[gmx-users] Re: Folding rate

[KS Rotondi]

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
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>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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>>    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>    ==============================__==========
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>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
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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
>
> ========================================
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