Skip to main content
SpringerLink
Log in
Book cover

TRP Channels pp 1–21Cite as

Molecular Evolution Bioinformatics Toward Structural Biology of TRPV1-4 Channels

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1987))

Abstract

Bioinformatics is a very resourceful tool to understand evolution of membrane proteins, such as transient receptor potential channels. Expert bioinformatics users rely on specialized scripting and programming skills. Several web servers and standalone tools are available for nonadvanced users willing to develop projects to understand their system of choice. In this case, we present a desktop-based protocol to develop evostructural hypotheses based on basic bioinformatics skills and resources, specifically for a small subgroup of TRPV channels, which can be further implemented for larger datasets.

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   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   169.99
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. Liang J, Naveed H, Jimenez-Morales D et al (2012) Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta 1818:927–941

    Article  CAS  Google Scholar 

  2. Bill RM, Henderson PJF, Iwata S et al (2011) Overcoming barriers to membrane protein structure determination. Nat Biotechnol 29:335–340

    Article  CAS  Google Scholar 

  3. Pierri CL, Parisi G, Porcelli V (2010) Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. Biochim Biophys Acta 1804:1695–1712

    Article  CAS  Google Scholar 

  4. Kozma D, Simon I, Tusnády GE (2013) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res 41:D524–D529

    Article  CAS  Google Scholar 

  5. Liao M, Cao E, Julius D et al (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–112

    Article  CAS  Google Scholar 

  6. Huynh KW, Cohen MR, Jiang J et al (2016) Structure of the full-length TRPV2 channel by cryo-EM. Nat Commun 7:11130

    Article  CAS  Google Scholar 

  7. Zubcevic L, Herzik MA, Chung BC et al (2016) Cryo-electron microscopy structure of the TRPV2 ion channel. Nat Struct Mol Biol 23:1–9

    Article  Google Scholar 

  8. Arinaminpathy Y, Khurana E, Engelman DM et al (2009) Computational analysis of membrane proteins: the largest class of drug targets. Drug Discov Today 14:1130–1135

    Article  CAS  Google Scholar 

  9. Fuchs A, Martin-Galiano AJ, Kalman M et al (2007) Co-evolving residues in membrane proteins. Bioinformatics 23:3312–3319

    Article  CAS  Google Scholar 

  10. Gromiha MM, Ou Y-Y (2013) Bioinformatics approaches for functional annotation of membrane proteins. Brief Bioinform 15(2):155–168

    Article  Google Scholar 

  11. Lundstrom K (2006) Structural genomics for membrane proteins. Cell Mol Life Sci 63:2597–2607

    Article  CAS  Google Scholar 

  12. Marks DS, Colwell LJ, Sheridan R et al (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One 6:e28766

    Article  CAS  Google Scholar 

  13. Forrest LR, Tang CL, Honig B (2006) On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 91:508–517

    Article  CAS  Google Scholar 

  14. Holder M, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet 4:275–284

    Article  CAS  Google Scholar 

  15. Grishin NV (2012) Membrane protein structure predictions for exploration. Cell 149:1424–1425

    Article  CAS  Google Scholar 

  16. Nugent T, Jones DT (2012) Membrane protein structural bioinformatics. J Struct Biol 179:327–337

    Article  CAS  Google Scholar 

  17. Montell C (2001) Physiology, phylogeny, and functions of the TRP superfamily of cation channels. Sci STKE 2001(90):re1

    CAS  PubMed  Google Scholar 

  18. Saito S, Shingai R (2006) Evolution of thermoTRP ion channel homologs in vertebrates. Physiol Genomics 27:219–230

    Article  CAS  Google Scholar 

  19. Saito S, Fukuta N, Shingai R et al (2011) Evolution of vertebrate transient receptor potential vanilloid 3 channels: opposite temperature sensitivity between mammals and western clawed frogs. PLoS Genet 7:e1002041

    Article  CAS  Google Scholar 

  20. Saito S, Ohkita M, Saito CT et al (2016) Evolution of heat sensors drove shifts in thermosensation between xenopus species adapted to different thermal niches. J Biol Chem 291:11446–11459

    Article  CAS  Google Scholar 

  21. Saito S, Tominaga M (2017) Evolutionary tuning of TRPA1 and TRPV1 thermal and chemical sensitivity in vertebrates. Temperature (Austin) 4:141–152

    Article  Google Scholar 

  22. Doñate-Macián P, Perálvarez-Marín A (2014) Dissecting domain-specific evolutionary pressure profiles of transient receptor potential vanilloid subfamily members 1 to 4. PLoS One 9:e110715

    Article  Google Scholar 

  23. Peng G, Shi X, Kadowaki T (2015) Evolution of TRP channels inferred by their classification in diverse animal species. Mol Phylogenet Evol 84:145–157

    Article  CAS  Google Scholar 

  24. Sardar P, Kumar A, Bhandari A et al (2012) Conservation of tubulin-binding sequences in TRPV1 throughout evolution. PLoS One 7:e31448

    Article  CAS  Google Scholar 

  25. Andrade MA, Sander C (1997) Bioinformatics: from genome data to biological knowledge. Curr Opin Biotechnol 8(6):675–683

    Article  CAS  Google Scholar 

  26. Edwards YJK, Cottage A (2003) Bioinformatics methods to predict protein structure and function: a practical approach. Mol Biotechnol 23:139–166

    Article  CAS  Google Scholar 

  27. Liu Y, Lu F, Jiang H et al (2017) Positive selection acted on the extracellular transmembrane linkers of heat receptors during evolution. J Therm Biol 64:86–91

    Article  CAS  Google Scholar 

  28. Palovcak E, Delemotte L, Klein ML et al (2015) Comparative sequence analysis suggests a conserved gating mechanism for TRP channels. J Gen Physiol 146:37–50

    Article  CAS  Google Scholar 

  29. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  Google Scholar 

  30. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    Article  CAS  Google Scholar 

  31. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948

    Article  CAS  Google Scholar 

  32. Katoh K, Misawa K, ichi KK et al (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  Google Scholar 

  33. Edgar RC, Batzoglou S (2006) Multiple sequence alignment. Curr Opin Struct Biol 16:368–373

    Article  CAS  Google Scholar 

  34. Zhang X, Ren W, DeCaen P et al (2012) Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel. Nature 486:130–134

    Article  CAS  Google Scholar 

  35. Ashkenazy H, Erez E, Martz E et al (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38:W529–W533

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain

    Pau Doñate-Macián & Alex Perálvarez-Marín

  2. Institute of Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, Scotland, UK

    Alba Crespi-Boixader

Authors
  1. Pau Doñate-Macián
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alba Crespi-Boixader
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alex Perálvarez-Marín
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alex Perálvarez-Marín .

Editor information

Editors and Affiliations

  1. Instituto de Biología, Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain

    Antonio Ferrer-Montiel

  2. Experimental Anesthesiology and Pain Research, Department of Anesthesiology and Intensive Care Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany

    Tim Hucho

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Doñate-Macián, P., Crespi-Boixader, A., Perálvarez-Marín, A. (2019). Molecular Evolution Bioinformatics Toward Structural Biology of TRPV1-4 Channels. In: Ferrer-Montiel, A., Hucho, T. (eds) TRP Channels. Methods in Molecular Biology, vol 1987. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9446-5_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9446-5_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9445-8

  • Online ISBN: 978-1-4939-9446-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation