[gmx-users] Re: Folding rate

João M. Damas jmdamas at itqb.unl.pt
Sat Dec 31 01:40:50 CET 2011 

As it was pointed out, the literature is vast on this subject.

Moreover, calculating folding rates from simulations is not a trivial
subject, and it relies on many assumptions (e.g. what is considered
"folded", that the sampling obtained is enough). Even for small peptides,
"enough sampling" may mean several hundreds of microsseconds, something not
accessible to everyone.

For a very recent article on the subject, check out:

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How
Fast-Folding Proteins Fold, *Science* 334:517-520.
http://dx.doi.org/10.1126/science.1208351

Regards,
João

On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi <ksr at chemistry.umass.edu>wrote:

> As Justin pointed out, there is a vast literature on this topic, you need
> to ask yourself what you seek, and look at many review articles to find
> some reasonable starting points for you own needs and designs. Beyond that,
> it's a lot of hard work...
>
> On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>
> Thanks for your advice... Could you please refer me some papers regarding
> this ....
>
> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi <ksr at chemistry.umass.edu>wrote:
>
>> No, there is no way to use such data to determine the folding rate of the
>> intact protein. If you used a fragment approach you could potentially (read
>> lots of papers on REMD) isolate nucleation sites, but minus the tertiary
>> interaction scheme you could not tell a compelling story. Now, if you want
>> to find nucleation sites and see if there are spatially proximal sites and
>> simulate them together... You might begin to tell a story.
>>
>> Ken
>>
>>
>> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
>>
>>
>>>
>>> bharat gupta wrote:
>>>
>>>> Thanks for your reply. I want to whether does it make any sense or is
>>>> it possible to simulate fragments of proteins and find their folding rate
>>>> and then correlate it to folding rate of whole protein ??
>>>>
>>>
>>> Simulating arbitrary parts of a protein may or may not produce any
>>> relevant information, likely the latter.  Independently folding domains
>>> might be simulated in isolation, but if there is a chance that the peptide
>>> sequences have any effect on neighboring residues or even more distal
>>> sites, you'll never produce anything useful.
>>>
>>> -Justin
>>>
>>>  On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>>> jalemkul at vt.edu>> wrote:
>>>>   bharat gupta wrote:
>>>>       Hi,
>>>>       I want to know whether it's possible to calculate the folding
>>>>       rate of 20 residue peptide folding into a beta-hairpin using
>>>>       gromacs ??
>>>>   Anything is possible ;)  But seriously, there is existing literature
>>>>   on such topics, I suspect you can find methodology that will suit
>>>>   your needs.
>>>>   -Justin
>>>>   --     ==============================**__==========
>>>>   Justin A. Lemkul
>>>>   Ph.D. Candidate
>>>>   ICTAS Doctoral Scholar
>>>>   MILES-IGERT Trainee
>>>>   Department of Biochemistry
>>>>   Virginia Tech
>>>>   Blacksburg, VA
>>>>   jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>>   http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>>   <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>> >
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>>>> --
>>>> Bharat
>>>> Ph.D. Candidate
>>>> Room No. : 7202A, 2nd Floor
>>>> Biomolecular Engineering Laboratory
>>>> Division of Chemical Engineering and Polymer Science
>>>> Pusan National University
>>>> Busan -609735
>>>> South Korea
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>>>> Mobile no. - 010-5818-3680
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>>>>
>>>
>>> --
>>> ==============================**==========
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>
>>> ==============================**==========
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>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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