[gmx-users] Urea induced denaturation and urea force fields.

Krzysztof Kuczera kkuczera at ku.edu
Mon Mar 28 17:49:33 CEST 2016

I think the reason your urea molecules moved away from the protein is 
the concentration gradient introduced through your solvation scheme  - 
since [urea] = 0 in the bulk, we can expect the molecules to 
spontaneously diffuse there. Probably solvating with an equilibrated 
water+urea box with high urea concentration would work better - see 
how-to's section of gromacs  website  for using mixed solvents

On 3/25/16 10:34 PM, Sagar Khavnekar wrote:
> Dear Gromacs Users,
> I have some questions about MD simulations we performed following our
> crystallographic investigations into urea induced denaturation.
> We have performed some crystallographic experiments to capture initial
> phases of urea induced denaturation of HEWL.
> We have observed initial changes in protein structure such as breaking of
> structurally important h bonds as a result of urea binding. We further
> wanted to see if similar structural alterations occur when we simulate
> native structure in the presence of these urea molecules, the positions of
> which are taken from the crystal structure.
> hence we prepared a starting system as follows
> we superposed native structure onto HEWL structure from the urea complex.
> Hence in starting system HEWL is in native conformation along with urea
> molecules which are observed in the case of complex.
> we solvated this starting system in tip3p water and performed energy
> minimization. we had restrained urea molecules during equilibration. for
> production MD we removed these restrains onto urea molecules. it was
> observed that urea molecules fly away from their positions soon after
> starting production MD.
> hence we restrained urea molecules in order to see local changes that these
> urea molecules will bring out in the native structure if they are present
> at crystallographically observed positions. I would like to get opinions
> from the gromacs community about this approach of restraining urea
> molecules for observation of local dynamics or for observation of possible
> conformational transition from native HEWL to the one in complex with urea.
> Now the question that has come up after review of our manuscript is that
> aret these retrains introducing crystallographic artifacts into MD.
> Another question is if urea molecules are flying off then is it due to
> force field that might be biased by many solution studies which suggest
> that urea denatures by weak interactions in contrast to strong interactions
> such as we have observed in our crystallographic study. for the purpose of
> information resolution of our structures is 1.6 Ang.
> Another thing I would like to have experts opinion about is as follows.
> In our opinion the best thing to do MD without restraining urea molecules
> will be to simulate nanocrystal spanning few unit cells in 9M urea/ But it
> will be computationally expensive. We do not have enough computing power to
> carry out such a massive simulation. Hence, will it be sensible to say we
> didn't do it due to lack of computing power?
> further most of MD simulations start from Protein molecule in mixed solvent
> of water and urea. but in reality when you dissolve protein in 9 molar urea
> protein has its solvation shell around itself. Hence isnt it better to
> perform denaturation simulation starting from hydrated protein with few
> hydration shells around it? and if we do so are present force fields able
> to account for urea water diffusion, especially the penetration of urea
> into hydration shell of protein?
> PS we used amber 99 ildn

Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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