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Working with Peptides

Working with Peptides

CcpNmr Analysis contains several features which should make life easier for people working with peptides.

Multiplets

Peptide spectra often contain undecoupled peaks which are split into multiplets. Find out about our Multiplets feature to see how you can group your peaks into multiplets. This way, the Chemical Shift reported in your Chemical Shift List will always be at the centre of the multiplet and you won't have to place an artificial placeholder peak between the two actual multiplet components as a surrogate.

We have also introduced a 2D multiplet peak picker. If you go to File / Preferences and then go to the Peaks tab, you can set your Default nD peak picker to PeakPicker2DMultiplets. This will act exactly the same as our normal PeakPickerNd peak picker, but for 2D spectra it will automatically group close peaks into multiplets.

Working with non-canonical Amino Acids

This is a common occurrence for people working with peptides. In principle, if you are simply assigning your protein, you can just go ahead and create the NmrResidues and NmrAtoms that you need as you want. The ResidueType box can be set to anything, so you can give your residue a different name. Similarly, the AtomName can be set to anything, so as long as you know what each atom in your non-canonical amino acid is called, you can name these as you wish.

You may decide that you would like to have not only an NmrChain, but also a Chain of your peptide in your project. This would, for example, allow you to create all possible NmrAtoms from the Chain very easily. And if you are going to be doing structure calculations you will need a Chain, too. In order to add a non-canonical amino acid to your Chain, you need to have a ChemComp .xml file for this amino acid. This is a file which contains all the information about the atoms: their names, how they are bonded to one another, possible differences in protonation state, magnetically equivalent groups, prochiral atoms, where/how the amino acid is linked to neighbouring amino acids in a chain etc. Find out about how to access existing ChemComp files for non-canonical amino acids or create your own on our Creating Non-canonical Amino Acid ChemComps page.

Once you have your ChemComp file you will then need to add it to your project and create your Chain using so-called ccpCodes rather than the standard 1-letter amino acid code. Have a look at our Creating Chains with non-canonical Amino Acids page to find out how you can do this.

Reference Chemical Shifts

If you are not so familiar with the average Chemical Shift values for the standard amino acids, you can easily look these up at Main Menu / Molecules / Reference Chemical Shifts (or shortcut RC) and correlate the Reference Chemical Shifts with the mouse cross-hairs in your spectra. Have a look at our Reference Chemical Shifts webpage for more information.

In addition, we have created a NEF file containing a 20-amino acid chain with all the Reference Chemical Shifts. You can import this into your project and then use this to create marks on your spectrum by dragging one of the NmrResidues/NmrAtoms onto a SpectrumDisplay.

You can also use the NEF file containing a 20-amino acid chain with all the Reference Chemical Shifts in conjunction with the Creating Peaks from NmrResidues macro introduced below to create a set of peaks at the Reference Chemical Shift positions which you can then easily move onto the actual peak positions in your spectrum.

Creating Peaks from NmrResidues

More information on this soon...

Creating a structure calculation PeakList from a Noesy spectrum with multiplets

When conducting structure calculations you generally need to provide the structure calculation program with a Noesy Peak List and a matching Chemical Shift List. However, if your Noesy spectrum contains multiplets (which may well be the case when working with unlabelled peptides), then the peaks in your Noesy spectrum (which are the multiplet components) won't match the Chemical Shifts in the Chemical Shift List (which match the centre of the multiplet). In addition, you may have some peaks which are split into multiplets and others which are not. Our CreateNoesyPeakListFromMultiplets macro will take your Noesy PeakList and create from it a new PeakList in which any peaks belonging to multiplets are replaced by peaks located at the multiplet centre and for which the heights and volumes are the sum of the heights and volumes of the component peaks of the multiplet. This PeakList can now be used together with a ChemicalShiftList to run a structure calculation.