Hi Bharat, In addition to the good comments from Chris, mind that to understand the molecular nature of experimental observations like yours requires quite a bit of statistics. With just two cases - wild type and insertion - there is too much uncertainty to claim that possible differences you observe between the two in a limited (or even infinite) stretch of time are linked to the difference in the test tube. Part of them might, but the answer could well be hid in some unexpected property that is overwhelmed by a seemingly obvious difference. You would need to have experimental and simulation data on a whole series of mutants to be able to regress one to the other, and hope that the differences manisfest themselves in properties that can be assessed in simulations on the time scales accessible.
Cheers, Tsjerk On Tue, Mar 22, 2011 at 2:02 AM, <chris.ne...@utoronto.ca> wrote: > Dear Bharat: > > I hope that this doesn't impede others giving you advice about how to go > about doing what you want to do, but here's my two cents for what it's > worth: > > My suggestion is to forget about trying to do that. 3-ns simulations are not > going to give you equilibrium populations of conformational basins (and > neither would 3-us simulations, I suspect). Not every question is amenable > to MD on the currently available timescales. > > If you really want to try to do it, I would find out what conformations lead > to flourescence and see if you get more drift away from those conformations > in some models with longer loops. But again, I think it's probably going to > be a waste of time. > > Chris. > > -- original message -- > > Hi, > > I simulated a protein (GFP) with one of its loop replaced with a longer loop > . After simulating for some 5 to 10 models with different loop sequences , I > decided to carry out wet-lab experiments for one model on the basis of > simulation result. The analysis of simulation was done in the following way > :- > > 1) Comparison of RMSD values of backbone - for both GFP wild type and loop > replaced (mutated GFP) > 2) Comparison of RMSF of the residues common to both the proteins. > 3) Visual Inspection of entry of water into GFP. > > The simulation was carried out for 3ns for both the proteins. > > After that I did the wet-lab experiment for the modeled structure and I > found the fluorescence to be 50% of the wild type. > > Now I want to investigate the reason for this reduction in fluorescence > ??... How can this be quantified using MD. > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46010 at yahoo.com > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
