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PDBsum entry 2b0x
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Signaling protein
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PDB id
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2b0x
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Theoretical model |
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PDB id:
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Signaling protein
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Title:
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Theoretical model of platelet-activating factor receptor (pafr)
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Structure:
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Platelet activating factor receptor. Chain: a. Synonym: paf-r
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Source:
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Homo sapiens. Human. Cell_line: xenopus oocyte, cos-7 cell. Tissue: leukocyte
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Authors:
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C.S.Gui,W.L.Zhu,G.Chen,X.M.Luo,O.H.Liew,C.M.Puah,J.H.Shen, K.X.Chen,H.L.Jiang
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Key ref:
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C.Gui
et al.
(2007).
Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: molecular modeling and molecular dynamics simulation studies.
Proteins,
67,
41-52.
PubMed id:
DOI:
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Date:
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15-Sep-05
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Release date:
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04-Oct-05
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PROCHECK
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Headers
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References
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P25105
(PTAFR_HUMAN) -
Platelet-activating factor receptor
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Seq:
Struc:
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342 a.a.
342 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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DOI no:
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Proteins
67:41-52
(2007)
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PubMed id:
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Understanding the regulation mechanisms of PAF receptor by agonists and antagonists: molecular modeling and molecular dynamics simulation studies.
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C.Gui,
W.Zhu,
G.Chen,
X.Luo,
O.W.Liew,
C.M.Puah,
K.Chen,
H.Jiang.
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ABSTRACT
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Platelet-activating factor receptor (PAFR) is a member of G-protein coupled
receptor (GPCR) superfamily. Understanding the regulation mechanisms of PAFR by
its agonists and antagonists at the atomic level is essential for designing PAFR
antagonists as drug candidates for treating PAF-mediated diseases. In this
study, a 3D model of PAFR was constructed by a hierarchical approach integrating
homology modeling, molecular docking and molecular dynamics (MD) simulations.
Based on the 3D model, regulation mechanisms of PAFR by agonists and antagonists
were investigated via three 8-ns MD simulations on the systems of apo-PAFR,
PAFR-PAF and PAFR-GB. The simulations revealed that binding of PAF to PAFR
triggers the straightening process of the kinked helix VI, leading to its
activated state. In contrast, binding of GB to PAFR locks PAFR in its inactive
state.
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Selected figure(s)
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Figure 3.
Figure 3. Structures of (a) model 2-PAF complex, (b) model 2-GB
complex, (c) model 3-PAF complex, (d) model 3-GB complex, (e)
PAF (top) and GB (bottom).
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Figure 9.
Figure 9. Schematic representation of the mechanism of PAFR
activation.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2007,
67,
41-52)
copyright 2007.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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Q.Luo,
Y.Yao,
W.W.Han,
Y.H.Zhou,
and
Z.S.Li
(2009).
Homology modeling of a novel epoxide hydrolase (EH) from Aspergillus niger SQ-6: structure-activity relationship in expoxides inhibiting EH activity.
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J Mol Model,
15,
1125-1132.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
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Links
