Advertisement

Optimizing GPCR Two-Dimensional Topology from Contact Map

  • Hongjie Wu
  • Dadong Dai
  • Huaxiang Shen
  • Ru Yang
  • Weizhong Lu
  • Qiming Fu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10956)

Abstract

Comparative folding G-protein coupled receptors are hampered by distant homology and limited experimental templates. In order to explore the possibility of ab initio modeling, we proposed an optimization method of GPCR two-dimensional topologies based on the contact map that does not apply to any homologous templates or fragments, using a cost-effective 2D helix topology phase. The approach was evaluated in 12 solved GPCRs, our method has seven advantages over SWISS-MODEL, and the overall RMSD was reduced by about 20%.

Keywords

GPCR topology Protein prediction Optimization 

Notes

Acknowledgements

This paper is supported by the National Natural Science Foundation of China (61772357, 61502329, 61672371), Jiangsu 333 talent project and top six talent peak project (DZXX-010), Suzhou Foresight Research Project (SYG201704, SNG201610) and the Postgraduate Research & Practice Innovation Program of Jiangsu Province (SJCX17_0680).

References

  1. 1.
    Fillmore, D.: It’s a GPCR world. Mod. Drug Discov. 11, 24–28 (2004)Google Scholar
  2. 2.
    Takeda, S., Kadowaki, S., Haga, T., Takaesu, H., Mitaku, S.: Identification of G protein-coupled receptor genes from the human genome sequence. FEBS Lett. 520(1–3), 97–101 (2002)CrossRefGoogle Scholar
  3. 3.
    Kufareva, I., Katritch, V., Participants of GD., Stevens, R.C., Abagyan, R.: Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 22(8), 1120–1139 (2014)CrossRefGoogle Scholar
  4. 4.
    Kufareva, I., Rueda, M., Katritch, V., Stevens, R.C., Abagyan, R.: Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19(8), 1108–1126 (2011)CrossRefGoogle Scholar
  5. 5.
    Zhang, J., Yang, J., Jang, R., Zhang, Y.: GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure 23(8), 1538–1549 (2015)CrossRefGoogle Scholar
  6. 6.
    Wu, H., et al.: Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science 344(6179), 58–64 (2014)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Electronic and Information EngineeringSuzhou University of Science and TechnologySuzhouChina
  2. 2.Jiangsu Province Key Laboratory of Intelligent Building Energy EfficiencySuzhou University of Science and TechnologySuzhouChina

Personalised recommendations