Dear Anselm,
thanks for the useful comments and for suggesting existing literature.
I will surely read those.
I hope others will give insightful comments on other questions soon.
thanks
On Mon, May 10, 2021 at 6:08 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Dear Vaibhav,
>
> I just want to comment to your question 2 very shortly: yes.
>
> The difference in experimentally found micelle stability, which depended
> on the nature of the counterion (Li+, Na+, K+), has been also
> investigated computationally by MD and was called sodium effect (DOI
> 10.1002/chem.201001150).
> Our own investigations showed an influence of the nature of the
> surrounding ions (Li+, Na+, K+) upon fibrillar amyloid-beta oligomers
> (DOI 10.1007/s00894-018-3920-4), which is also known from experiment.
> Of course, there might be more literature about that topic available.
>
> In short, the different metal ions interacted in the simulations with
> neighboring carboxylate groups in different ways, i.e. bridging vs.
> non-bridging, which will in turn affected the stability of the overall
> protein (complex).
>
> Best regards,
>
> Anselm
>
>
> On 05/07/2021 08:07 AM, Vaibhav Dixit wrote:
> > Dear All,
> > I am seeing some differences in the position of counterions with tleap
> that
> > I think might have some impact on how conformations evolve during MD.
> > This protein has an FMN co-factor.
> > Following are the differences that I'm observing and some associated
> > questions.
> > Differences:
> > 1) with ff14sb/tip3p, Na+ ions are placed away from the dianionic FMN
> > phosphate group.
> > 2) with ff19sb/opc, Na+ ions are placed close to FMN that form close
> > contact during equilibration. This ion doesn't move away from FMN during
> a
> > 40ns MD.
> > 3) with ff19sb/opc, K+ ions are placed far away from FMN (may be due to
> > large Van der Waals radii of K+).
> >
> > questions:
> > 1) Since most exp. are done in KPi buffer to mimic intracellular
> > conditions, why do many studies use Na+ ions for such proteins? Is it
> not
> > better to always use K+ ions and avoid using Na+ (unless there are other
> > reasons for using them)?
> > 2) Can the differences in the choice of these counterions have a
> > significant impact on the dynamics of the protein and complexes? (I think
> > it may). There is some literature on ions vs. no ions (here
> > <https://academic.oup.com/peds/article/14/10/747/1498769>and here
> > <https://academic.oup.com/peds/article/14/10/747/1498769>), but I can't
> > find comparisons between Na+ vs K+.
> > 3) Is it possible to selectively include/exclude a region where
> counterions
> > can be placed by tleap?
> > 4) Is there a difference between the two commands "solvatebox mol opc 10"
> > and solvatebox mol *opcbox *10"? the first did not give any error and
> > simulations are running fine, but not sure if it is correct usage.
> >
> > Looking forward to valuable suggestions and tips from the list.
> > thank you and best regards.
> > Vaibhav
> >
> >
>
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Wed May 12 2021 - 09:30:02 PDT
