I-PINE, CO shifts
Ivan S. Podkorytov
Hi Woonghee,
May I ask you a couple of questions about assignment
http://zavot.nmrfam.wisc.edu/upload/script/users/210311_031905_371162/results
?
1) The file
protein_backbone_assignment.txt
contains almost complete assignment with probabilities P > 0.99. Also, the file
sparky_ExportfromPolyScope2---march-11---HNCACB-12.txt
contains almost complete assignment. In contrast, the file
sparky_ExportfromPolyScope2---march-11---HN(CA)CO-24.txt
contains only question marks “?-?-?” and no any assigned signal. What does it mean?
2) As an example. According to protein_backbone_assignment.txt, HIS-20 and GLU-21 are assigned (with very high probabilities of 1.000 and 0.997) as follows:
20 HIS 1.000 8.315 113.69
21 GLU 0.997 8.242 117.31
However, basing on CO shifts I would say that this assignment is incorrect. The HSQC peaks (8.315, 113.69) and (8.242, 117.31) have CO shifts at {175.536 and 176.357} and {175.289 and 177.036}, respectively (see the file sparky_ExportfromPolyScope2---march-11---HN(CA)CO-24.txt). The difference 175.536 - 175.289 = 0.247 ppm is big enough to reject the assignment. Does I-PINE server take into account CO shifts?
3) In PINE-SPARKY.2 automation, one can define ppm tolerances N tol., C tol., and H tol. Is it possible to define the tolerances on I-PINE server?
Thank you. Have a good weekend!
Ivan.
Lee, Woonghee
Dear Ivan,
1) The file
protein_backbone_assignment.txt
contains almost complete assignment with probabilities P > 0.99. Also, the file
sparky_ExportfromPolyScope2---march-11---HNCACB-12.txt
contains almost complete assignment. In contrast, the file
sparky_ExportfromPolyScope2---march-11---HN(CA)CO-24.txt
contains only question marks “?-?-?” and no any assigned signal. What does it mean?
It means it doesn’t have any robust assignments for CO.
2) As an example. According to protein_backbone_assignment.txt, HIS-20 and GLU-21 are assigned (with very high probabilities of 1.000 and 0.997) as follows:
20 HIS 1.000 8.315 113.69
21 GLU 0.997 8.242 117.31
However, basing on CO shifts I would say that this assignment is incorrect. The HSQC peaks (8.315, 113.69) and (8.242, 117.31) have CO shifts at {175.536 and 176.357} and {175.289 and 177.036}, respectively (see the file sparky_ExportfromPolyScope2---march-11---HN(CA)CO-24.txt). The difference 175.536 - 175.289 = 0.247 ppm is big enough to reject the assignment. Does I-PINE server take into account CO shifts?
CO shifts are completely ignored I presume. Because you don’t provide a partner experiment like HNCO. HN(CA)CO couldn’t determine (i-1) vs (i) for the peaks on the strip because of that. Also, 0.247 is not big for heavy atoms.
3) In PINE-SPARKY.2 automation, one can define ppm tolerances N tol., C tol., and H tol. Is it possible to define the tolerances on I-PINE server?
I-PINE uses harmonic potential for the different shifts higher than certain level and the user does not need to provide tolerances. Those tolerances in PINE-SPARKY.2 is for putting assignment labels not for I-PINE automated assignments.
Best,
Woonghee
--
Woonghee Lee, I.E.I.P., M.S., Ph.D.
Assistant Professor
Department of Chemistry
University of Colorado Denver
1151 Arapahoe St. (Science Bldg.) Rm 4128A
Denver, CO 80217-3364, USA
Office: +1-303-315-7672
https://poky.clas.ucdenver.edu
https://clas.ucdenver.edu/chemistry/woonghee-lee
Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
P.O. Box 173364 (USPS)
Denver, CO 80204, USA
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