Look at this paper where the simulation was done on a protein dimer: http://www.ncbi.nlm.nih.gov/pubmed/17027497
On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 18/07/2011 3:08 PM, Kavyashree M wrote: > >> Dear users, >> >> I am working on a protein which is a dimer (in the crystal structure), >> predicted according top PISA. >> and some of the homologous proteins are dimers (covalent /non-covalent) >> some are monomers. >> There has not been any literature regarding the fact that the functional >> unit is a dimer, ie the enzyme >> is not functional when the dimeric interface is disturbed due to >> mutations. Also the active sites are not >> shared among the dimeric partners. In this situation is it meningful to do >> a simulation of monomers alone >> and try to get some information. >> > > The dimeric interface might be so hydrophobic the protein would unfold - > but unlikely given the homology evidence. It could certainly perturb the > structure significantly, and perhaps such perturbations connect with the > activity. Only detailed understanding of the structure and function can help > you decide about this. > > > In general is it necessary to simulate only the functional oligomers or >> monomer also can be done ? >> > > Depends on the system, and depends what you wish to learn. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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