AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Nov 12 2009 - 16:29:13 CST


i think it is still an open research question whether it is true for most
proteins and unlikely that such a general statement would be true for all
proteins.

On Thu, Nov 12, 2009 at 4:59 PM, Chih-Ying Lin <chihying_at_usc.edu> wrote:

>
>
>
> 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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