Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations

Yıl: 2013 Cilt: 37 Sayı: 3 Sayfa Aralığı: 449 - 463 Metin Dili: İngilizce İndeks Tarihi: 29-07-2022

Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations

Öz:
$beta_2$ -Adrenergic receptor ($beta_2$ AR) is a G protein-coupled receptor that is highlyexible and able to recognize a wide range of ligands through its conformational variations. Active and inactive conformations revealed by recent crystallographic experiments do not provide a complete dynamic picture of the receptor, especially in the binding site. In this study, molecular dynamics (MD) simulation through a residue-based coarse-grained model is used as an alternative and e cient method to explore a wider conformational search space. The system was composed of $beta_2$AR embedded into a 1-palmitoyl-2-oleoyl-phosphatidylcholine membrane bilayer with surrounding water. A total of 6 s of simulation at constant NPT was performed for a system of 6868 coarse-grained beads. The system reached equilibrium at around 0.1s. The overall 3-dimensional structure was well preserved throughout the simulation. Local residue-baseductuations were in good agreement with fully atomistic MD simulations. Four distinct snapshots were selected and reverse-mapped to all-atom representations with around 65,000 atoms. Each reverse-mapped system was later subjected to 100 ns of MD simulation for equilibration. Root mean square deviation clustering analysis yielded distinct receptor conformers for the binding site regions, which were suggested to be alternative representations of the binding pocket and thus were proposed as plausible targets in docking-based virtual screening experiments for the discovery of novel antagonists.
Anahtar Kelime:

Konular: Mühendislik, Kimya
Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık
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APA ÇAKAN S, AKDO GAN E (2013). Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. , 449 - 463.
Chicago ÇAKAN Sibel,AKDO GAN Ebru Demet Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. (2013): 449 - 463.
MLA ÇAKAN Sibel,AKDO GAN Ebru Demet Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. , 2013, ss.449 - 463.
AMA ÇAKAN S,AKDO GAN E Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. . 2013; 449 - 463.
Vancouver ÇAKAN S,AKDO GAN E Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. . 2013; 449 - 463.
IEEE ÇAKAN S,AKDO GAN E "Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations." , ss.449 - 463, 2013.
ISNAD ÇAKAN, Sibel - AKDO GAN, Ebru Demet. "Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations". (2013), 449-463.
APA ÇAKAN S, AKDO GAN E (2013). Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. Turkish Journal of Chemistry, 37(3), 449 - 463.
Chicago ÇAKAN Sibel,AKDO GAN Ebru Demet Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. Turkish Journal of Chemistry 37, no.3 (2013): 449 - 463.
MLA ÇAKAN Sibel,AKDO GAN Ebru Demet Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. Turkish Journal of Chemistry, vol.37, no.3, 2013, ss.449 - 463.
AMA ÇAKAN S,AKDO GAN E Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. Turkish Journal of Chemistry. 2013; 37(3): 449 - 463.
Vancouver ÇAKAN S,AKDO GAN E Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations. Turkish Journal of Chemistry. 2013; 37(3): 449 - 463.
IEEE ÇAKAN S,AKDO GAN E "Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations." Turkish Journal of Chemistry, 37, ss.449 - 463, 2013.
ISNAD ÇAKAN, Sibel - AKDO GAN, Ebru Demet. "Exploring distinct binding site regions of $beta_2$-adrenergic receptor via coarse-grained molecular dynamics simulations". Turkish Journal of Chemistry 37/3 (2013), 449-463.