Should VDW not (incorrectly) favor in-register-parallel over
parallel-displaced and T-shaped geometries for aromatic rings?
http://www.jbc.org/content/273/25/15458.long
And how does the Hamiltonian at all account for cation-pi?
I do agree that other parts of the force field might lead to configurations
that are stabilized by pi-based interactions in real life though not in
simulation, and that disrupting the associated pi-based interaction may
thereby have an experimental effect.
On Fri, Oct 19, 2018 at 6:50 AM Christina Bergonzo <cbergonzo.gmail.com>
wrote:
> Hi,
>
> I wanted to give a more nuanced look at the pi-pi and cation-pi interaction
> in MD force fields.
>
> While there is no explicit force field term for pi-pi or cation-pi
> interactions, you can of course look for their effects, which are indeed
> represented using MD - otherwise my DNA duplexes would be in trouble!
> Force fields rely on van der Waals to pick up the effects of these
> interactions, and generally they can capture those effects - of course,
> this is modulated by the desired level of accuracy.
>
> You can take a look at these papers to get an understanding of the issue
> w.r.t. QM:
> https://www.ncbi.nlm.nih.gov/pubmed/22260616
> https://link.springer.com/content/pdf/bbm%3A978-3-319-15382-7%2F1.pdf
>
> Here is an example where we measured base eversion pathways, noted a
> cation-pi interaction, and experimental collaborators made the mutation to
> disrupt it, causing catalytic activity of the protein with an (aromatic)
> damaged DNA base to decrease, but leaving the activity of the
> (non-aromatic) apurinic damage intact:
> https://academic.oup.com/nar/article/44/2/683/2468125
>
> And here is an example of base stacking in RNA, where it is argued that
> pi-pi stacking is overstabilized:
> http://www.pnas.org/content/110/42/16820
>
> http://www.pnas.org/content/pnas/suppl/2013/09/11/1309392110.DCSupplemental/pnas.201309392SI.pdf
>
>
> For analysis of these types of interactions, I would make sure to look at
> not only the energies but also the distances and geometries of pi-pi or
> cation-pi binding pairs.
>
> Hope this helps,
> Christina
>
> On Thu, Oct 18, 2018 at 11:27 PM Chris Neale <candrewn.gmail.com> wrote:
>
> > Be careful... atomistic force fields typically don't have any pi electron
> > effects in the Hamiltonian, so why would you analyze for them? In fact,
> > most atomistic force fields do a pretty terrible job at pi-based effects
> > like aromatic stacking. Same goes for cation-pi interactions.
> >
> > On Thu, Oct 18, 2018 at 8:08 PM Meng Wu <wumeng.shanghaitech.edu.cn>
> > wrote:
> >
> > > Dear all,
> > >
> > > I have MD for my channel protein and substrate molecules and I have
> > > used the "lie" command to calculate the EELEC and EVDW terms. Now I
> want
> > to
> > > analysis like the pi-pi interactions or aromatic interactions between
> the
> > > substrates and protein & residue to residue in protein, could anybody
> > give
> > > me some suggestions? Thank you in advance!
> > >
> > > Best regards,
> > > Meng Wu
> > >
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>
>
> --
> --------------------------------------------------------------
> Christina Bergonzo
> Research Chemist
> NIST/IBBR NRC Postdoctoral Researcher
> --------------------------------------------------------------
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Received on Fri Oct 19 2018 - 14:00:03 PDT
