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Setting Up NmrResidues

Setting up NmrResidues

Setting up your NmrResidues is the first step required for the Backbone Assignment of a protein. We start the assignment process by assigning each peak in an HSQC or other base spectrum to NmrResidues and NmrAtoms which we use as placeholders until (over the course of the assignment process) we can assign them to actual residues and atoms. Go to NmrResidues for more information on how NmrResidues, NmrAtoms and NmrChains are used in Analysis.

Make sure all the peaks in your 2D (HSQC) base sepctrum have been picked, for example, by holding down Shift and Ctrl (Cmd on a Mac) while left-dragging the mouse over the complete spectrum area (go to Peak Picking for more information on peak picking).

Type SN or go to Assign / Set up NmrResidues. Select the (HSQC) peak list you want to use to set up your NmrResidues. Select the NmrChain you would like your NmrResidues to be added to. By default, this is the @- chain. If you want to use a different NmrChain, you can create a new one, by opening up NmrChains in the sidebar and double-clicking on New NmrChain. Then select Create New (rather than Clone from) and give your NmrChain a name. Once you have selected both your source peak list and your NmrChain you can click Okay to set up your NmrResidues.

The program creates a set of NmrResidues and NmrAtoms in your chosen NmrChain. If you open your NmrChain in the sidebar you will now see that it contains all the NmrResidues and these in turn contain the NmrAtoms that have just been created. These are now your provisional atom names until you have managed to assign them. Any other peaks in other spectra which stem from the same nuclei can (or indeed should) be assigned to these same NmrAtoms.

Each peak has now also been given a peak label. Our base spectrum is generally a spectrum (such as an HSQC) in which the two atoms associated with each peak must be bonded to one another and belong to the same residue. Therefore, the two dimensions of each peak are labelled with the same NmrResidue (currently an arbitrary number preceeded by an @ symbol to indicate that this is a temporary number until we have made an assignment). But each dimension is assigned a different NmrAtom; in the case of an HSQC these are generally named either H or N. (The NmrAtom names are derived from the Axis Codes - change these in the Dimensions tab of the Spectrum Properties dialog, opend by double-clicking on a spectrum in the sidebar.) Typically, the peak label is something like @63H, N, meaning that the NmrResidue is @63 in both dimensions and the NmrAtom names in the two dimensions are H and N.

By default, all the peaks in an HSQC spectrum are given H and N atom names. Of course you are likely to have some peaks in your spectrum which derive from Asn, Gln or Trp side chains. You can change the atom names to HD2x/y, ND2 etc. at any time. Simply double-click on the NmrAtom in the sidebar to bring up the Edit NmrAtom diaglog box, choose a different atom name and click Apply or Okay.