From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 26 2007 - 08:19:13 CDT
Prabhu,
Yup.. I do have a complete unfolding trajectory.. so that's not a problem.
Cheers,
Arun
On 9/26/07, E. Prabhu Raman <
eraman_at_gmu.edu<https://mail.google.com/mail?view=cm&tf=0&to=eraman@gmu.edu>>
wrote:
>
> Neelanjana:
> >see if it is stable over an extended period of time.
> > If you
> > find that the energy is stable too, then you "may" think that you have
> > encountered a transition state. However, a lot of caution is
> > required in
> > your treatment...
>
> I do not understand your point of finding a stable state. During a
> constant temperature run, the transition state will be populated for a
> "short" time right? (as by definition the transition state is the maximum of
> Free energy as a function of the reaction coordinate) Then why are we
> detecting a stable state? (I think by this, we will end up detecting the
> equilibrium state at the simulation temperature and not the transition
> state)
>
> Arun: You have complete unfolding trajectory right? i.e you start from a
> fairly folded state and end at a unfolded state where most native contacts
> are lost ? Because if the trajectory is not complete, then detecting the
> transition state(s) using snapshots showing steep buildup of reaction
> coordinate might not be right.
>
> -Prabhu
>
> E.Prabhu Raman
> Ph.D Student, Bioinformatics & Computational Biology
> George Mason University
>
> ----- Original Message -----
> From: Arun Krishnan < krishnan_at_ttck.keio.ac.jp<https://mail.google.com/mail?view=cm&tf=0&to=krishnan@ttck.keio.ac.jp>
> >
> Date: Wednesday, September 26, 2007 0:56 am
> Subject: Re: namd-l: Determining Transition State from an Unfolding
> Simulation
>
> > Hi Prabhu and Neelanjana,
> >
> > Thanks for your inputs... Shall try them out and let you know what
> > I get. To
> > answer Neelanjana's point, yes, my unfolding simulation does seem
> > to follow
> > the same pathway as has been shown in literature... so am fairly
> > confidentabout it being right.
> >
> > Cheers,
> >
> > Arun
> >
> > On 9/24/07, E. Prabhu Raman <eraman_at_gmu.edu<https://mail.google.com/mail?view=cm&tf=0&to=eraman@gmu.edu>>
> wrote:
> > >
> > > Using Snapshots of a trajectory of Kinetics simulation at a constant
> > > temperature, a method called Progress Variable Cluster has been
> > used to
> > > pin-point the structures of the transition state ensemble(TSE).
> > > REF : Chemical Physics Volume 307, Issues 2-3, 27 December 2004,
> > Pages> 251-258
> > > The basic idea being that the passage through the transition
> > state can be
> > > identified by the time-point(s) that record a maximal change in
> > a suitable
> > > reaction coordinate (example Rg, or number of native contacts)
> > > However,I WOULD CAUTION that this approach,to my best knowledge
> > has been
> > > tried for Coarse Grained Model folding studies and more importantly
> > > lots(~100) of independent trajectories were used to get a
> > picture of the
> > > TSE.
> > > I assume that you might not have too many unfolding
> > trajectories. But
> > > since this procedure is easy to apply, you can try it out and
> > compare your
> > > TSE from any experimental available data(phi-values).
> > > The reference given above uses a clustering algorithm to cluster
> > similar> structures. A first pass at TSE determination could be
> > not to cluster, but
> > > simply pick out the structures that record the steepest
> > buildup(or down) of
> > > the reaction coordinate and look at the structures to see if it
> > is any
> > > meaningful at all.
> > >
> > > Best
> > > Prabhu
> > >
> > > E.Prabhu Raman
> > > Ph.D Student, Bioinformatics & Computational Biology
> > > George Mason University
> > >
> > > ----- Original Message -----
> > > From: Neelanjana Sengupta <senguptan_at_gmail.com<https://mail.google.com/mail?view=cm&tf=0&to=senguptan@gmail.com>
> >
> > > Date: Sunday, September 23, 2007 7:33 pm
> > > Subject: Re: namd-l: Determining Transition State from an Unfolding
> > > Simulation
> > >
> > > > Hi,
> > > >
> > > > This would work (if at all) assuming your unfolding pathway
> > > > retraces the
> > > > protein folding pathway. If you figure out a way to determine if
> > > > this is
> > > > what is going on (figuring this out would indeed be non-trivial),
> > > > you may
> > > > then closely examine the timeline of a unfolding parameter
> > (Rg, for
> > > > instance) and see if it is stable over an extended period of time.
> > > > If you
> > > > find that the energy is stable too, then you "may" think that
> > you have
> > > > encountered a transition state. However, a lot of caution is
> > > > required in
> > > > your treatment...
> > > >
> > > > Would be great if others share their thought too!
> > > >
> > > > Cheers,
> > > > Neelanjana
> > > >
> > > > On 9/23/07, Arun Krishnan < krishnan_at_ttck.keio.ac.jp<https://mail.google.com/mail?view=cm&tf=0&to=krishnan@ttck.keio.ac.jp>>
> wrote:
> > > > >
> > > > > Hi All,
> > > > >
> > > > > Is there a way to calculate the transition state structure from
> > > > Unfolding> data? From the plot of RMSD vs time maybe?
> > > > > Or is there some other way? Any pointers would be much
> > appreciated.> > >
> > > > > Cheers,
> > > > >
> > > > > Arun
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > >
> > >
> >
> >
> >
> > --
> > ***********************************************
> > Arun Krishnan, Ph.D,
> > Assistant Professor,
> > Institute for Advanced Biosciences,
> > Keio University,
> > Center Building,
> > Tsuruoka, Yamagata 997-0035
> > Japan
> > Phone: +81 (0)235-29-0824
> > Email: krishnan_at_ttck.keio.ac.jp<https://mail.google.com/mail?view=cm&tf=0&to=krishnan@ttck.keio.ac.jp>
> > URL: http://www.iab.keio.ac.jp/~krishnan
> > **********************************************
> >
>