Re: protein unfolding

From: jose correa (corrjose_at_gmail.com)
Date: Thu Jan 21 2010 - 11:03:27 CST

IDear Andrew
I am agree with you, to reproduce the biological conditions is better. But,
i am working now under this conditions (heat), i hope reach the goald under
this, if not, i need to chang as you say.
Vest wishes
Josť

2010/1/21 Andrew Emerson <a.emerson_at_cineca.it>

> Hi Jose
>
> I think we should continue this discussion off the NAMD list.
>
> You are right at such high temperatures water would boil. But on the other
> hand is superheated water at 600K that much more realistic? And then there
> is the point that Axel made that classical force-fields such as Charmm are
> not intended to be used at temperatures far away from standard conditions,
> i.e. 300K.
>
> If you really want to study unfolding I think a more elegant approach is
> to replicate what biochemists do in the lab and introduce into the solvent
> a denaturing agent such as urea. In this way you can persuade the protein to
> unfold but at much lower temperatures and in shorter time intervals (e.g.
> less than 400K). A quick web search will turn up a few hits but I can
> provide some references if you are interested.
>
> best wishes
> Andy
>
> jose correa wrote:
>
>> Dear Andy
>> I start with NTP (150 ps) and then NTV, but the protein was unfolded
>> inmediatelly with NTV. I ask it to a colleage who sugest me that, it is
>> preferible start and mantain NTV due to with NTP, the water are boiling and
>> the protein-water contats dissapear, then, it yield data not reliable. But,
>> if you think or have a paper that report this condition (NTP), I can try--001485f5cec87df65d047dafaea7--

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:42 CST