Abstract
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.
Highlights
Ca2+-ATPase, adenosine triphosphate (ATP), which is a serine type lipid, is a transporter protein in the plasma membrane which acts as calcium (Ca2+) remover from the cells and its action is vital for regulating the amount of Ca2+ within the cells [1]
Having smaller Root mean square deviation (RMSD), as has been observed in a previous simulation work [31], it is seen from Fig. 3 that system 4 with protein 2 is more stable than the systems with protein 1
The results indicate that the protein 2 with the initial structure obtained by X-ray diffraction is more stable than protein 1 with the initial structure obtained by electron microscopy (EM)
Summary
Ca2+-ATPase, adenosine triphosphate (ATP), which is a serine type lipid, is a transporter protein in the plasma membrane which acts as calcium (Ca2+) remover from the cells and its action is vital for regulating the amount of Ca2+ within the cells [1]. It is thought that the Ca2+-ATPase has 10 segments that cross the plasma lipid bilayer membrane, with both termini, namely C and N (shown in Fig. 1), remaining inside the cell. At the C terminus, there is a long ‘tail’ of between 70 and 200 amino acids in length [2]. This tail is responsible for regulating the pump operation [2]. ATP binds tightly to Ca2+ ions but does not remove Ca2+ at a very fast rate [3]
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