I am using a structure-based alignment, and I want to model a sequence based on a template, but I want to model my sequence with inverted polarity to the template. That is, I want to model starting from the C-term of the template backwards to its N-term. If I invert my sequence in the alignment, the result is structurally sound, but now they are obviously bonded incorrectly.
For example, my template is: >P1;1u19 structureX:1u19.stripped:33:A:65:A: rhodopsin: Bovine: 2.20: 0.200 EPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQH*
and my sequence is (n)-FVFKIVIVIGILPLLNLVGVVKLI-(coo) but I want the F positioned near the H end and the ile positioned near the glu in the template etc. How would I go about doing this?
Hi,
If I understand your problem correctly you need to change the template instead of the target sequence since you want to reverse the order of the residues in the structure, essentially creating a new fold (mirror image?). A quick solution would be to use only C-alphas coordinates from the original template and reverse their order in the PDB file. You start with coordinates for the c-term H C-alpha, which now becomes an n-term H in the new template and end with the coordinates for the n-term E C-alpha, which now becomes a c-term E. This step is basically just text editing (remember to renumber the residues and reverse the template sequence in the alignment). Now you can use this new C-alpha template to model your target sequence. I guess there is no way around loosing the rest of the structure (backbone and sidechain atoms) since anyway their positions are not likely to be compatible with the "new fold". Not sure if this is what you want.
Best,
Roberto
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://sanchezlab.org/
> -----Original Message----- > From: modeller_usage-bounces@salilab.org [mailto:modeller_usage- > bounces@salilab.org] On Behalf Of Peter C. Lai > Sent: Thursday, October 13, 2005 3:52 PM > To: modeller_usage@salilab.org > Subject: [modeller_usage] howto reverse polarity > > I am using a structure-based alignment, and I want to model a sequence > based on a template, but I want to model my sequence with inverted > polarity > to the template. That is, I want to model starting from the C-term of the > template backwards to its N-term. If I invert my sequence in the > alignment, > the result is structurally sound, but now they are obviously bonded > incorrectly. > > For example, my template is: > >P1;1u19 > structureX:1u19.stripped:33:A:65:A: rhodopsin: Bovine: 2.20: 0.200 > EPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQH* > > and my sequence is (n)-FVFKIVIVIGILPLLNLVGVVKLI-(coo) but I want the F > positioned near the H end and the ile positioned near the glu in the > template > etc. How would I go about doing this? > > -- > Peter C. Lai > Cesium Hyperfine Enterprises > http://cowbert.2y.net/ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage
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Peter C. Lai -
Roberto Sanchez