Sir, My aim was to find out the difference between the monomer protein and monomer of the dimer. it was for a preliminary analysis of the dynamics of the structure and not a detailed study. But whatever the aim is, if the protein is stable during the simulation then can a comparison be made for the dynamics of protein from different sources.
Thank you With Regards M. Kavyashree On Mon, Jul 18, 2011 at 6:22 PM, Ragothaman Yennamalli <ragotha...@gmail.com > wrote: > 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 >> > > > > -- > 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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