Molecular dynamic simulation of Ca2+-ATPase interacting with lipid bilayer membrane
- Author(s): Samaneh Davoudi 1 ; Sepideh Amjad-Iranagh 2 ; Mahdi Zaeifi Yamchi 3
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View affiliations
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Affiliations:
1:
Chemical Engineering Department, Amirkabir University of Technology, Tehran, Iran;
2: Department of Chemistry, Amirkabir University of Technology, Tehran, Iran;
3: Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
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Affiliations:
1:
Chemical Engineering Department, Amirkabir University of Technology, Tehran, Iran;
- Source:
Volume 9, Issue 2,
April 2015,
p.
85 – 94
DOI: 10.1049/iet-nbt.2013.0073 , Print ISSN 1751-8741, Online ISSN 1751-875X
In biomedical and drug delivery treatments, protein Ca2+-ATPase in the lipid bilayer (plasma) membrane plays a key role by reducing multidrug resistance of the cancerous cells. The lipid bilayer membrane and the protein Ca2+-ATPase were simulated by utilising the Gromacs software and by applying the all-atom/united atom and coarse-grained models. The initial structure of Ca2+-ATPase was derived from X-ray diffraction and electron microscopy patterns and was placed in a simulated bilayer membrane of dipalmitoylphosphatidylcholine. The conformational changes were investigated by evaluating the root mean square deviation, root mean square fluctuation, order parameter, diffusion coefficients, partial density, thickness and area per lipid.
Inspec keywords: molecular configurations; drug delivery systems; lipid bilayers; molecular dynamics method; proteins; molecular biophysics; biomembranes
Other keywords: multidrug resistance; diffusion coefficients; area per lipid; partial density; order parameter; dipalmitoylphosphatidylcholine; conformational changes; ATPase; biomedical treatments; plasma membrane; electron microscopy patterns; mean square deviation; root mean square fluctuation; cancerous cells; lipid bilayer membrane; Gromacs software; coarse grained models; X-ray diffraction; thickness; drug delivery treatments; protein; molecular dynamic simulation
Subjects: Biomolecular structure, configuration, conformation, and active sites; Cellular biophysics; Biomolecular interactions, charge transfer complexes; Natural and artificial biomembranes; Biomolecular dynamics, molecular probes, molecular pattern recognition
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