From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Tue Sep 25 2007 - 23:56:52 CDT
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 confident
about it being right.
Cheers,
Arun
On 9/24/07, E. Prabhu Raman <eraman_at_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>
> 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> 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 URL: http://www.iab.keio.ac.jp/~krishnan **********************************************
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