Skip to main content
SpringerLink
Log in

Protein-Protein Docking Using Evolutionary Information

  • Protocol
  • First Online:
Protein Complex Assembly

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1764))

Abstract

The structural modeling of protein complexes by docking simulations has been attracting increasing interest with the rise of proteomics and of the number of experimentally identified binary interactions. Structures of unbound partners, either modeled or experimentally determined, can be used as input to sample as extensively as possible all putative binding modes and single out the most plausible ones. At the scoring step, evolutionary information contained in the joint multiple sequence alignments of both partners can provide key insights to recognize correct interfaces. Here, we describe a computational protocol based on the InterEvDock web server to exploit coevolution constraints in protein-protein docking methods. We provide methodology guidelines to prepare the input protein structures and generate improved alignments. We also explain how to extract and use the information returned by the server through the analysis of two representative examples.

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

Access this chapter

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 139.99
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

Institutional subscriptions

References

  1. Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7(3):188–197. https://doi.org/10.1038/nrm1859

    Article  PubMed  CAS  Google Scholar 

  2. Vajda S, Kozakov D (2009) Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 19(2):164–170. https://doi.org/10.1016/j.sbi.2009.02.008

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Dreze M, Charloteaux B, Milstein S, Vidalain PO, Yildirim MA, Zhong Q, Svrzikapa N, Romero V, Laloux G, Brasseur R, Vandenhaute J, Boxem M, Cusick ME, Hill DE, Vidal M (2009) ‘Edgetic’ perturbation of a C. Elegans BCL2 ortholog. Nat Methods 6(11):843–849. https://doi.org/10.1038/nmeth.1394

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  4. Wang Y, Sahni N, Vidal M (2015) Global edgetic rewiring in cancer networks. Cell Syst 1(4):251–253. https://doi.org/10.1016/j.cels.2015.10.006

    Article  PubMed  CAS  Google Scholar 

  5. Kadota Y, Amigues B, Ducassou L, Madaoui H, Ochsenbein F, Guerois R, Shirasu K (2008) Structural and functional analysis of SGT1-HSP90 core complex required for innate immunity in plants. EMBO Rep 9(12):1209–1215. https://doi.org/10.1038/embor.2008.185

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ, Critical Assessment of PI (2003) CAPRI: a critical assessment of predicted interactions. Proteins 52(1):2–9. https://doi.org/10.1002/prot.10381

    Article  PubMed  CAS  Google Scholar 

  7. Wodak SJ, Janin J (2017) Modeling protein assemblies: critical assessment of predicted interactions (CAPRI) 15 years hence.: 6TH CAPRI evaluation meeting April 17-19 Tel-Aviv, Israel. Proteins 85(3):357–358. https://doi.org/10.1002/prot.25233

    Article  PubMed  CAS  Google Scholar 

  8. Lensink MF, Velankar S, Wodak SJ (2017) Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition. Proteins 85(3):359–377. https://doi.org/10.1002/prot.25215

    Article  PubMed  CAS  Google Scholar 

  9. Huang SY (2014) Search strategies and evaluation in protein-protein docking: principles, advances and challenges. Drug Discov Today 19(8):1081–1096. https://doi.org/10.1016/j.drudis.2014.02.005

    Article  PubMed  CAS  Google Scholar 

  10. Yu J, Vavrusa M, Andreani J, Rey J, Tuffery P, Guerois R (2016) InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. Nucleic Acids Res 44(W1):W542–W549. https://doi.org/10.1093/nar/gkw340

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Aloy P, Ceulemans H, Stark A, Russell RB (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 332(5):989–998

    Article  CAS  PubMed  Google Scholar 

  12. Levy ED, Boeri Erba E, Robinson CV, Teichmann SA (2008) Assembly reflects evolution of protein complexes. Nature 453(7199):1262–1265. https://doi.org/10.1038/nature06942

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Faure G, Andreani J, Guerois R (2012) InterEvol database: exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res 40(Database issue):D847–D856. https://doi.org/10.1093/nar/gkr845

    Article  PubMed  CAS  Google Scholar 

  14. Ofran Y, Rost B (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23(2):e13–e16. https://doi.org/10.1093/bioinformatics/btl303

    Article  PubMed  CAS  Google Scholar 

  15. Res I, Mihalek I, Lichtarge O (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 21(10):2496–2501. https://doi.org/10.1093/bioinformatics/bti340

    Article  PubMed  CAS  Google Scholar 

  16. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A 106(1):67–72. https://doi.org/10.1073/pnas.0805923106

    Article  PubMed  Google Scholar 

  17. Marks DS, Hopf TA, Sander C (2012) Protein structure prediction from sequence variation. Nat Biotechnol 30(11):1072–1080. https://doi.org/10.1038/nbt.2419

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D (2015) Large-scale determination of previously unsolved protein structures using evolutionary information. elife 4:e09248. https://doi.org/10.7554/eLife.09248

    Article  PubMed  PubMed Central  Google Scholar 

  19. Andreani J, Faure G, Guerois R (2012) Versatility and invariance in the evolution of homologous heteromeric interfaces. PLoS Comput Biol 8(8):e1002677. https://doi.org/10.1371/journal.pcbi.1002677

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Andreani J, Faure G, Guerois R (2013) InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. Bioinformatics 29(14):1742–1749. https://doi.org/10.1093/bioinformatics/btt260

    Article  PubMed  CAS  Google Scholar 

  21. Garzon JI, Lopez-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P (2009) FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 25(19):2544–2551. https://doi.org/10.1093/bioinformatics/btp447

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A (2013) Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics 29(24):3158–3166. https://doi.org/10.1093/bioinformatics/btt560

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Yu J, Andreani J, Ochsenbein F, Guerois R (2017) Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI rounds 28-35. Proteins 85(3):378–390. https://doi.org/10.1002/prot.25180

    Article  PubMed  CAS  Google Scholar 

  24. Nakamura Y, Umehara T, Tanaka A, Horikoshi M, Padmanabhan B, Yokoyama S (2007) Structural basis for the recognition between the regulatory particles Nas6 and Rpt3 of the yeast 26S proteasome. Biochem Biophys Res Commun 359(3):503–509. https://doi.org/10.1016/j.bbrc.2007.05.138

    Article  PubMed  CAS  Google Scholar 

  25. Hwang H, Vreven T, Janin J, Weng Z (2010) Protein-protein docking benchmark version 4.0. Proteins 78(15):3111–3114. https://doi.org/10.1002/prot.22830

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Tesmer JJ, Sunahara RK, Gilman AG, Sprang SR (1997) Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gsalpha.GTPgammaS. Science 278(5345):1907–1916

    Article  CAS  PubMed  Google Scholar 

  27. Lensink MF, Mendez R, Wodak SJ (2007) Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 69(4):704–718. https://doi.org/10.1002/prot.21804

    Article  PubMed  CAS  Google Scholar 

  28. Mosca R, Ceol A, Aloy P (2013) Interactome3D: adding structural details to protein networks. Nat Methods 10(1):47–53. https://doi.org/10.1038/nmeth.2289

    Article  PubMed  CAS  Google Scholar 

  29. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server):W244–W248. https://doi.org/10.1093/nar/gki408

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Alva V, Nam SZ, Soding J, Lupas AN (2016) The MPI bioinformatics toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res 44(W1):W410–W415. https://doi.org/10.1093/nar/gkw348

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 54:5 6 1–5 6 37. https://doi.org/10.1002/cpbi.3

    Article  Google Scholar 

  32. Yu J, Picord G, Tuffery P, Guerois R (2015) HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinformatics 31(23):3850–3852. https://doi.org/10.1093/bioinformatics/btv441

    Article  PubMed  CAS  Google Scholar 

  33. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191. https://doi.org/10.1093/bioinformatics/btp033

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18(Suppl 1):S71–S77

    Article  PubMed  Google Scholar 

  35. Teichmann SA (2002) The constraints protein-protein interactions place on sequence divergence. J Mol Biol 324(3):399–407

    Article  CAS  PubMed  Google Scholar 

  36. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, Huang ES (2004) Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13(1):190–202. https://doi.org/10.1110/ps.03323604

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951–960. https://doi.org/10.1093/bioinformatics/bti125

    Article  PubMed  Google Scholar 

  38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    Article  PubMed  CAS  Google Scholar 

  39. Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C (2011) OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 39(Database):D289–D294. https://doi.org/10.1093/nar/gkq1238

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France

    Aravindan Arun Nadaradjane, Raphael Guerois & Jessica Andreani

Authors
  1. Aravindan Arun Nadaradjane
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Raphael Guerois
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jessica Andreani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Raphael Guerois or Jessica Andreani .

Editor information

Editors and Affiliations

  1. MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom

    Joseph A. Marsh

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Nadaradjane, A.A., Guerois, R., Andreani, J. (2018). Protein-Protein Docking Using Evolutionary Information. In: Marsh, J. (eds) Protein Complex Assembly. Methods in Molecular Biology, vol 1764. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7759-8_28

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7759-8_28

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7758-1

  • Online ISBN: 978-1-4939-7759-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation