Hi Watson and others,
Many thanks for the paper list. I am following the papers from Pavel
Jungwirth group.
Moreover, I am very curious to hear thoughts of practitioners - the persons
who do protein+Bilayer simulations and how they deal with salt concentration
issue??
Any thoughts will be highly appreciated.
Thanks again,
--- Lalit
On Mon, Mar 1, 2010 at 9:03 AM, David Watson <dewatson.olemiss.edu> wrote:
> On Mar 1, 2010, at 8:43 AM, Lalit Dubey wrote:
>
> > Hi Jason,
> >
> > Thats truly the way to think about the role of ions in a protein+Bilayer
> > simulation at first. Thanks. But whats the judgement or say, convention
> as
> > of now. We can think of a 'protein' as a generic one. Nothing especial.
> (All
> > polar residues are towards outside surface and hydrophobic ones
> > are buried inside). [Mine is pkc with +1e charge].
> >
> > Whats the motivation for those who do protein + Bilayer simulations to
> add
> > or just to not add salt concentration in the system??
> >
> > Mine was that it hardly matters in such a big system and contemporary
> others
> > are not treating it (as a critical factor) and still doing
> protein+Bilayer
> > simulations. Moreover, our experience with other similar systems shows
> > little effect on salt concentration.[I am going to write individually to
> all
> > those who have published such a work however I want initial motivation
> > factors that makes the judgement at first].
> >
> > yeah, I have to address this question as raised in a seminar.
> >
>
> I remember reading (on this list, I believe) about detrimental effects of
> too much salt, namely the salt "crystallizing" during the simulation.
>
> Here's a cherry-picked list of a quick SciFinder search
>
> Ion Specificity at the Peptide Bond: Molecular Dynamics Simulations of
> N-Methylacetamide in Aqueous Salt Solutions
> By Heyda, Jan; Vincent, Jordan C.; Tobias, Douglas J.; Dzubiella, Joachim;
> Jungwirth, Pavel
> From Journal of Physical Chemistry B (2010), 114(2), 1213-1220.
>
> Effect of counterions on the structure of reverse micelles according to the
> data of molecular-dynamic simulation
> By Mudzhikova, G. V.; Brodskaya, E. N.
> From Colloid Journal (2009), 71(6), 803-809.
>
> Salt Dependence of an α-Helical Peptide Folding Energy Landscapes
> By Xiong, Kan; Asciutto, Eliana K.; Madura, Jeffry D.; Asher, Sanford A.
> From Biochemistry (2009), 48(45), 10818-10826.
>
> Molecular dynamics simulation of effect of salt on the compromise of
> hydrophilic and hydrophobic interactions in sodium dodecyl sulfate micelle
> solutions
> By Gao, Jian; Ren, Ying; Ge, Wei
> From Chinese Journal of Chemical Engineering (2009), 17(4), 654-660.
>
> Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane
> By Vacha, Robert; Siu, Shirley W. I.; Petrov, Michal; Bockmann, Rainer A.;
> Barucha-Kraszewska, Justyna; Jurkiewicz, Piotr; Hof, Martin; Berkowitz, Max
> L.; Jungwirth, Pavel
> From Journal of Physical Chemistry A (2009), 113(26), 7235-7243.
>
> > Thanks again,
> > --- Lalit
> >
> >
> > On Sun, Feb 28, 2010 at 6:40 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
> >
> >> On Sun, Feb 28, 2010 at 6:35 PM, Lalit Dubey <dubey.lalit.gmail.com>
> >> wrote:
> >>> Hello Florent,
> >>>
> >>> Thanks for the quick response!
> >>>
> >>> Yes, indeed putting counter ions to neutralize the whole system is
> >> required
> >>> for full PME calculation of electrostatic forces.
> >>> This part is fine. I have added counter ions. My systems are neutral.
> >>>
> >>> My question concerns with the effect of *'physiological concentration
> of
> >>> salt'* (say, NaCl) on the configuration of protein.
> >>
> >> Maybe yes, maybe no. Depends on your system. Evaluating even
> >> classical laws on that number of interacting particles is inherently
> >> chaotic and with the right set of variables anything can happen.
> >>
> >> Look for experimental data about your protein -- do they control the
> >> salt concentration? Do they say what happens to the activity when
> >> it's absent? Do they address it?
> >>
> >> I'm guessing if you're looking to publish this data, a reviewer may
> >> ask that exact same question, and the only way of addressing it really
> >> is to run those simulations. But again, maybe not if salt is known
> >> not to be a large factor. All-in-all, this is a very long non-answer.
> >> That's my $0.02.
> >>
> >> As a side note, when a system is not formally neutral, a "neutralizing
> >> plasma". This is how, for instance, softcore potential TI is handled
> >> when the net charge of the system changes (I'm pretty sure).
> >>
> >>
> >> Good luck!
> >> Jason
> >>
> >> --
> >> ---------------------------------------
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
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Received on Mon Mar 01 2010 - 12:30:02 PST
