I had a homology model protein, that I needed to dock with solved protein structure (which is inhibitor of the build model). The crystallography structure consist of homologus hexamer in its structure, my doubt is I need to take the whole protein complex for docking studies or is it enough to take a single subunit? If single subunit is enough what was the reason to take a single sub-unit? (crystal structure are build in different physiological condition; if we choose single subunit is the predicted results are accurate?)
Hello Babajan,
It is very common that crystal structures are deposited as number of chains since they are solved as it is in the unit cell or crystal packing units. Just check the pdb structure is containing hexameric subunits and not they are multimer in the real life situation. Unless you know that the mulimerization is crucial for the protein's fuction, you can study with a single subunit which is sufficient. I would also compare each of the subunits by aligning the structures and I will get the informations out of it!
Good luck.
F
First you have to find the active sites of that protein through casp p
Software tool
Dear Friends, before answering the question.. try to read question properly.. i am not asking about protein-protein docking server or active site prediction.... and @bhattacharya.. gromacs and namd not used in docking simulation , its used to perform MD simulation in different environment... and i request you all to read question properly before the answer
Hello Babajan,
It is very common that crystal structures are deposited as number of chains since they are solved as it is in the unit cell or crystal packing units. Just check the pdb structure is containing hexameric subunits and not they are multimer in the real life situation. Unless you know that the mulimerization is crucial for the protein's fuction, you can study with a single subunit which is sufficient. I would also compare each of the subunits by aligning the structures and I will get the informations out of it!
Good luck.
If all six chains are identical then u can dock into any chain. But is important to know formation this complex in biological scenario. As u said it is inhibitor (or substrate??) u have to be more specific in targeting. Also check for the localization and presence of any specific protein binding domain.
Dear Babajan,
Continue to ans (for If single subunit is enough what was the reason to take a single sub-unit?) added by Ananda.
Consider following example
Case 1 Hemoglobin which consist of 4 sub units. Considering either Alpha or beta is enough because here functionality is located at every individual chain. Considering any chain will represent same for its second counter part.
Case 2 Chitinase consist of many chains that vary with organism. Here considering individual chain is absolutely wrong because here functionality center formed by incorporation of two or more units and of course each constituting unit will play significantly while docking.
The idea is study your molecule properly and confirm whether multimerization is important for only structural stability or has any functional importance also and decide accordingly.
In case 2 keeping multi chin PDB file under docking may cause error. You can avoid such condition by creating your own single (non contiguous mix of contributing residues of various chains) chain (virtually assumed by software) PDB file.
Hope this will clarify you the subject.
Dear friends thanks for your valid information, all your answers aims with selection of single templet in homologous structure, If we had multimer with non-homologous structure then what what was the situation.
for example i need to dock my protein with 30s Ribosomal subunit, as seen the structure of 30s ribosomal structure it nearly consist of 20 subunits in its structure; then what was situation of docking of these proteins
I dont understand... Is ur protein is homo-multimer or hetero-multimer. If hetero-multimer. Then its all down to importance of formation of such hetero-multimer
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