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Application of a Membrane Protein Structure Prediction Web Service GPCRM to a Gastric Inhibitory Polypeptide Receptor Model

  • Ewelina Rutkowska
  • Przemyslaw Miszta
  • Krzysztof Mlynarczyk
  • Jakub Jakowiecki
  • Pawel Pasznik
  • Slawomir Filipek
  • Dorota Latek
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10209)

Abstract

A novel versatile tool named GPCRM has been developed. It targets structure prediction of a distinct protein family of G protein-coupled receptors (GPCRs). In principle, GPCRM builds a GPCR model using a MODELLER-based homology modeling procedure. In addition, that commonly used procedure was improved by using comparison of sequence profiles, multiple template structures and the extensive loop refinement in Rosetta. We applied our method to predict a three dimensional structure of a gastric inhibitory polypeptide receptor (GIPR) from the secretin-like class B of human GPCRs. The GIPR model was also tested in an ensemble docking study in which we investigated plausible interactions of four potential antagonists with that receptor. Out of those four ligands we suggested ChEMBL_1933363 as the most potent antagonist of GIPR based on the Glide docking results.

Keywords

Gastric inhibitory polypeptide receptor GIPR Antagonist ChEMBL_1933363 GPCRM G protein-coupled receptors Membrane proteins MODELLER Rosetta Structure prediction Homology modeling 

Notes

Acknowledgments

The current study was financed by National Science Centre in Poland, the SONATA grant no. DEC-2012/07/D/NZ1/04244.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Ewelina Rutkowska
    • 1
  • Przemyslaw Miszta
    • 1
  • Krzysztof Mlynarczyk
    • 1
  • Jakub Jakowiecki
    • 1
  • Pawel Pasznik
    • 1
  • Slawomir Filipek
    • 1
  • Dorota Latek
    • 1
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland

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