With regards to run a monomeric simulation as resonable or not, I would agree with Mark that it depends what you wish to learn, and depends on what your hypothesis is. Ragothaman
On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M <hmkv...@gmail.com> wrote: > Thank you Sir, > > The interface is connected by salt bridges and hydrogen bonding > interactions and not severely > hydrophobic. I tried simulating the monomers it stayed quite stable without > unfolding till 50ns. > Even the other structure which are reported to be dimer is a reported as a > trimer in solution. > Another one is a part of a bifunctional protein which is an octamer. So > Because of all these > confusions I through some information could be obtained from a monomeric > simulation.. > Is it reasonable? > > > Thanking you > With Regards > M. Kavyashree > > On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli < > ragotha...@gmail.com> wrote: > >> 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> >>> >> >> >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> 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 >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
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