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 >
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