Hi,
I need to model a protein with the lysine all straight (stuck-up?). How can I say to modeller that only create models with the lysine in that form?? This Lysine is known to be like that. Thanks!!
Omar
Hi Omar,
Presumably if you know the rotamer the lysine adopts it is from a solved crystal structure, with good B-factors for the atoms? Anyway, Coot is a crystallographic model building program that lets you play with rotamers ( http://www.biop.ox.ac.uk/coot/).
Cheers, James
On 9 October 2010 05:38, Omar Piña pibe05@gmail.com wrote:
> > Hi, > > I need to model a protein with the lysine all straight (stuck-up?). How can > I say to modeller that only create models with the lysine in that form?? > This Lysine is known to be like that. Thanks!! > > Omar > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
You probably need to tune Modeller to set all lysine rotamers to the the straight conformation on the fly, otherwise you may get biased models -especially if the Lys residues are buried within the protein. If this isn't the case and you just want to adjust a few side-chains on the surface then you can use Chimera (read section "Angles, Rotamers and Clashes"http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html). With Chimera you can correct interactively every residue you like and also see what steric clashes or H-bonds are formed by every rotamer. I use it a lot to improve my models or adjust side-chains in the active site.
Otherwise you will need a more drastic solution (not sure if possible), namely tuning Modeller to do that directly. Modeller Caretaker is the designated person to answer that question.
best, Thomas
On 10 October 2010 22:39, James Irving irving.james@gmail.com wrote:
> Hi Omar, > > Presumably if you know the rotamer the lysine adopts it is from a solved > crystal structure, with good B-factors for the atoms? Anyway, Coot is a > crystallographic model building program that lets you play with rotamers ( > http://www.biop.ox.ac.uk/coot/). > > Cheers, > James > > > On 9 October 2010 05:38, Omar Piña pibe05@gmail.com wrote: > >> >> Hi, >> >> I need to model a protein with the lysine all straight (stuck-up?). How >> can I say to modeller that only create models with the lysine in that form?? >> This Lysine is known to be like that. Thanks!! >> >> Omar >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >> > > > -- > Dr. James Irving PhD > Research Associate > Cambridge Institute of Medical Research > Wellcome Trust/MRC Building > University of Cambridge > Hills Road > Cambridge CB2 0XY > UK > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
On 10/8/10 9:38 PM, Omar Piña wrote: > I need to model a protein with the lysine all straight (stuck-up?). How > can I say to modeller that only create models with the lysine in that > form?? This Lysine is known to be like that. Thanks!!
For any modeling in Modeller, you need to think about the set of spatial restraints that correspond to your desired geometry. By "stuck-up" I presume you mean a specific rotamer for which you know chi1, chi2 etc. So you just create a few restraints on those dihedrals. If you're doing this during a comparative modeling run with automodel, you'd build those restraints in the special_restraints() routine. The only complication is that Modeller already builds homology-derived sidechain restraints, so you'd have to remove those first using Restraints.unpick() and Restraints.condense().
I've attached a simple modification of the basic automodel example from http://salilab.org/modeller/9v8/manual/node16.html which modifies it to restrain the first Lys residue (residue 15) to have both chi1 and chi2 be 0 +/ 0.1 radians.
Ben Webb, Modeller Caretaker
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James Irving -
Modeller Caretaker -
Omar Piña -
Thomas Evangelidis