[gmx-users] constant protonation state MD

shahid nayeem msnayeem at gmail.com
Mon May 6 06:47:23 CEST 2013 

It is a peptide.
Shahid


On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen <jesorensen at ucsd.edu> wrote:

> Shahid,
>
> This must be system dependent then because there are experimental methods,
> e.g. NMR and CD, that can help determine the secondary structure of
> proteins/peptides are various pH ranges.
> What is your system? A peptide? A globular protein?
>
> Best,
> Jesper
>
> On May 3, 2013, at 7:33 PM, shahid nayeem <msnayeem at gmail.com> wrote:
>
> > Thanks a lot Erik and Baptista
> > I am interested in simulating the change in secondary structure which is
> > supposed to be influenced by the change in the pH environment of the
> cell.
> > Experimentally it is not known but it has been proposed by many that the
> > change in pH leads to change in conformation. I did constant protonation
> > state MD at two different pH. I got an alpha helix converting to beta
> sheet
> > at higher pH but not at lower pH. I am bothered to prove the reliability
> of
> > the simulation results as experimentally it cant be established.
> >
> > Shahid
> >
> >
> > On Sat, May 4, 2013 at 5:46 AM, <baptista at itqb.unl.pt> wrote:
> >
> >> Hi Shahid,
> >>
> >> As Erik said, it depends... on your system, on the process you are
> >> studying in that system, on the property you think it's relevant to
> study
> >> that process, etc.
> >>
> >> If your question refers to the (de)protonation of acidic and basic
> groups
> >> usually occuring in aqueous solution, there are methods to perform what
> is
> >> called constant-pH MD, where the protonation states of those groups
> change
> >> in a discrete or continuous way along the simulation. If you are
> >> interested, start with the corresponding GROMACS how-to (
> >> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
> <http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation>)
> >> and then search the literature.
> >>
> >> In any case, you don't need any of that fancy stuff unless you have
> >> reasons to think that the properties you want to study in your system
> are
> >> strongly dependent on protonation-conformation coupling effects. In some
> >> cases you may be suspicious about the effect of the protonation state of
> >> one group (e.g., a histidine), but that can be simply tested by
> performing
> >> two constant-protonation MD simulations, one for each state (you can
> even
> >> try to use a linear response approximation on top of that). But in most
> >> cases you don't need even that.
> >>
> >> For what it's worth: I was one of the first to develop and apply
> >> constant-pH MD and I don't bother to use it most of the time... :)
> >>
> >> Best,
> >> Antonio
> >>
> >>
> >> On Fri, 3 May 2013, Erik Marklund wrote:
> >>
> >> Yes that's what lambda dynamics does. I mentioned it since it addresses
> >>> the interplay between protonation and structure. So to answer your
> original
> >>> question: it depends.
> >>>
> >>> Erik
> >>>
> >>> On 3 May 2013, at 15:27, shahid nayeem <msnayeem at gmail.com> wrote:
> >>>
> >>> If I know correctly in lambda dynamics the dynamics of
> >>>> protonation/deprotonation equilibria is accounted for while my
> question
> >>>> relates to the typical constant protonation MD where each titratable
> >>>> group
> >>>> remains in one protonation state throughout the simulation. Please
> >>>> educate
> >>>> me
> >>>> Shahid
> >>>>
> >>>>
> >>>> On Fri, May 3, 2013 at 6:22 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> >>>> wrote:
> >>>>
> >>>> I don't have one in mind. It's a delicate question and perhaps I
> >>>>> shouldn't
> >>>>> have phrased it the way I did. Nevertheless, the pKa of most side
> chains
> >>>>> mean that their protonation will be dominated by one state for most
> pH
> >>>>> values. pKa-shifts and complicated interplay between protonation and
> >>>>> structure cause exceptions to this and you should be aware that such
> >>>>> things
> >>>>> may in some cases be important. Also consider the timescales of
> >>>>> pH-depedent
> >>>>> structural changes and the length of your simulations. You could
> check
> >>>>> out
> >>>>> the papers on lambda dynamics by C. Brooks III for an interesting
> take
> >>>>> on
> >>>>> sampling multiple protonation states.
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Erik
> >>>>>
> >>>>> On 3 May 2013, at 14:05, shahid nayeem <msnayeem at gmail.com> wrote:
> >>>>>
> >>>>> Thanks a lot Erik. Could I get some reference based on which you say
> >>>>>> that
> >>>>>> much of the structural biology will be largely unaffected.
> >>>>>>
> >>>>>> Shahid
> >>>>>>
> >>>>>>
> >>>>>> On Fri, May 3, 2013 at 1:05 PM, Erik Marklund <erikm at xray.bmc.uu.se
> >
> >>>>>>
> >>>>> wrote:
> >>>>>
> >>>>>>
> >>>>>> There's no general answer to that. Proton conductivity measurements,
> >>>>>>> for
> >>>>>>> instance, will be horribly wrong without dynamic protonation. Much
> >>>>>>> (but
> >>>>>>>
> >>>>>> not
> >>>>>
> >>>>>> all) structural biology, however, will be largely unaffected.
> >>>>>>>
> >>>>>>> Erik
> >>>>>>>
> >>>>>>> On 3 May 2013, at 04:30, shahid nayeem <msnayeem at gmail.com> wrote:
> >>>>>>>
> >>>>>>> Dear all
> >>>>>>>>
> >>>>>>>> Can someone enlighten me on the reliability of the results
> obtained
> >>>>>>>>
> >>>>>>> from
> >>>>>
> >>>>>> constant protonation state (assigned by different pKa value at
> >>>>>>>>
> >>>>>>> different
> >>>>>
> >>>>>> pH) MD simulation. Also want to know its reliability in case of
> >>>>>>>>
> >>>>>>> implicit
> >>>>>
> >>>>>> solvation model such as PB/GB calculation.
> >>>>>>>>
> >>>>>>>> Shahid
> >>>>>>>> --
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> >>> --
> >> Antonio M. Baptista
> >> Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
> >> Av. da Republica - EAN, 2780-157 Oeiras, Portugal
> >> phone: +351-214469619         email: baptista at itqb.unl.pt
> >> fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~**baptista
> <http://www.itqb.unl.pt/~baptista>
> >> ------------------------------**------------------------------**
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