Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana

Akinori Hirashima, Hongwei Huang

研究成果: ジャーナルへの寄稿学術誌査読

29 被引用数 (Scopus)

抄録

AY333178 (from Periplaneta americana, 628 AAs) was selected as a target octopamine receptor (OAR) class OAR2 for this study using Discovery Studio (DS Modeling1.1/1.2, Accelrys Inc.). Blast similarity search was performed and identified that AY333178 contains N-terminal domain of GPCR. Based upon Blast and Pfam results, Rhodopsin 1U19 (protein data bank) was considered as an ideal homologue and used as a template for homology modeling due to its higher X-ray resolution at 2.2 Å. Sequence alignment between AY333178 and 1U19 was done using Align123 followed by a manual modification. The final alignment was carefully evaluated and evidenced to be matching the conserved residue data for class A GPCR fairly well. The 3D model of AY333178 was generated with MODELER, and further refined using CHARMm. Superimposition of the model was done over the template 1U19. Two fairly consistent profiles were observed demonstrating AY333178 model was reasonable and could be employed for the further docking study. Agonist docking into OAR2 model was done using LigandFit. The superimposition of two top poses of representative agonists was performed with a soft surface generated. Those models are considered to be used in designing new leads for hopefully more active compounds. Further research on the comparison of models for the agonists may elucidate the mechanisms of OAR2-ligand interactions.

本文言語英語
ページ(範囲)185-190
ページ数6
ジャーナルComputational Biology and Chemistry
32
3
DOI
出版ステータス出版済み - 6月 1 2008

!!!All Science Journal Classification (ASJC) codes

  • 構造生物学
  • 生化学
  • 有機化学
  • 計算数学

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