A molecular model and Monte Carlo simulation of flavivirus envelope building block

[Display omitted] ► A full molecular model of flavivirus envelope building block is constructed. ► Monte Carlo optimisation of the model in the implicit membrane is performed. ► The roles of stem and anchor residues are explained based on structure. ► Inhibitor binding site is stabilized in the open...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2012-08, Vol.425 (2), p.207-211
Main Authors: Osolodkin, Dmitry I., Kozlovskaya, Liubov I., Palyulin, Vladimir A., Pentkovski, Vladimir M., Karganova, Galina G., Zefirov, Nikolay S.
Format: Article
Language:English
Subjects:
Computer Simulation
Crystallography, X-Ray
Dengue virus
Dengue Virus - chemistry
Envelope proteins
Flavivirus
Implicit membrane
Models, Molecular
Molecular dynamics
Monte Carlo Method
Monte Carlo simulations
Protein Structure, Tertiary
Viral Envelope Proteins - chemistry
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Summary:[Display omitted] ► A full molecular model of flavivirus envelope building block is constructed. ► Monte Carlo optimisation of the model in the implicit membrane is performed. ► The roles of stem and anchor residues are explained based on structure. ► Inhibitor binding site is stabilized in the open state by M protein. A molecular model of mature dengue virus envelope building block consisting of two E and two M protein subunits is constructed. Monte Carlo optimisation is performed for the model in the implicit membrane system. Interactions between the ectodomains and membrane parts of E and M proteins are studied, and possible role of conserved residues is suggested. The opening of E protein detergent binding site and its fixation in the open state by the M non-structured loop is observed.
ISSN:0006-291X
1090-2104
DOI:10.1016/j.bbrc.2012.07.069