acad Sci USA 95: 12825–12831.
  • 27
    Witting PK, Mauk AG, Lay PA ( 2002) Role of tyrosine-103 in myoglobin peroxidase activity: kinetic and steady-state studies on the reaction of wild-type and variant recombinant human myoglobins with H2O2. Biochemistry 41: 11495–11503.
  • 28
    Carlsen CU, Skovgaard IM, Skibsted LH ( 2003) Pseudoperoxidase activity of myoglobin: kinetics and mechanism of the peroxidase cycle of myoglobin and H2O2 and 2,2-Azino-bis(3-ethylbenzthiazoline-6-sulfonate) as substrates. J Agric Food Chem 51: 5815–5823.
  • 29
    Dwyer MA, Looger LL, Hellinga HW ( 2008) Retraction of “computational design of a biologically active enzyme.” Science 319: 569.
  • 30
    Reedy CJ, Gibney BR ( 2004) Heme protein assemblies. Chem Rev 104: 617–649.
  • 31
    Wilson JR, Caruana DJ, Gilardi G ( 2003) Engineering redox functions in a nucleic acid binding protein. Chem Commun 356–357.
  • 32
    Webb EC ( 1992) Recommendations of the nomenclature committee of the International union of biochemistry and molecular biology. Enzyme nomenclature. San Diego: Academic Press, p 862.
  • 33
    Dimitrov JD, Roumenina LT, Doltchinkova VR, Mihaylova NM, Lacroix-Desmazes S, Kaveri SV, Vassilev TL ( 2007) Antibodies use heme as a cofactor to extend their pathogen elimination activity and to acquire new effector functions. J Biol Chem 282: 26696–26706.
  • 34
    Choma CT, Lear JD, Nelson MJ, Dutton PL, Robertson DE, DeGrado WF ( 1994) Design of a heme-binding four-helix bundle. J Am Chem Soc 116: 856–865.
  • 35
    Robertson DE, Farid RS, Moser CC, Urbauer JL, Mulholland SE, Pidikiti R, Lear JD, Wand AJ, DeGrado WF, Dutton PL ( 1994) Design and synthesis of multi-haem proteins. Nature 368: 425–432.
  • 36
    Arnold PA, Shelton WR, Benson DR ( 1997) Peptide helix induction in a self-assembling hemoprotein model. J Am Chem Soc 119: 3181–3182.
  • 37
    Huffman DL, Rosenblatt MM, Suslick KS ( 1998) Synthetic heme-peptide complexes. J Am Chem Soc 120: 6183–6184.
  • 38
    Gibney BR, Dutton PL ( 1999) Histidine placement in de novo-designed heme proteins. Protein Sci 8: 1888–1898.
  • 39
    Rau HK, DeJonge N, Haehnel W ( 2000) Combinatorial synthesis of four-helix bundle hemoproteins for tuning of cofactor properties. Angew Chem Int Ed 39: 250–253.
  • 40
    Koder RL, Valentine KG, Cerda J, Noy D, Wand AJ, Dutton PL ( 2006) Nativelike structure in designed four α-helix bundles driven by buried polar interactions. J Am Chem Soc 128: 14450–14451.
  • 41
    Adams PA ( 1990) The peroxidasic activity of the haem octapeptide microperoxidase-8 (MP-8): the kinetic mechanism of the catalytic reduction of H2O2 by MP-8 using 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulphonate)(ABTS) as reducing substrate. J Chem Soc Perkin Trans 2: 1407–1414.
  • 42
    Tsuruzono M, Obataya I, Ueno A, Mihara H ( 2003) Design and peroxidase-like activity of 3 alpha-helix hemoproteins. Peptide Sci 2002: 367–368.
  • 43
    Broo KS, Nilsson H, Nilsson J, Baltzer L ( 1998) Substrate recognition and saturation kinetics in de novo designed histidine-based four-helix bundle catalysts. J Am Chem Soc 120: 10287–10295.
  • 44
    Bolon DN, Mayo SL ( 2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98: 14274–14279.
  • 45
    Yamauchi A, Nakashima T, Tokuriki N, Hosokawa M, Nogami H, Arioka S, Urabe I, Yomo T ( 2002) Evolvability of random polypeptides through functional selection within a small library. Protein Eng 15: 619–626.
  • 46
    Kunitake T, Okahata Y ( 1976) Catalytic hydrolysis by synthetic polymers. Adv Polym Sci 20: 159–221.
  • 47
    Clouet A, Darbre T, Reymond JL ( 2006) Combinatorial synthesis, selection, and properties of esterase peptide dendrimers. Biopolymers 84: 114–123.
  • 48
    Patel SC ( 2008) PhD Thesis. NJ: Princeton University.
  • 49
    O'Loughlin TL, Patrick WM, Matsumura I ( 2006) Natural history as a predictor of protein evolvability. Protein Eng Des Sel 19: 439–442.
  • 50
    O'Brien PJ, Herschlag D ( 1999) Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol 6: R91–R105.
  • 51
    Aharoni A, Gaidukov L, Khersonsky O, Gould SM, Roodveldt C, Tawfik DS ( 2005) The “evolvability” of promiscuous protein functions. Nat Genet 37: 73–76.
  • 52
    Axe DD ( 2004) Estimating the prevalence of protein sequences adopting functional enzyme folds. J Mol Biol 341: 1295–1315.
  • 53
    Petrounia PP, Arnold FH ( 2000) Designed evolution of enzymatic properties. Curr Opin Biotechnol 11: 325–330.
  • 54
    Smith GP ( 1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317.
  • 55
    Roberts RW, Szostak JW ( 1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA 94: 12297–12302.
  • 56
    Tawfik DS, Griffiths AD ( 1998) Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16: 652–656.
  • 57
    Arnold FH, Georgiou G ( 2003) Methods in molecular biology—directed enzyme evolution—screening and selection methods. Totowa, NJ: Humana Press, pp 3–84.
  • 58
    Studier FW ( 2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207–234.
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