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Novel Computational Methodologies for Structural Modeling of Spacious Ligand Binding Sites of G-Protein-Coupled Receptors : Development and Application to Human Leukotriene B4 Receptor
Joint Authors
Source
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-12-10
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Medicine
Information Technology and Computer Science
Abstract EN
This paper describes a novel method to predict the activated structures of G-protein-coupled receptors (GPCRs) with high accuracy, while aiming for the use of the predicted 3D structures in in silico virtual screening in the future.
We propose a new method for modeling GPCR thermal fluctuations, where conformation changes of the proteins are modeled by combining fluctuations on multiple time scales.
The core idea of the method is that a molecular dynamics simulation is used to calculate average 3D coordinates of all atoms of a GPCR protein against heat fluctuation on the picosecond or nanosecond time scale, and then evolutionary computation including receptor-ligand docking simulations functions to determine the rotation angle of each helix of a GPCR protein as a movement on a longer time scale.
The method was validated using human leukotriene B4 receptor BLT1 as a sample GPCR.
Our study demonstrated that the proposed method was able to derive the appropriate 3D structure of the active-state GPCR which docks with its agonists.
American Psychological Association (APA)
Ishino, Yoko& Harada, Takanori. 2012. Novel Computational Methodologies for Structural Modeling of Spacious Ligand Binding Sites of G-Protein-Coupled Receptors : Development and Application to Human Leukotriene B4 Receptor. The Scientific World Journal،Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-490929
Modern Language Association (MLA)
Ishino, Yoko& Harada, Takanori. Novel Computational Methodologies for Structural Modeling of Spacious Ligand Binding Sites of G-Protein-Coupled Receptors : Development and Application to Human Leukotriene B4 Receptor. The Scientific World Journal No. 2012 (2012), pp.1-11.
https://search.emarefa.net/detail/BIM-490929
American Medical Association (AMA)
Ishino, Yoko& Harada, Takanori. Novel Computational Methodologies for Structural Modeling of Spacious Ligand Binding Sites of G-Protein-Coupled Receptors : Development and Application to Human Leukotriene B4 Receptor. The Scientific World Journal. 2012. Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-490929
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-490929