Re: protein unfolding -- Phi MD

From: Leandro Martínez (
Date: Wed Nov 29 2006 - 10:51:50 CST

Hi Wei,
I'm not a specialist in protein unfolding simulation either. However,
I recently performed some simulations of protein denaturation
and I'm now also working
on the determination of transition states. I have read in a review
written by Valerie Daggett (I'm not sure she idealized the technique
in the first place) a interesting idea: Run a simulation with high
temperature, in order to induce denaturation (as is usually done).
Then, you get you intermediates from this simulation and run for
each intermediate a new simulation at room temperature. Supposedly,
if the intermediate is before the transition state, the RMSD relative
to the native structure will decrease and the structure will return
to a structure similar to the native one. If the intermediate obtained
from the high-temperature simulation is after the transition state, then
the structure will diverge from the native structure. By narrowing the
search between unfolding intermediates that return to the native
state or diverge from it you can identify the first transition state.
This idea is described in this review:
V. Daggett, Protein Folding Simulation, Chem. Rev. 2006, 106, 1898-1916.
If you determine the transition state you can check which residues
are important to it and compare to experimental phi values.
Best regards,

Leandro Martinez
Institute of Chemistry
State University of Campinas, Brazil
Initial confiugurations for molecular dynamics:
Convergent algorithms for protein alignment:

On 11/28/06, Wei Fu <> wrote:
> Dear NAMD users,
> I am trying to determine the transition state ensemble during protein
> unfolding event by phi value
> obtained from experiment by MD with NAMD. I guess that I need to
> add an additional term obtained from the measured phi values to a standard
> molecular mechanics potential function. I wonder if there is a script in
> NAMD to do this? Or I just need to run a standard MD, then use phi value
> to analyze trajectory? I am new to inverstigate protein unfolding event,
> any idea will be highly appreciated!
> Wei

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