Then there is a wealth of papers that describe secondary structure
determination from the experimental point of view that you should look for.
NMR and CD would be the first obvious methods that come to mind, but there are
probably others as well.
These should be able to help you validate or inval
It is a peptide.
Shahid
On Mon, May 6, 2013 at 4:46 AM, Jesper Sørensen 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
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 na
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
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
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 wrote:
> If I know correctly in lambda dynamics the dynamics of
> protonation/d
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, Ma
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 structur
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 wrote:
> There's no general answer to that. Proton conductivity measurements, for
> instance, will be horrib
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 wrote:
> Dear all
>
> Can someone enl
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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