[gmx-users] about salt concentration

[ran friedman]

Dear Thomas,

Both the amount of salt and the ionic composition are important for
specific interactions between ions and the protein surface. However, the
overall effect on the structure and shape of a globular protein will
probably not change so much.

@Article{Friedman2011b,
author = "Friedman, R",
title = {Ions and the protein surface revisited: extensive molecular
dynamics simulations and analysis of protein structures in alkali-chloride
solutions},
journal = "J Phys Chem B",
year = "2011",
volume = "115",
pages = "9213-9223"
}

Ran

Message: 6
Date: Thu, 11 Oct 2012 23:41:11 +0300
From: Thomas Evangelidis <tevang3 at gmail.com>
Subject: Re: [gmx-users] about salt concentration
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <CAACvdx0aTpQQ+Jrwk2JQJE0p5s5GL9zMbNNmHQC2yt7G54_LZQ at mail.gmail.com>
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Thanks Chris, very good points. I would like to add a potential drawback
for not using salt taken from my experience:

I simulated a coiled coil with one end having charge +12 and the other
zero. I ran a simulation with just 12 Cl- counter ions which tended to
cluster near the positively charged tail. In that simulation the
electrostatic potential in the box was uneven and that resulted to spurious
protein movement at the positively charged end.

I am now preparing a simulation with 0.15 M NaCl and zero net charge to see
the effect on protein dynamics. But I haven't seen many papers using excess
salt concentrations and that makes me worry about the validity of the
results I will get.

Thomas



On 11 October 2012 20:22, Christopher Neale <chris.neale at mail.utoronto.ca
>wrote:

> There are 4 reasons that I can think of:
>
> A) Didn't consider it or know how to do it
> B) Repeating a previous simulation (possibly with some modifications) --
> e.g. simulation a protein in a lipid bilayer
> using lipid parameters that have been shown to give the desired area per
> lipid in the absence of salt but which
> have not been evaluated in the presence of salt.
> C) No parameters for desired salts, such as the common phosphate buffered
> saline, in some force fields.
> D) Trying to avoid unexpected and sometimes difficult to understand
> effects of salt binding to the protein, salt
> entry into a channel, etc. This is probably misguided because such things
> are possible once you have even a single
> counter-ion, but it is the reason that I have avoided the use of excess
> salt in the past. However, in my more recent
> work I have started adding excess salt around the concentrations that you
> mention.
>
> I'm sure that there are lots of other reasons.
>
> Chris.
>
> -- original message --
>
> Dear GROMACS users,
>
> In most of the papers that compare the results from MD with NMR data the
> authors use just counter ions to neutralize the system. However, a salt
> concentration of 0.10-0.15 M would be closer to the buffer solution used
in
> the NMR experiment. Why then people don't use more salt in their
> simulations? Do they want to avoid ff inaccuracies or to be able to use a
> shorter cutoff for the short range interactions? I would be very
interested
> to know the reason.
>
> thanks,
> Thomas
>
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--

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/


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