[gmx-users] Helix to coil

[Justin A. Lemkul]

simon sham wrote:
> Hi,
> Does anyone know the time scale for helical to random coil transition? I 
> have done one simulation and noticed that one helical turn of a helix in 
> the crystal structure becomes a loop in the simulation. Have anyone seen 
> something like this before?
> 

It depends on simulation conditions, force field (some are prone to erroneous 
secondary structure conversion or other biases), the nature of the protein 
itself, whether or not the crystal structure is particularly accurate, and 
probably more factors that I am not thinking of.  Also, one event is not 
necessarily representative of a population of states, hence multiple simulations 
from independent starting velocities would be necessary to derive converged 
results.  If it happens consistently, you may have a real phenomenon, otherwise, 
you may have just simulated the outlier in the data set.

Short answer - no easy answer :)

-Justin

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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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