Skip to main content
SpringerLink
Log in
Book cover

G Protein-Coupled Receptors in Drug Discovery pp 295–311Cite as

Experiment-Guided Molecular Modeling of Protein–Protein Complexes Involving GPCRs

  • Protocol

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1335))

Abstract

Experimental structure determination for G protein-coupled receptors (GPCRs) and especially their complexes with protein and peptide ligands is at its infancy. In the absence of complex structures, molecular modeling and docking play a large role not only by providing a proper 3D context for interpretation of biochemical and biophysical data, but also by prospectively guiding experiments. Experimentally confirmed restraints may help improve the accuracy and information content of the computational models. Here we present a hybrid molecular modeling protocol that integrates heterogeneous experimental data with force field-based calculations in the stochastic global optimization of the conformations and relative orientations of binding partners. Some experimental data, such as pharmacophore-like chemical fields or disulfide-trapping restraints, can be seamlessly incorporated in the protocol, while other types of data are more useful at the stage of solution filtering. The protocol was successfully applied to modeling and design of a stable construct that resulted in crystallization of the first complex between a chemokine and its receptor. Examples from this work are used to illustrate the steps of the protocol. The utility of different types of experimental data for modeling and docking is discussed and caveats associated with data misinterpretation are highlighted.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R (2011) Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19(8):1108–1126

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  2. Wu B, Chien EYT, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330(6007):1066–1071. doi:10.1126/science.1194396

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Kufareva I, Chen Y-C, Ilatovskiy AV, Abagyan R (2012) Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem 12(17):1869–1882. doi:10.2174/1568026611209061869

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Kamal JKA, Chance MR (2008) Modeling of protein binary complexes using structural mass spectrometry data. Protein Sci 17(1):79–94

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Goldsmith SC, Guan JQ, Almo S, Chance M (2001) Synchrotron protein footprinting: a technique to investigate protein–protein interactions. J Biomol Struct Dyn 19(3):405–418

    Article  CAS  PubMed  Google Scholar 

  6. Xu G, Chance MR (2004) Radiolytic modification of acidic amino acid residues in peptides: probes for examining protein–protein interactions. Anal Chem 76(5):1213–1221

    Article  CAS  PubMed  Google Scholar 

  7. Guan J-Q, Chance MR (2005) Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci 30(10):583–592

    Article  CAS  PubMed  Google Scholar 

  8. Dong M, Lam PCH, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ (2007) Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol 72(2):280–290

    Article  CAS  PubMed  Google Scholar 

  9. Chen Q, Pinon DI, Miller LJ, Dong M (2009) Molecular basis of glucagon-like peptide 1 docking to its intact receptor studied with carboxyl-terminal photolabile probes. J Biol Chem 284(49):34135–34144. doi:10.1074/jbc.M109.038109

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Chen Q, Pinon DI, Miller LJ, Dong M (2010) Spatial approximations between residues 6 and 12 in the amino-terminal region of glucagon-like peptide 1 and its receptor: a region critical for biological activity. J Biol Chem 285(32):24508–24518. doi:10.1074/jbc.M110.135749

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Miller LJ, Chen Q, Lam PC-H, Pinon DI, Sexton PM, Abagyan R, Dong M (2011) Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. J Biol Chem 286(18):15895–15907. doi:10.1074/jbc.M110.217901

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Dong M, Lam PCH, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller LJ (2011) Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem 286(27):23888–23899

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Coin I, Katritch V, Sun T, Xiang Z, Siu FY, Beyermann M, Stevens RC, Wang L (2013) Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell 155(6):1258–1269. doi:10.1016/j.cell.2013.11.008

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Wittelsberger A, Corich M, Thomas BE, Lee B-K, Barazza A, Czodrowski P, Mierke DF, Chorev M, Rosenblatt M (2006) The mid-region of parathyroid hormone (1–34) serves as a functional docking domain in receptor activation†. Biochemistry 45(7):2027–2034. doi:10.1021/bi051833a

    Article  CAS  PubMed  Google Scholar 

  15. Pham V, Sexton PM (2004) Photoaffinity scanning in the mapping of the peptide receptor interface of class II G protein-coupled receptors. J Pept Sci 10(4):179–203. doi:10.1002/psc.541

    Article  CAS  PubMed  Google Scholar 

  16. Grunbeck A, Huber T, Abrol R, Trzaskowski B, Goddard WA, Sakmar TP (2012) Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor. ACS Chem Biol 7(6):967–972. doi:10.1021/cb300059z

    Article  CAS  PubMed  Google Scholar 

  17. Grunbeck A, Sakmar TP (2013) Probing G protein-coupled receptor–ligand interactions with targeted photoactivatable cross-linkers. Biochemistry 52(48):8625–8632. doi:10.1021/bi401300y

    Article  CAS  PubMed  Google Scholar 

  18. Buck E, Wells JA (2005) Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor. Proc Natl Acad Sci U S A 102(8):2719–2724. doi:10.1073/pnas.0500016102

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Hagemann IS, Miller DL, Klco JM, Nikiforovich GV, Baranski TJ (2008) Structure of the complement factor 5a receptor–ligand complex studied by disulfide trapping and molecular modeling. J Biol Chem 283(12):7763–7775. doi:10.1074/jbc.M709467200

    Article  CAS  PubMed  Google Scholar 

  20. Monaghan P, Thomas BE, Woznica I, Wittelsberger A, Mierke DF, Rosenblatt M (2008) Mapping peptide hormone–receptor interactions using a disulfide-trapping approach†. Biochemistry 47(22):5889–5895. doi:10.1021/bi800122f

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Dong M, Xu X, Ball AM, Makhoul JA, Lam PCH, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ (2012) Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J 26:5092–5105

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM (2014) Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: Molecular modeling and experimental validation. Proc Natl Acad Sci U S A 111(50):E5363–E5372. doi:10.1073/pnas.1417037111

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Pellequer J-L, Chen S-wW (2006) Multi-template approach to modeling engineered disulfide bonds. Proteins 65(1):192–202. doi:10.1002/prot.21059

    Article  CAS  PubMed  Google Scholar 

  24. Skelton NJ, Quan C, Reilly D, Lowman H (1999) Structure of a CXC chemokine-receptor fragment in complex with interleukin-8. Structure 7(2):157–168, http://dx.doi.org/10.1016/S0969-2126(99)80022-7

    Article  CAS  PubMed  Google Scholar 

  25. Johnston CA, Siderovski DP (2007) Structural basis for nucleotide exchange on Gαi subunits and receptor coupling specificity. Proc Natl Acad Sci 104(6):2001–2006. doi:10.1073/pnas.0608599104

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Johnston CA, Kimple AJ, Giguère PM, Siderovski DP (2008) RETRACTED: structure of the parathyroid hormone receptor C terminus bound to the G-protein dimer Gβ1γ2. Structure 16(7):1086–1094. doi:10.1016/j.str.2008.04.010

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Veldkamp CT, Seibert C, Peterson FC, De la Cruz NB, Haugner JC III, Basnet H, Sakmar TP, Volkman BF (2008) Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12. Sci Signal 1(37):ra4. doi:10.1126/scisignal.1160755

    Article  PubMed Central  PubMed  Google Scholar 

  28. Millard Christopher J, Ludeman Justin P, Canals M, Bridgford Jessica L, Hinds Mark G, Clayton Daniel J, Christopoulos A, Payne Richard J, Stone Martin J (2014) Structural basis of receptor sulfotyrosine recognition by a CC chemokine: the N-terminal region of CCR3 bound to CCL11/Eotaxin-1. Structure 22(11):1571–1581, http://dx.doi.org/10.1016/j.str.2014.08.023

    Article  CAS  PubMed  Google Scholar 

  29. Johnston CA, Siderovski DP (2012) Retraction for Johnston and Siderovski. Structural basis for nucleotide exchange on Gαi subunits and receptor coupling specificity. Proc Natl Acad Sci U S A 109(5):1808. doi:10.1073/pnas.1200173109

    CAS  PubMed  Google Scholar 

  30. Johnston Christopher A, Kimple Adam J, Giguère Patrick M, Siderovski David P (2011) Retraction notice to: structure of the parathyroid hormone receptor C terminus bound to the G-protein dimer Gβ1γ2. Structure 19(8):1200. doi:10.1016/j.str.2011.07.010

    Article  Google Scholar 

  31. Kufareva I, Salanga CS, Handel TM (2015) Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies. Immunol Cell Biol 93(4):372–383

    Article  CAS  PubMed  Google Scholar 

  32. Orry AJW, Abagyan R (2012) Preparation and refinement of model protein–ligand complexes. Methods Mol Biol 857:351–373

    Article  CAS  PubMed  Google Scholar 

  33. Totrov M, Abagyan R (2001) Protein–ligand docking as an energy optimization problem. In: Raffa RB (ed) Drug-receptor thermodynamics: introduction and applications. Wiley, Chichester, pp 603–624

    Google Scholar 

  34. Fernandez-Recio J, Totrov M, Abagyan R (2002) Soft protein–protein docking in internal coordinates. Protein Sci 11(2):280–291

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Abagyan R, Totrov M (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235(3):983–1002

    Article  CAS  PubMed  Google Scholar 

  36. Totrov M, Abagyan R (1994) Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol 1(4):259–263

    Article  CAS  PubMed  Google Scholar 

  37. Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM (2015) Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science 347:1117–1122. doi:10.1126/science.1261064

    Article  CAS  PubMed  Google Scholar 

  38. Bottegoni G, Kufareva I, Totrov M, Abagyan R (2009) Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem 52(2):397–406

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Totrov M, Abagyan R (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 18:178–184

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Totrov M (2008) Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Drug Design 71(1):15–27. doi:10.1111/j.1747-0285.2007.00605.x

    Article  CAS  Google Scholar 

  41. Kufareva I, Katritch V, Stevens Raymond C, Abagyan R (2014) Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 22(8):1120–1139. doi:10.1016/j.str.2014.06.012

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  42. Arnautova YA, Abagyan RA, Totrov M (2011) Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins 79(2):477–498. doi:10.1002/prot.22896

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Veldkamp CT, Ziarek JJ, Peterson FC, Chen Y, Volkman BF (2010) Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure-based drug design. J Am Chem Soc 132(21):7242–7243. doi:10.1021/ja1002263

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  44. Totrov M, Abagyan R (1997) Flexible protein–ligand docking by global energy optimization in internal coordinates. Proteins 1:215–220

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

Authors thank Martin Gustavsson, Lauren G. Holden, Ling Qin, Yi Zheng, and other members of Handel lab at UCSD for valuable input regarding the disulfide trapping assay in application to chemokine receptor interactions. This work is partially supported by National Institutes of Health grants R01 GM071872, U01 GM094612, U54 GM094618, and R01 AI118985. We apologize to many researchers whose work could not be acknowledged appropriately due to space limitations.

Author information

Authors and Affiliations

  1. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, MC 0684, 9500 Gilman Drive, San Diego, La Jolla, CA, 92093, USA

    Irina Kufareva, Tracy M. Handel & Ruben Abagyan

Authors
  1. Irina Kufareva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tracy M. Handel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ruben Abagyan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ruben Abagyan .

Editor information

Editors and Affiliations

  1. Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA

    Marta Filizola

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Kufareva, I., Handel, T.M., Abagyan, R. (2015). Experiment-Guided Molecular Modeling of Protein–Protein Complexes Involving GPCRs. In: Filizola, M. (eds) G Protein-Coupled Receptors in Drug Discovery. Methods in Molecular Biology, vol 1335. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2914-6_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2914-6_19

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2913-9

  • Online ISBN: 978-1-4939-2914-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation