Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor

J Comput Aided Mol Des. 2006 Jul-Aug;20(7-8):463-70. doi: 10.1007/s10822-006-9065-z. Epub 2006 Oct 13.

Abstract

It is well known that G protein-coupled receptors are prime targets for drug discovery. At the present time there is only one protein from this class that has an X-ray crystal structure, bovine rhodopsin. Crystal structures of rhodopsin have become invaluable templates for the modeling of class-A G protein-coupled receptors as they likely represent the overall topology of this family of proteins. However, because of low sequence homology within the class and the inherent mobility of integral membrane proteins, it is unlikely that this single structural template reflects the ensemble of conformations accessible for any given receptor. We have devised a procedure based upon comparative modeling that uses induced fit modeling coupled with binding site expansion. The modeling protocol enables an ensemble approach to binding mode prediction. The utility of models for beta-2 adrenergic receptor will be discussed.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Cattle
  • Humans
  • Hydrogen Bonding
  • Models, Molecular*
  • Molecular Sequence Data
  • Receptors, Adrenergic, beta-2 / chemistry*
  • Rhodopsin / chemistry
  • Sequence Alignment

Substances

  • Receptors, Adrenergic, beta-2
  • Rhodopsin