AMBER Archive (2009)

Subject: Re: [AMBER] Increase Temperature to 550 K

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Nov 12 2009 - 15:59:11 CST


Hi
"Increasing Temperature Accelerates Protein Unfolding
Without Changing the Pathway of Unfolding"

Can this statement be applied on all proteins?

Thank you

Lin

Ferguson et al. Simulation and experiment at high temperatures:
Ultrafast folding of a thermophilic protein by
nucleation-condensation. Journal of Molecular Biology 2005, 347,
855-870.

Day et al. Increasing Temperature Accelerates Protein Unfolding
Without Changing the Pathway of Unfolding 2002, 22, 189-203.

Thank you, regards, Francois

----- Original Message -----
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Date: Thursday, November 12, 2009 6:23 am
Subject: Re: [AMBER] Increase Temperature to 550 K
To: AMBER Mailing List <amber_at_ambermd.org>

> Dave is right of course, and the only reason we need to know what
> you want
> to learn is to respond to your question "is this trustworthy?". I
> can't try
> to answer that without knowing what it is you are deciding to trust.
>
> On Thu, Nov 12, 2009 at 7:55 AM, case <case_at_biomaps.rutgers.edu>
> wrote:
> > On Thu, Nov 12, 2009, FyD wrote:
> > >
> > > So what would you answer to the work of V. Daggett ?
> > > 498 K = 225 C
> >
> > You can read Prof. Daggett's papers to find out, although the
> explanation> is probably not in every paper. She is not directly
> comparing her
> > simulation to an experiment carried out at 498K, but rather is
> using high
> > temperature simulations (with special, artificial, conditions to
> keep the
> > density of water the same as at room temperature) to speed up
> dynamical> processes. There is a long discussion and set of tests
> to support the
> > argument that the pathways of unfolding are not qualitatively
> affected by
> > such a temperature change.
> >
> > This (broadly speaking) would be Daggett's answer to Carlos'
> question,> "what
> > do you want to learn"? We don't know what your answer is; and,
> of course,
> > it
> > may not be necessary for us to know that.
> >
> > ...dac
> >
> >
> > _______________________________________________
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> >
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