Dear Mahesh, Instead of bothering with the secondary structure assignments why may try to superpose your structures and then view your RMSD plots(Superpose program in CCP4 can do the trick). You might then be better off focusing on the regions with high RMSD. Regards
On Sat, Oct 19, 2013 at 3:20 AM, krish <krishna....@gmail.com> wrote: > Hi Mahesh, > > If you have made these screen shots using pymol, then you really need to be > careful before you jump to conclude anything from these secondary structural > changes (Matt already mentioned it). Assign secondary structures using DSSP > or see the secondary structure restraints in the structure while refining. > Manual refining of these areas is really important (I mean careful > inspection) and once you think these regions you highlighted have proper > restraints, then you can conclude to a CERTAIN extent. > > I would perform MD simulation runs after energy minimization for each > structure for 10 to 15 nanoseconds and see whether these small perturbations > (what you have depicted) are really there. These runs with identical > parameters should give you clear hints how much your protein in different > states is stable with time. Also, you can figure out other structural > changes with longer simulation times if at all if your protein is dynamic. > > Hope this helps! > > Krish > > > On Fri, Oct 18, 2013 at 2:52 PM, Mahesh Lingaraju <mxl1...@psu.edu> wrote: >> >> Hello experts >> >> Attached is an image showing different crystal structures of the same >> protein in diffrent states (mutant vs substrate bound vs unliganded) and >> highlighted are little changes in secondary structure. I was wondering how >> real such small changes are and if they are real could they be enough to >> perturb the energy potential of the protein significantly. >> I apologize if this is a naive question as this is clearly not my area of >> expertise. >> >> Thanks for your input >> >> Mahesh >> >> >> >> > > -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता संरचनात्मक जीवविज्ञान प्रयोगशाला डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र हैदराबाद, ५००, ००१ और राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७
