Engineering oxidoreductases: Maquette proteins designed from scratch

Biochemical Society Transactions

Volumn 40, Issue 3, 2012, Pages 561-566

  Lichtenstein, Bruce R ^a   Farid, Tammer A ^a   Kodali, Goutham ^a   Solomon, Lee A ^a   Anderson, J L Ross ^b   Sheehan, Molly M ^a   Ennist, Nathan M ^a   Fry, Bryan A ^a   Chobot, Sarah E ^c   Bialas, Chris ^a   Mancini, Joshua A ^a   Armstrong, Craig T ^b   Zhao, Zhenyu ^a   Esipova, Tatiana V ^a   Snell, David ^d   Vinogradov, Sergei A ^a   Discher, Bohdana M ^a   Moser, Christopher C ^a   Dutton, P Leslie ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

^c Department of Obstetrics Gynecology   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

Author keywords

Electron transfer; Maquette; Oxidoreductase; Protein design; Protein engineering; Synthetic protein

Indexed keywords

NANOMATERIAL; OXIDOREDUCTASE; SCAFFOLD PROTEIN; TITANIUM DIOXIDE;

ALPHA HELIX; AMINO ACID SEQUENCE; CATALYSIS; CONFERENCE PAPER; ELECTRON TRANSPORT; ENERGY TRANSFER; ENZYME ACTIVITY; HYDROPHILICITY; HYDROPHOBICITY; LIGHT HARVESTING SYSTEM; MOLECULAR MIMICRY; OXIDATION; OXYGEN AFFINITY; PHOTOCHEMISTRY; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN LOCALIZATION; PROTEIN SYNTHESIS; PROTEIN TERTIARY STRUCTURE; REDUCTION; SITE DIRECTED MUTAGENESIS;

OXIDATION-REDUCTION; OXIDOREDUCTASES; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SYNTHETIC BIOLOGY;

EID: 84861499435     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120067     Document Type: Conference Paper

References (43)

1. Kosiol, C. and Goldman, N. (2011) Markovian and non-Markovian protein sequence evolution: aggregated markov process models. J. Mol. Biol. 411, 910-923
2. Muller, H.J. (1964) The relation of recombination to mutational advance. Mutat. Res. 1, 2-9
3. Darwin C. (1872) Origin of Species by Means of Natural Selection, Earlton House, New York
4. Choi, J.M., Kang, S.Y., Bae, W.J., Jin, K.S., Ree, M. and Cho, Y. (2007) Probing the roles of active site residues in the 3′-5′ exonuclease of the Werner syndrome protein. J. Biol. Chem. 282, 9941-9951 (Pubitemid 47104567)
5. Choi, Y.H., Matsuzaki, R., Suzuki, S. and Tanizawa, K. (1996) Role of conserved Asn-Tyr-Asp-Tyr sequence in bacterial copper/2,4,5- trihydroxyphenylalanyl quinone-containing histamine oxidase. J. Biol. Chem. 271, 22598-22603 (Pubitemid 26304700)
6. Cooperman, B.S., Baykov, A.A. and Lahti, R. (1992) Evolutionary conservation of the active-site of soluble inorganic pyrophosphatase. Trends Biochem. Sci. 17, 262-266
7. Menon, B.R.K., Davison, P.A., Hunter, C.N., Scrutton, N.S. and Heyes, D.J. (2010) Mutagenesis alters the catalytic mechanism of the light-driven enzyme protochlorophyllide oxidoreductase. J. Biol. Chem. 285, 2113-2119
8. O'Farrell, H.C., Musayev, F.N., Scarsdale, J.N. and Rife, J.P. (2012) Control of substrate specificity by a single active site residue of the KsgA methyltransferase. Biochemistry 51, 466-474
9. Rungsrisuriyachai, K. and Gadda, G. (2010) Role of asparagine 510 in the relative timing of substrate bond cleavages in the reaction catalyzed by choline oxidase. Biochemistry 49, 2483-2490
10. Azoitei, M.L., Ban, Y.E.A., Julien, J.P., Bryson, S., Schroeter, A., Kalyuzhniy, O., Porter, J.R., Adachi, Y., Baker, D., Pai, E.F. and Schief, W.R. (2012) Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. J. Mol. Biol. 415, 175-192
11. Hedstrom, L., Szilagyi, L. and Rutter, W.J. (1992) Converting trypsin to chymotrypsin: the role of surface loops. Science 255, 1249-1253
12. O'Donoghue, P., Sheppard, K., Nureki, O. and Soll, D. (2011) Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proc. Natl. Acad. Sci. U.S.A. 108, 20485-20490
13. Villiers, B. and Hollfelder, F. (2011) Directed evolution of a gatekeeper domain in nonribosomal peptide synthesis. Chem. Biol. 18, 1290-1299
14. Yip, S.H.C., Foo, J.L., Schenk, G., Gahan, L.R., Carr, P.D. and Ollis, D.L. (2011) Directed evolution combined with rational design increases activity of GpdQ toward a non-physiological substrate and alters the oligomeric structure of the enzyme. Protein Eng. Des. Sel. 24, 861-872
15. Jiang, L., Althoff, E.A., Clemente, F.R., Doyle, L., Rothlisberger, D., Zanghellini, A., Gallaher, J.L., Betker, J.L., Tanaka, F., Barbas, C.F. et al. (2008) De novo computational design of retro-aldol enzymes. Science 319, 1387-1391 (Pubitemid 351354873)
16. Siegel, J.B., Zanghellini, A., Lovick, H.M., Kiss, G., Lambert, A.R., Clair, J.L.S., Gallaher, J.L., Hilvert, D., Gelb, M.H., Stoddard, B.L. et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329, 309-313
17. Simons, K.T., Bonneau, R., Ruczinski, I. and Baker, D. (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Struct. Funct. Genet. (Suppl. 3), 171-176 (Pubitemid 29463528)
18. Richter, F., Leaver-Fay, A., Khare, S.D., Bjelic, S. and Baker, D. (2011) De novo enzyme design using Rosetta3. PLoS ONE 6, e19230
19. Korendovych, I.V., Kulp, D.W., Wu, Y.B., Cheng, H., Roder, H. and DeGrado, W.F. (2011) Design of a switchable eliminase. Proc. Natl. Acad. Sci. U.S.A. 108, 6823-6827
20. Sigman, J.A., Kwok, B.C. and Lu, Y. (2000) From myoglobin to heme-copper oxidase: design and engineering of a Cu-B center into sperm whale myoglobin. J. Am. Chem. Soc. 122, 8192-8196
21. Koder, R.L. and Dutton, P.L. (2006) Intelligent design: the de novo engineering of proteins with specified functions. Dalton Trans., 3045-3051
22. Regan, L. and DeGrado, W.F. (1988) Characterization of a helical protein designed from first principles. Science 241, 976-978
23. Gibney, B.R., Rabanal, F., Reddy, K.S. and Dutton, P.L. (1998) Effect of four helix bundle topology on heme binding and redox properties. Biochemistry 37, 4635-4643 (Pubitemid 28217182)
24. Robertson, D.E., Farid, R.S., Moser, C.C., Urbauer, J.L., Mulholland, S.E., Pidikiti, R., Lear, J.D., Wand, A.J., DeGrado, W.F. and Dutton, P.L. (1994) Design and synthesis of multi-heme proteins. Nature 368, 425-431
25. Razeghifard, A.R. and Wydrzynski, T. (2003) Binding of Zn-chlorin to a synthetic four-helix bundle peptide through histidine ligation. Biochemistry 42, 1024-1030
26. Gibney, B.R., Mulholland, S.E., Rabanal, F. and Dutton, P.L. (1996) Ferredoxin and ferredoxin-heme maquettes. Proc. Natl. Acad. Sci. U.S.A. 93, 15041-15046 (Pubitemid 27009548)
27. Summa, C.M., Rosenblatt, M.M., Hong, J.K., Lear, J.D. and DeGrado, W.F. (2002) Computational de novo design, and characterization of an A2B2 diiron protein. J. Mol. Biol. 321, 923-938
28. Magistrato, A., DeGrado, W.F., Laio, A., Rothlisberger, U., VandeVondele, J. and Klein, M.L. (2003) Characterization of the dizinc analogue of the synthetic diiron protein DF1 using ab initio and hybrid quantum/classical molecular dynamics simulations. J. Phys. Chem. B 107, 4182-4188
29. Sharp, R.E., Moser, C.C., Rabanal, F. and Dutton, P.L. (1998) Design, synthesis, and characterization of a photoactivatable flavocytochrome molecular maquette. Proc. Natl. Acad. Sci. U.S.A. 95, 10465-10470 (Pubitemid 28413090)
30. Lichtenstein, B.R. (2010) A New Approach to Understanding Biological Control of Quinone Electrochemistry. Ph.D. Thesis, University of Pennsylvania, Philadelphia, PA, U.S.A.
31. Li, W.W., Hellwig, P., Ritter, M. and Haehnel, W. (2006) De novo design, synthesis, and characterization of quinoproteins. Chem. Eur. J. 12, 7236-7245 (Pubitemid 44460928)
32. Grosset, A.M., Gibney, B.R., Rabanal, F., Moser, C.C. and Dutton, P.L. (2001) Proof of principle in a de novo designed protein maquette: an allosterically regulated, charge-activated conformational switch in a tetra-α-helix bundle. Biochemistry 40, 5474-5487 (Pubitemid 32458249)
33. Koder, R.L., Anderson, J.L. R., Solomon, L.A., Reddy, K.S., Moser, C.C. and Dutton, P.L. (2009) Design and engineering of an O2 transport protein. Nature 458, 305-309
34. Hokanson, S.C. (2010) Deconvoluting the Engineering and Assembly Instructions for Complex III Activity. Ph.D. Thesis, University of Pennsylvania, Philadelphia, PA, U.S.A.
35. Moser, C.C., Keske, J.M., Warncke, K., Farid, R.S. and Dutton, P.L. (1992) Nature of biological electron transfer. Nature 355, 796-802
36. Anderson, J.L.R., Koder, R.L., Moser, C.C. and Dutton, P.L. (2008) Controlling complexity and water penetration in functional de novo protein design. Biochem. Soc. Trans. 36, 1106-1111
37. Huang, S.S., Gibney, B.R., Stayrook, S.E., Dutton, P.L. and Lewis, M. (2003) X-ray structure of a maquette scaffold. J. Mol. Biol. 326, 1219-1225 (Pubitemid 36263393)
38. Koder, R.L., Valentine, K.G., Cerda, J., Noy, D., Smith, K.M., Wand, A.J. and Dutton, P.L. (2006) Nativelike structure in designed four α-helix bundles driven by buried polar interactions. J. Am. Chem. Soc. 128, 14450-14451 (Pubitemid 44749832)
39. Discher, B.M., Koder, R.L., Moser, C.C. and Dutton, P.L. (2003) Hydrophilic to amphiphilic design in redox protein maquettes. Curr. Opin. Chem. Biol. 7, 741-748 (Pubitemid 37486119)
40. Chen, X.X., Moser, C.C., Pilloud, D.L., Gibney, B.R. and Dutton, P.L. (1999) Engineering oriented heme protein maquette monolayers through surface residue charge distribution patterns. J. Phys. Chem. B 103, 9029-9037 (Pubitemid 129613958)
41. Topoglidis, E., Discher, B.M., Moser, C.C., Dutton, P.L. and Durrant, J.R. (2003) Functionalizing nanocrystalline metal oxide electrodes with robust synthetic redox proteins. ChemBioChem 4, 1332-1339 (Pubitemid 38036415)
42. Pilloud, D.L., Chen, X.X., Dutton, P.L. and Moser, C.C. (2000) Electrochemistry of self-assembled monolayers of iron protoporphyrin IX attached to modified gold electrodes through thioether linkage. J. Phys. Chem. B 104, 2868-2877
43. Chen, X.X., Discher, B.M., Pilloud, D.L., Gibney, B.R., Moser, C.C. and Dutton, P.L. (2002) De novo design of a cytochrome b maquette for electron transfer and coupled reactions on electrodes. J. Phys. Chem. B 106, 617-624 (Pubitemid 35276180)