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Rosetta and the Design of Ligand Binding Sites

Part of the Methods in Molecular Biology book series (MIMB,volume 1414)

Abstract

Proteins that bind small molecules (ligands) can be used as biosensors, signal modulators, and sequestering agents. When naturally occurring proteins for a particular target ligand are not available, artificial proteins can be computationally designed. We present a protocol based on RosettaLigand to redesign an existing protein pocket to bind a target ligand. Starting with a protein structure and the structure of the ligand, Rosetta can optimize both the placement of the ligand in the pocket and the identity and conformation of the surrounding sidechains, yielding proteins that bind the target compound.

Key words

  • Computational design
  • Protein/small molecule interaction
  • Sequence optimization
  • Protein design
  • Ligand docking

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References

  1. Leader B, Baca QJ, Golan DE (2008) Protein therapeutics: a summary and pharmacological classification. Nat Rev Drug Discov 7(1):21–39. doi:10.1038/nrd2399

    CAS  CrossRef  PubMed  Google Scholar 

  2. Knudsen KE, Scher HI (2009) Starving the addiction: new opportunities for durable suppression of AR signaling in prostate cancer. Clin Cancer Res 15(15):4792–4798. doi:10.1158/1078-0432.CCR-08-2660

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  3. Baeumner AJ (2003) Biosensors for environmental pollutants and food contaminants. Anal Bioanal Chem 377(3):434–445. doi:10.1007/s00216-003-2158-9

    CAS  CrossRef  PubMed  Google Scholar 

  4. Morin A, Kaufmann KW, Fortenberry C, Harp JM, Mizoue LS, Meiler J (2011) Computational design of an endo-1,4-beta-xylanase ligand binding site. Protein Eng Des Sel 24(6):503–516. doi:10.1093/protein/gzr006

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  5. Morin A, Meiler J, Mizoue LS (2011) Computational design of protein-ligand interfaces: potential in therapeutic development. Trends Biotechnol 29(4):159–166. doi:10.1016/j.tibtech.2011.01.002

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  6. Jackel C, Kast P, Hilvert D (2008) Protein design by directed evolution. Annu Rev Biophys 37:153–173. doi:10.1146/annurev.biophys.37.032807.125832

    CAS  CrossRef  PubMed  Google Scholar 

  7. Nannemann DP, Birmingham WR, Scism RA, Bachmann BO (2011) Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis. Future Med Chem 3(7):809–819. doi:10.4155/fmc.11.48

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  8. Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D (2013) Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501(7466):212–216. doi:10.1038/nature12443

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  9. Feldmeier K, Hocker B (2013) Computational protein design of ligand binding and catalysis. Curr Opin Chem Biol 17(6):929–933 doi: 10.1016/j.cbpa.2013.10.002

    Google Scholar 

  10. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D (2005) Progress in modeling of protein structures and interactions. Science 310(5748):638–642. doi:10.1126/science.1112160

    CAS  CrossRef  PubMed  Google Scholar 

  11. 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 YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovic 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

    Google Scholar 

  12. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Design of a novel globular protein fold with atomic level accuracy. Science 302(5649):1364–1368 doi: 10.1126/science.1089427

    Google Scholar 

  13. Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D (2012) Principles for designing ideal protein structures. Nature 491(7423):222–227. doi:10.1038/nature11600

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  14. Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 38(16):5601–5608 doi: 10.1093/nar/gkq283

    Google Scholar 

  15. Sammond DW, Bosch DE, Butterfoss GL, Purbeck C, Machius M, Siderovski DP, Kuhlman B (2011) Computational design of the sequence and structure of a protein-binding peptide. J Am Chem Soc 133(12):4190–4192. doi:10.1021/ja110296z

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  16. Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332(6031):816–821. doi:10.1126/science.1202617

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  17. 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(5868):1387–1391. doi:10.1126/science.1152692

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  18. 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(7192):190–195. doi:10.1038/nature06879

    CrossRef  PubMed  Google Scholar 

  19. Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, 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. doi:10.1126/science.1190239

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  20. Allison B, Combs S, DeLuca S, Lemmon G, Mizoue L, Meiler J (2014) Computational design of protein-small molecule interfaces. J Struct Biol 185(2):193–202. doi:10.1016/j.jsb.2013.08.003

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  21. Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D (2011) RosettaScripts: a scripting language interface to the rosetta macromolecular modeling suite. PLoS One 6(6):20161. doi:10.1371/journal.pone.0020161

    Google Scholar 

  22. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65(3):538–548. doi:10.1002/prot.21086

    CAS  CrossRef  PubMed  Google Scholar 

  23. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385(2):381–392. doi:10.1016/j.jmb.2008.11.010

    CAS  CrossRef  PubMed  Google Scholar 

  24. Lemmon G, Meiler J (2012) Rosetta Ligand docking with flexible XML protocols. Methods Mol Biol 819:143–155. doi:10.1007/978-1-61779-465-0_10

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  25. DeLuca S, Khar K, Meiler J (2015) Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand. PLoS One 10(7):e0132508. doi: 10.1371/journal.pone.0132508

    Google Scholar 

  26. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33. doi:10.1186/1758-2946-3-33

    CrossRef  PubMed  PubMed Central  Google Scholar 

  27. Kothiwale S, Mendenhall JL, Meiler J (2015) BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform 7:47. doi: 10.1186/s13321-015-0095-1

  28. Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B 58(Pt 3 Pt 1):380–388 doi: 10.1107/S0108768102003890

    Google Scholar 

  29. Hawkins PC, 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. doi:10.1021/ci100031x

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  30. Labute P (2010) LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops. J Chem Inf Model 50(5):792–800. doi:10.1021/ci900508k

    CAS  CrossRef  PubMed  Google Scholar 

  31. Ebejer JP, Morris GM, Deane CM (2012) Freely available conformer generation methods: how good are they? J Chem Inf Model 52(5):1146–1158. doi:10.1021/ci2004658

    CAS  CrossRef  PubMed  Google Scholar 

  32. Nivon LG, Moretti R, Baker D (2013) A Pareto-optimal refinement method for protein design scaffolds. PLoS One 8(4), e59004. doi:10.1371/journal.pone.0059004

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  33. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. doi:10.1002/jcc.20084

    CAS  CrossRef  PubMed  Google Scholar 

  34. Sheffler W, Baker D (2009) RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci 18(1):229–239. doi:10.1002/pro.8

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Lawrence MC, Colman PM (1993) Shape complementarity at protein/protein interfaces. J Mol Biol 234(4):946–950. doi:10.1006/jmbi.1993.1648

    CAS  CrossRef  PubMed  Google Scholar 

  36. Stranges PB, Kuhlman B (2013) A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Sci 22(1):74–82. doi:10.1002/pro.2187

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  37. Nivon LG, Bjelic S, King C, Baker D (2014) Automating human intuition for protein design. Proteins 82(5):858–866. doi:10.1002/prot.24463

    CAS  CrossRef  PubMed  Google Scholar 

  38. Combs SA, Deluca SL, Deluca SH, Lemmon GH, Nannemann DP, Nguyen ED, Willis JR, Sheehan JH, Meiler J (2013) Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc 8(7):1277–1298. doi:10.1038/nprot.2013.074

    CAS  CrossRef  PubMed  Google Scholar 

  39. Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D (2013) High-resolution comparative modeling with RosettaCM. Structure 21(10):1735–1742. doi:10.1016/j.str.2013.08.005

    CAS  CrossRef  PubMed  Google Scholar 

  40. 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(12):2785–2794. doi:10.1110/ps.062353106

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  41. Henrich S, Salo-Ahen OM, Huang B, Rippmann FF, Cruciani G, Wade RC (2010) Computational approaches to identifying and characterizing protein binding sites for ligand design. J Mol Recognit 23(2):209–219. doi:10.1002/jmr.984

    CAS  PubMed  Google Scholar 

  42. Lemmon G, Meiler J (2013) Towards ligand docking including explicit interface water molecules. PLoS One 8(6), e67536. doi:10.1371/journal.pone.0067536

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  43. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190. doi:10.1101/gr.849004

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  44. DeLano WL (2007) The PyMOL Molecular Graphics System 1.0 edn. DeLano Scientific LLC, Palo Alto, CA, USA

    Google Scholar 

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Acknowledgements

This work was supported through NIH (R01 GM099842, R01 DK097376, R01 GM073151) and NSF (CHE 1305874). RM is further partially supported by grant from the RosettaCommons.

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Correspondence to Jens Meiler .

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Moretti, R., Bender, B.J., Allison, B., Meiler, J. (2016). Rosetta and the Design of Ligand Binding Sites. 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_4

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  • DOI: https://doi.org/10.1007/978-1-4939-3569-7_4

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