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Author:

Chen, Lei (Chen, Lei.) | Gong, Weikang (Gong, Weikang.) | Han, Zhongjie (Han, Zhongjie.) | Zhou, Wenxue (Zhou, Wenxue.) | Yang, Shuang (Yang, Shuang.) | Li, Chunhua (Li, Chunhua.) (Scholars:李春华)

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EI Scopus SCIE

Abstract:

Opioid receptors, a kind of G protein-coupled receptors (GPCRs), mainly mediate an analgesic response via allosterically transducing the signal of endogenous ligand binding in the extracellular domain to couple to effector proteins in the intracellular domain. The delta opioid receptor (DOP) is associated with emotional control besides pain control, which makes it an attractive therapeutic target. However, its allosteric mechanism and key residues responsible for the structural stability and signal communication are not completely clear. Here we utilize the Gaussian network model (GNM) and amino acid network (AAN) combined with perturbation methods to explore the issues. The constructed fcfGNMMD, where the force constants are optimized with the inverse covariance estimation based on the correlated fluctuations from the available DOP molecular dynamics (MD) ensemble, shows a better performance than traditional GNM in reproducing residue fluctuations and cross-correlations and in capturing function-ally low-frequency modes. Additionally, fcfGNM(MD) can consider implicitly the environmental effects to some extent. The lowest mode can well divide DOP segments and identify the two sodium ion (important allosteric regulator) binding coordination shells, and from the fastest modes, the key residues important for structure stabilization are identified. Using fcfGNMMD combined with a dynamic perturbation-response method, we explore the key residues related to the sodium ion binding. Interestingly, we identify not only the key residues in sodium ion binding shells but also the ones far away from the perturbation sites, which are involved in binding with DOP ligands, suggesting the possible long-range allosteric modulation of sodium binding for the ligand binding to DOP. Furthermore, utilizing the weighted AAN combined with attack perturbations, we identify the key residues for allosteric communication. This work helps strengthen the understanding of the allosteric communication mechanism in delta opioid receptor and can provide valuable information for drug design.

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Author Community:

  • [ 1 ] [Chen, Lei]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 2 ] [Gong, Weikang]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 3 ] [Han, Zhongjie]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 4 ] [Zhou, Wenxue]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 5 ] [Yang, Shuang]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China
  • [ 6 ] [Li, Chunhua]Beijing Univ Technol, Fac Environm & Life Sci, Beijing 100124, Peoples R China

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Source :

JOURNAL OF CHEMICAL INFORMATION AND MODELING

ISSN: 1549-9596

Year: 2022

Issue: 24

Volume: 62

Page: 6727-6738

5 . 6

JCR@2022

5 . 6 0 0

JCR@2022

ESI Discipline: CHEMISTRY;

ESI HC Threshold:53

JCR Journal Grade:1

CAS Journal Grade:2

Cited Count:

WoS CC Cited Count: 4

SCOPUS Cited Count: 4

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 4

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