I have antigen as a protein and antibody as ligand, now I want to run this protein-protein simulation by using GROMACS. How can I prepare my antigen and antibody by Gromacs?
Supplementary questions to clarify any doubt:
1) Do you have any experimental structure (ie NMR or Xray) of the Ab::Ag complex?
If not, you have to build a model of the complex before starting any simulation with GROMACS. If this is the case:
2) Is there any homolog complex experimental structure to use as template, in order to perform an homology modeling or threading job?
If not (you don't know how the antigen is orientated in respect of antibody molecule), you have to build a model with a protein-protein docking software
Dario: thank you so much for your response well i have Xray structure reported in PDB . 3uzv is the reported structure . it have two chains , chain A as protein and i want to make chain B (anti-dengue Mab 4E11) as ligand .
Ok Sidra, we have a crystal, sounds good!!! But...
In the pdb 3UZV the antibody portion is a Fv fragment. If you want to perform a simulation I expect (in my personal experience) great alteration about the reciprocal motion between the variable domains VH and VL. The avalaibility of a Fab fragment would be better, since the presence of additonal domains CL and CH1 renders the Ab::Ag complex more stable (see http://www.ncbi.nlm.nih.gov/pubmed/23240736).
Anyway, before running GROMACS you have to pre-process your pdb:
* remove the solvent
* the ethanol molecule is important for the antigen interaction? Carefully read the related paper
* the chain B, representing the Fv fragment, should be splitted in two separated chains (one for VH domain and another for the VL domain)
* you have to fill the gaps internal to the structure, for example the missing residues 343-345 of the antigen molecule (you can accomplish such task through a loop modeling job with MODELLER). Don't worry about missing residues at N-term or C-term.
Thank you too. After the above mentioned pre-processing step, to perform a MD on GROMACS with only proteins (even if they are distinct protomers) is quite easy.
I suggest you to follow, as a guideline, the tutorial at Bevan lab (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html).
The main difference, in your case, is that you will obtain three different topology and position restraint files for the three protein chains. They are generated automatically from the pdb2gmx command; furthermore, a fourth topology file (called topol.top) will be generated and it contains the specific calls for the previous. So you have to don't worry about.
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