Assign NOEs based on structural information

Assign NOEs

It is possible in Analysis to assign NOE peaks based on information from structures. This is useful if we e.g. have a NOE peak list that is only partly assigned or has ambiguous assignments, for which we want to make further assignments or reduce the level of ambiguity.. The structure models that are used for this structure based NOE assignment may have been generated from a structure calculation program like ARIA based on the projects’ NOE peak lists and chemical shift lists, or could stem from other sources such as homology modeling or databases.

The NOE peaks can be assigned, or ambiguities be resolved, based on the distances between the 1H atoms in the structure. If one of the 1H resonances in a peak dimension assignment is assigned to an atom in the structure, the distance will automatically be calculated for each of the assignment possibilities in the other 1H dimension. The procedure to make the assignments can be done as follows:

• • Make sure that the structure and assigned molecule are connected to the same Molecular system.

  • Go to the NOESY spectrum and click ‘a’ over a peak you want to assign to raise the Assignment: Assignment Panel popup for that peak.

  • Set the structure in the upper right pulldown menu in the Assignment: Assignment Panel popup.

  • Click [Show on Structure] to see assignment possibilities in the structure viewer. How the structure viewer works is found here.

  • Based on the distance (|Dist|) column in the Assignment: Assignment Panel popup, assign the peak dimensions based on the distances between the atoms in the assignments (This assignment is often based upon the shortest distance).

Note: Because we have a structure loaded in the project, the Assignment: Assignment Panel popup will show distances between the atoms assigned to the different peak 1H dimensions. Distances only appear in the |Dist| column if you have an appropriate structure set at the top and then only if there are through-space transfers in particular dimensions of the peak’s experiment (See Figure 1).

Figure 1. The Assignment: Assignment Panel popup with distances in the |Dist| column. The distance between the 10TyrHd* and the 9SerH is here shown to be 6.122 Å.

Assign NOEs in a more detailed manner

An alternative, more detailed, method of assigning NOE peaks goes via the Assignment: NOE contributions popup accessible through M: Assignment: NOE Contributions:

This functionality is designed to make the whole process of comparing NOE peaks to a structural model efficient and the general way to use it is to do as follows:

•   Go to the {Peak List & Display Settings} tab and choose the peak list for the NOESY experiment in the “NOE Peak List:” pulldown menu.

•   Double click in the |Use?| column in the lower table for the relevant window, so that it becomes "Yes".

•   Set the ''Structure Display:" pulldown menu (choose e.g. "Assigned" to show assigned peaks in the structure viewer)

•   Set the structure in the “Structure:” pulldown menu.

•   Set other properties of choice and move on to the {Peak Assignments} tab.

•   Select a peak in the spectrum window and in the Assignment: NOE Contributions popup click [Selected Peak]. This will show you, in terms of the close chemical shifts and distances from the selected structure, what the likely NOE assignments are.

‣    An alternative approach to see the likely NOE assignments to a peak would be to click on a peak row in the ‘NOE Peaks’ table the Assignment: NOE Contributions popup. The lower table ‘Possible Assignments’ will now show the possible resonance assignments.

•   To assign a peak to a resonance, select the resonance in the table cell and click [Assign Selected].

•   To remove a resonance from a peak dimension, click [Delete Assignment]. You will see that the upper table, the spectrum window and the structure view will update to reflect the new assignment.

In cases where the resonance assignments are not so clear for a peak, click [Predict Peaks]. This command will use the selected structure and the known chemical shift values to predict the positions of peaks, near to the selected real peak:

The artificial peaks shown in the Figure above are labelled with the distance in the structure and are contained in an entirely separate list to the real peaks (so nothing is contaminated and they can be removed easily).

To confirm an assignment have a look at the "return" peaks that show the reciprocal connection (looking from the point of view of the other atom). To do this click [Find Reciprocal Peaks] and you will see that the spectrum window splits into separate strips, with the original location on the left. In the strips to the right you might now see positions with peaks that may possibly reciprocate the same proton-proton connection.