Open AccessMolecular dynamic simulation of Ca 2+ ‐ATPase interacting with lipid bilayer membrane
Author(s) -
Davoudi Samaneh,
AmjadIranagh Sepideh,
Zaeifi Yamchi Mahdi
Publication year - 2015
Publication title -
iet nanobiotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.366
H-Index - 38
eISSN - 1751-875X
pISSN - 1751-8741
DOI - 10.1049/iet-nbt.2013.0073
Subject(s) - lipid bilayer , molecular dynamics , biophysics , atpase , membrane , bilayer , chemistry , nanotechnology , physics , materials science , biology , biochemistry , enzyme , computational chemistry
In biomedical and drug delivery treatments, protein Ca 2+ ‐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 Ca 2+ ‐ATPase were simulated by utilising the Gromacs software and by applying the all‐atom/united atom and coarse‐grained models. The initial structure of Ca 2+ ‐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.