Protein crystallization has long been known to cause unnatural conformations in proteins due to the proteins been forced to adopt a highly dense rigid body interaction with other proteins in absence of bulk solvent. By unnatural I mean the conformations could perhaps be on the tail end of a Boltzmann distribution or have little representation in the solution ensemble. This is probably less often the case and the effects are usually more subtle. i.e. crystal contacts causing an alpha helix in the protein to adopt a slightly different 3D positioning than would actually occur.
NMR spectrscopy calculates structures using distance constraints and MD methods in solution to find highly represented conformers in the solution ensemble.
Proteins are inherently dynamic and access a wide range of conformations at room temperature in solution but they are still biasedly viewed as static structures. (See work by Dorothy Kern or Lewis Kay)
Comparing the RMSD progression of a structure over time during an MD simulation allows one to find the equilibrium or best fit relaxed states. Do these differ when starting from an X-ray or NMR and if so how.
On Wednesday, October 31, 2012 11:39:26 AM UTC-5, Nathan McCorkle wrote:
On Wed, Oct 31, 2012 at 6:44 AM, Josiah Zayner <josiah...@gmail.com> wrote:--
> I was doing some basic MD. I wanted to compare simulations of proteins that
> start from X-ray structures or NMR structures. One would predict that
> because of the nature of crystals that some X-ray structures might simulated
> differently due to starting in unnatural conformation. However, people think
> that X-ray crystallography is the gold standard in structural biology,
> predicting structure &c. when some of these structures are probably
> slightly, majorly off. I need to redo it though actually using NMR and X-ray
> structures from the same proteins instead of different proteins.
Are you saying that sometimes the way proteins crystallize isn't how
they are in situ, and you want to compare many different
crystallization methods with the structures produced to find your way
back to what they're really like in situ? Which you can then compare
with simulations?
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