[gmx-users] MD analysis

Justin Lemkul jalemkul at vt.edu
Mon Sep 22 20:35:16 CEST 2014

On 9/22/14 2:26 PM, Anu Chandran wrote:
> Dear all,
> I have carried out simulations of two homologous proteins (~38kDA) using
> Gromacs v4.5.3 using OPLS force field. The protein consists of three
> domains. Structural studies using cystallography reported earlier showed
> that the two proteins differ in the extent of orientations one domain can
> take with respect to other. However the reason for  this difference is not
> clear from the structure as the size of the domain and region connecting
> them is almost the same in both. The only difference between the two are 32
> residues spread over the sequence. Can anybody please suggest me as to how
> to go about with the MD analysis to find out the reason for this difference
> in the two structures ?
> Visualization of the structures extracted from the trajectory showed the
> domain to be flexible in two proteins but to different extents.

Start by quantifying this.  Unless you reproduce some experimental observable, 
looking for a mechanism behind it is useless without knowing if it is there. 
Also realize that a crystal environment is wildly different from a solution 
environment (and crystal packing effects can be very prominent); you generally 
won't see the same dynamics, so relating such flexibility back to the crystal 
structure may not even be possible.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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