Abstract
Recently, there have been several successful cases of introducing catalytic activity into proteins. One method that has been used successfully to achieve this is the theozyme placement and enzyme design algorithms implemented in Rosetta Molecular Modeling Suite. Here, we illustrate how to use this software to recapitulate the placement of catalytic residues and ligand into a protein using a theozyme, protein scaffold, and catalytic constraints as input.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Röthlisberger 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(7192):190–195
Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319(5868):1387–1391
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, Clair JLS, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329(5989):309–313
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban Y-EA, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487:545–574. doi:10.1016/B978-0-12-381270-4.00019-6
Tantillo DJ, Chen J, Houk KN (1998) Theozymes and compuzymes: theoretical models for biological catalysis. Curr Opin Chem Biol 2(6):743–750
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15(12):2785–2794
Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D (2011) De novo enzyme design using Rosetta3. PLoS ONE 6(5):e19230. doi:10.1371/journal.pone.0019230
Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D (2012) Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol 30(2):190–192
Radzicka A, Wolfenden R (1995) A proficient enzyme. Science 267(5194):90–93
Mak WS, Siegel JB (2014) Computational enzyme design: transitioning from catalytic proteins to enzymes. Curr Opin Struct Biol 27:87–94
Isorna P, Polaina J, Latorre-GarcÃa L, Cañada FJ, González B, Sanz-Aparicio J (2007) Crystal structures of Paenibacillus polymyxa β-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. J Mol Biol 371(5):1204–1218. doi:10.1016/j.jmb.2007.05.082
The PyMOL Molecular Graphics System, Version 1.5.0.5 Schrodinger, LLC
Spartan ’08, Wavefunction Inc., Irvine, CA
Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT (2010) Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 50(4):572–584
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd J, Brothers EN, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09. Gaussian, Inc., Wallingford, CT
O'Boyle NM, Vandermeersch T, Flynn CJ, Maguire AR, Hutchison GR (2011) Confab-Systematic generation of diverse low-energy conformers. J Cheminform 3:8
Acknowledgments
The authors would like to thank UC Davis, Sloan Foundation (BR2014-012), ARPA-E (DE-AR0000429), and CDFA (SCB14037) for funding.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Bertolani, S.J., Carlin, D.A., Siegel, J.B. (2016). Computational Introduction of Catalytic Activity into Proteins. In: Stoddard, B. (eds) Computational Design of Ligand Binding Proteins. Methods in Molecular Biology, vol 1414. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3569-7_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3569-7_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3567-3
Online ISBN: 978-1-4939-3569-7
eBook Packages: Springer Protocols