Re: Temperature dependent unfolding..

From: Giovanni Settanni (gs_at_mrc-lmb.cam.ac.uk)
Date: Thu Sep 06 2007 - 06:34:51 CDT

Hi Arun,

did you (very very roughly) check the expected unfolding time of
ubiquitin at high temperature extrapolating the Arrhenius's law (with
the brutal assumption that there are no solvent phase transitions as you
would not see them in the simulations)? It may be much larger than
12ns, and your simulations may be correct (even if they provide no
information about the unfolding pathways!). Ubiquitin has a very small
unfolding rate at 300K (0.001 s-1), I do not expect it to increase by
almost 12 orders of magnitudes with temperature alone. The authors of
the phys rev E probably did a temperature AND pressure induced unfolding.
Cheers

Gianni

-- 
Giovanni Settanni
Centre for Protein Engineering
MRC Centre
Hills Road,
Cambridge, UK
CB2 0QH
Phone: +44 1223 402133
Fax:   +44 1223 402140
Arun Krishnan wrote:
> Hi Monika,
> 
> I have uploaded all my config files to my website. You can get them from 
> here:
> 
> a) energy minimization: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/min.namd 
> <http://www.iab.keio.ac.jp/~krishnan/downloads/min.namd>
> b) heating to 300K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/heating.namd
> c) equilibration @300K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_300K.namd
> d) production @300K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/production_300K.namd 
> <http://www.iab.keio.ac.jp/~krishnan/downloads/production_300K.namd>
> e) heating to 520K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/heating_to_520K.namd
> f) equilibration @520K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/equilibrate_520K.namd
> g) production @520K: 
> http://www.iab.keio.ac.jp/~krishnan/downloads/production_520K.namd 
> <http://www.iab.keio.ac.jp/~krishnan/downloads/production_520K.namd>
> 
> I ran these under NPT.. so some of the comments in the files might not 
> make sense. (These were put in when I was initially doing an NVT ensemble).
> 
> Do let me know if you see anything wrong.
> 
> Thanks in advance.
> 
> Cheers,
> 
> Arun
> 
> On 9/5/07, *Monika Sharma* <mon_sharma_at_research.iiit.ac.in 
> <mailto:mon_sharma_at_research.iiit.ac.in>> wrote:
> 
>     hii!!
>     can you just write your conf file here the last part of the run?There
>     might be some problem in going from 300K to 500K.
>     regards,
>     monika
>     Arun Krishnan wrote:
>      > Dear NAMD list users,
>      >
>      > I have been trying to carry out unfolding simulations of Ubqiuitin. I
>      > use the top_all22_prot.inp and par_all22_prot.inp topology and
>      > parameter files.
>      > I did the following steps:
>      >
>      > a) Energy minimization
>      > b) Heating to 300K
>      > c) Equilibration for 50ps NPT
>      > d) Production run @300K for 1ns. NPT
>      > e) Heating to 500K
>      > f) Equilibration for 50ps NPT
>      > g Production run @500K for 12ns NPT
>      >
>      > Very surprisingly, I don't see the RMSD values changing (with respect
>      > to the final equilibrated frame at 300K) by greater than 4-5
>      > Angstroms. This is very weird. There is a paper in Physical Review E,
>      > 72, 051928, 2005 "Unfolding dynamics of the protein ubiquitin:
>     Insight
>      > from simulation" where they achieved drastic unfolding within 1ns
>      > for ubiquitin at 520K. I followed what they did and tried at 520K
>     too.
>      >
>      > I have used NPT throughout.. but I also used NVT and NVE ensembles..
>      > and in all cases it seems to be very stable. Does anyone have any
>      > pointers to what I might be doing wrong?
>      >
>      > Thanks in Advance,
>      >
>      > Arun
>      > -
>      >
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