Ion concentration and aggregation problem of the nuclear protein simulations

Date: Fri Dec 13 2019 - 09:19:07 CST

Dear all,

I am trying to create a representative physiological environment for a
protein which localizes in the human nucleus. However, I am not
completely sure regarding the type and concentration of the ions I
should use. I looked into the literature but couldn’t find an exact
answer to my question .

In the literature, mostly sodium ions with a concentration of 150 mM
(according to physiological concentration of the cell cytoplasm) was
used for nuclear proteins but since both potassium and sodium ions
concentrations are higher in the nucleus, shouldn't I use both of them
instead of only sodium ions?

In some experimental studies the concentration of the sodium, chloride
and potassium ions in the human urinary bladder epithelium cell
nucleus are approximately given as 23.4, 46.7 and 214.1,
respectively. Moreover, concentration of the sodium, chloride and
potassium ions in the human thyroid cell nucleus are approximately
given as 40.1, 36.5 and 249.6, respectively. Since concentrations of
these ions are different from cell to cell, how should I determine the
optimum selection for the concentration to use in my simulations? In
the molecular dynamics studies the most generally applied ion and
concentration is 150 mM NaCl for the nuclear proteins either. However,
DNA is heavily negatively charged. Based on the experimental data in
the literature (for bladder cell nucleus for example) I should use 23
mM of sodium, 214 mM of potassium and 46 mM of cloride ions. Thus, I
am considering of setting my system 200 to 250 mM KCl and 23 to 40
NaCl concentrations. I am a bit concerned that this would lead to salt
aggregates as it was reported that high concentrations (like 250 mM
KCl) can do that . Moreover, would it really represent the
physiological conditions.

Long story short what concentrations would you suggest me to use for
simulations that should represent the nucleus physiological conditions
in human body? Moreover, Should I neuralize the system or perform
constant pH simulations?

Any input or reference would be greatly appreciated. Thanks in advance,

Best regards,
Ceren Kılınç

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