[gmx-users] How to built a protein model basing on the X-ray diffraction structure at different pH environment

Ran Friedman ran at hemi.tau.ac.il
Wed Jan 12 15:28:05 CET 2005


Unfortunately there's no simple solution to this. An initial model can
be built by setting the protonation states according to the pH - you can
do it using pdb2gmx (in Gromacs). Then, you need to refine your model by
energy minimization. If you want to run an MD simulation, that might be
enough. However, if the pH that you need to work with is much smaller or
larger than the pH in which the protein was crystallised, the protein
may be deformed, and you may need to equilibrate it for a long time
before you get any meaningful model.


zjim wrote:

> Hi
> As both the basic and acidic amino acid will be different protonation
> state at different pH environment, the pH will greatly affect the
> structure and function of protein. while the positions of hydrogen is
> hard to be earned using X-ray diffraction method, Is there a way to
> built protein models at different pH environment basing on a X-ray
> diffraction structure?
> Maybe a soft will do, does somebody know it, please give some advice,.
> thank you in advice
> zhou jinming
> ShanghaiInstituteofOrganicChemistry
> ComputationalChemistryLab
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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