AMBER Archive (2008)

Subject: Re: AMBER: Question on AMBER MD Implications

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Oct 31 2008 - 11:51:21 CDT

in my opinion Levinthal's paradox was a straw man, not meant to be
reality but to show that such a system could not work.
furthermore, if landscape theory is correct about folding, one
advantage of MD (which is force-guided) is that it will benefit from
the funnel just as much as true proteins do, and thus avoid the
paradox.

On Fri, Oct 31, 2008 at 12:27 PM, Campbell, Patrick <pcampbell_at_msm.edu> wrote:
> Hello All,
>
> I have a quick question concerning the implications of MD with AMBER.
>
> I am aware of Anfinsen's dogma that the aa sequence can determine the
> folding pattern of a protein and also of Levinthal's paradox which states
> that for a polypeptide of length n amino acids, the possible number of
> folding possibilities is 4^n.
>
> My question then is this - Is it reasonable to state that for a
> given protein subjected to MD, the number of low energy states that are
> derived during the simulation can give a relatively small set of possible aa
> folded states in contradiction to Levinthal's paradox?
>
> I do look forward to your responses and have a great day!
>
> Pat Campbell
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