Using Structures to Assign NOE Contributions
This part of the Tutorial is based on the CcpnStructCourseD project.
An alternative, more detailed, method of looking at NOE assignments is via the M: Assignment: NOE Contributions option. This is designed to make the whole process of comparing NOE peaks to a structural model efficient. Select this and in the {Peak List & Display Settings} choose the "N-NOESY:182:1" for the NOESY experiment you are currently looking at, then double click the "Use?" column in the lower table for the relevant window, so that it becomes "Yes". Also set ''Structure Display:" to "Assigned" and "Mark Peak:" to true:
Now move to the {Peak Assignments} tab, select the peak in the spectrum window (left click & drag) and in the Assignment: NOE Contributions popup click [Selected Peak] (alternatively, just click on a row in the table). This will show you, in terms of the close chemical shifts and distances from the selected structure, what the likely NOE assignments are.
By clicking on the rows in the NOE peaks table you will see that several things happen automatically: The view of the selected windows (in this case the selected window2) zooms and marks the selected peak; the graphical structure view highlights the assigned atom connections from the peak; and the lower table of the NOE Contributions popup shows the structurally possible, shift-matched resonance pairs ordered in terms of shift and geometric distance. Select the first peak in the table (10Tyr) and you will see that the top row for the possible assignments is "9SerHbb", which is close in chemical shift and only 2.939 Angstroms away. Click on the "9SerHbb" for the second column in the table and then [Assign Selected]. You will see that the upper table, spectrum window and structure view all update to reflect the new assignment.
Next, in the upper table select peak number 4 (62Glu) and you will see that the assignment possibilities are not so clear cut. Here, selecting [Predict Peaks] will use the entered structure and the known chemical shift values to predict the positions of peaks, near to the selected real peak:
These artificial peaks are labelled with the structural distance and are contained in an entirely separate list to the real peaks (so nothing is contaminated and they can be removed easily). In this instance it is probably appropriate to assign the peak to both of the top assignment possibilities (from residues 62Glu and 31Ala). While holding down the 'Ctrl' key select both the "63AlaH" and "32LeuH" options in the table and click [Assign Selected]:
We can confirm that this double assignment was the correct thing to do by looking for "return" peaks that show the reciprocal connection (looking from the point of view of the other amide). Clicking on [Find Reciprocal Peaks] you will see that the spectrum window splits into separate panels, with the original amide location on the left. Strips 2-4 show other amide positions with peaks that may possibly reciprocate the same proton-proton connection. Peaks for 63AlaH and 32Leu are indeed present and confirm the assignment in the second dimension we just made. Note also that 36Leu shows a potential return peak, but this is too far away in the structure and so does not appear in the table.
Note that if we change peak assignments then we have the choice of making (or letting ARIA make) a new set of restraints. Alternatively we can curate the existing restraints using the [Update Assignment From Peak] button (see M:Structure:Restraints & Violations, {Restraints}), which will alter the distance restraint to reflect this new assignment.
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