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Again thanks all for your suggestions, Dear Herman For all the structures wt or mutant PISA is predicting to be a dimer. On Thu, Sep 10, 2015 at 5:54 PM, <[log in to unmask]> wrote: > Pankaj, > > Again a few remarks: > > - Is Pisa predicting a tetramer for the P6522 crystals, but not > for the D32 crystals? > > - Or is the putative tetramer present in both crystal forms? > > - Would some of the putative tetramer contacts become stronger > upon protonation at low pH? In that case one could consider changing the > residues involved to their protonated counterparts (e.g. Asp->Asn). > > > > Herman > > > > *Von:* CCP4 bulletin board [mailto:[log in to unmask]] *Im Auftrag von > *pankaj sharma > *Gesendet:* Donnerstag, 10. September 2015 14:01 > *An:* [log in to unmask] > *Betreff:* Re: [ccp4bb] How different space groups affect interaction > between symmetry mates of a protein and its mutant > > > > Thanks for your valuable suggestions, to be more precise this protein is > biologically dimeric in nature and we are getting same result through PISA. > But during stressed conditions this wt protein forms tetramers (As seen in > native gel), further mutant protein also forms tetramers under normal > conditions (i.e. in the absence of stress, like low pH), so can we assume > that the stronger interactions between symmetry mates seen in mutant w.e.t. > wt protein are the cause of formation of tetrameric population even in the > absence of stress in mutant. Further since PISA is predicting it to be > dimer can we predict the structure of higher order oligomerisation state > based on symmetry analysis results as well as by doing some mutations at > symmetry interface to prove that in solution also, these interactions > persists and are responsible for oligomerisation of this protein. Also I > want to add that mutations are not in the interaction interface. > > > > On Thu, Sep 10, 2015 at 4:51 PM, Pankaj Chauhan <[log in to unmask]> > wrote: > > Dear Pankaj, > > > > PISA is the good suggestion to know the correct symmetry related contacts. > > Is the mutation in between crystal contacts? When you superpose the two > structures, do you find any difference in them? There are few questions > that can give directions to next experiments to answer any biological > question. > > > > Pankaj > > > > > On Thursday, September 10, 2015, pankaj sharma <[log in to unmask]> > wrote: > > Dear all, > > I am solving crystal structure of a protein. wild type protein is solved > in H32 space group but its mutant is in p6522 space group. this protein is > known to exist in oligomeric states. Interaction between the symmetry mates > of mutant is twice (~86, 10H-bonds, 2 salt bridges) as compared to wild > type protein (~46, 4H-bond and 2 salt bridges). Further we carried out > native PAGE analysis where we found that an additional band corresponding > to oligomeric state is present in mutant protein but absent in wt protein. > > > > So, can we co-relate crystallization data with native PAGE results? or > > we should do further mutations based on crystal structure results? > > > > Further mutant protein exists in two populations native and oligomeric > state, thus if the interactions between mutant protein molecules are > sufficient to form oligomeric state then why all the mutant protein > molecules are not transforming from native to oligomeric state? > > > > -- > Sent from Gmail Mobile > > >