[gmx-users] about salt concentration

Fri Oct 12 16:11:55 CEST 2012

@Christopher Neale

The terminal part of the protein is folded in the starting conformation but
disordered under natural conditions. In the 150 ns simulation, the terminal
helices instead of unfolding, as the NMR experiments suggest, they turned
upwards interacting with the rest of the protein, which is something
unexpected.

@Vitaly Chaban

It's not about "repeating" the experiments. NMR captures phenomena in the
order of miliseconds whereas MD can reach up to microsends and nanoseconds.
Usually people who compare with NMR data use enhanced sampling MD methods
(as I am also planning to do) to reach these timescales. So it's rather
about complementing the experiments and explain them in greater detail.

But as you suggested, it's probably better to ask directly the people who
did such comparisons.

@Ran Friedman

Thank you Ran, nice work. However, it does not apply to the case I
described. My protein is intrinsically disordered and highly charged at one
end. I am wondering if the ion parameters you cite in your paper are
shipped with the main GROMACS release.

On 12 October 2012 09:09, ran friedman <ran.friedman at gmail.com> wrote:

> 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>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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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-- 

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

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/