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Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes

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  • Michael Leguèbe
  • Chuong Nguyen
  • Luciana Capece
  • Zung Hoang
  • Alejandro Giorgetti
  • Paolo Carloni

Abstract

Understanding how ligands bind to G-protein coupled receptors (GPCRs) provides insights into a myriad of cell processes and is crucial for drug development. Here we extend a hybrid molecular mechanics/coarse-grained (MM/CG) approach applied previously to enzymes to GPCR/ligand complexes. The accuracy of this method for structural predictions is established by comparison with recent atomistic molecular dynamics simulations on the human β2 adrenergic receptor, a member of the GPCRs superfamily. The results obtained with the MM/CG methodology show a good agreement with previous all-atom classical dynamics simulations, in particular in the structural description of the ligand binding site. This approach could be used for high-throughput predictions of ligand poses in a variety of GPCRs.

Suggested Citation

  • Michael Leguèbe & Chuong Nguyen & Luciana Capece & Zung Hoang & Alejandro Giorgetti & Paolo Carloni, 2012. "Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-7, October.
    • Handle: RePEc:plo:pone00:0047332
    DOI: 10.1371/journal.pone.0047332
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