Dihedral constraints
Introduction
Following on from generating dihedral restraints using an HNHA experiment, we will now generate backbone dihedral restraints in a different manner, from backbone chemical shifts. We will be using a program called DANGLE (Dihedral ANgles from Global Likelihood Estimates) which is embedded within Analysis. DANGLE estimates dihedral angles from chemical shifts in a similar manner to TALOS; i.e. it matches a chemical shift & sequence query to a structural database of known PHI/PSI angles and chemical shifts. However, DANGLE uses a different (Bayesian) method to produce an angle estimate and tolerance, compared to TALOS. The idea is to use Bayesian inference to infer what the range of likely PHI/PSI angles might be (using the chemical shifts) by checking all PHI/PSI combinations in 10 degree square bins to see how well such angles can be used to explain the data. Such an analysis allows for the user to see uncertainties in the angle predictions, including where the chemical shift to structure mapping is redundant and there are multiple regions in the ramachandran plot which could explain the chemical shift data.
DANGLE
To run DANGLE select M: Structure: DANGLE Predict Dihedrals. Note that at the top that the Chain should be set as "MS1:A", the Shift List as "ShiftList 1:1" and "Max No. of Islands:" as 2. This simply specifies which data to use and how strict the analysis should be. Using two islands means that we will reject predictions that result in more than two discrete regions of the Ramachandran plot:
To start the analysis press [Run Prediction] and accept "Run1" as the name for the job by pressing [OK] at the opportune moment. Please be aware that DANGLE will take several minutes to finish the calculation.
Once the calculation is over you will see that the main table filled in with PHI and PSI backbone dihedral angle predictions and their associated error ranges. Further, if you select a row in the main table you will see a plot in Ramachandran (PHI/PSI) space of where the likely angles are deemed to be. Click on the "9 Tyr" row and note that there is a lot of red colour in the chart, indicating that DANGLE was not able to make a distinct choice of PHI/PHI:
You should not use such a prediction in a structure calculation. Click on the [Next] button to get to "10 Arg". The prediction for this residue is somewhat better, and you could use this in a structure calculation (it has one discrete region) although the error bounds for such a dihedral restraint would be suitably large. Click [Next] once more to get to "11 Glu". This residue has a very precise range of predicted PHI/PSI angles:
Such a residue could be used in a structure calculation with a high degree of confidence and proportionately narrow error margins.
Note that DANGLE also predicts the secondary structure of the residues, but that this calculation is not made from the angles, but directly from the measured secondary structures in the shift-structure database. To make the restraints themselves simply press [Commit Constraints]. This will make a PHI/PHI dihedral angle restraint list in the selected constraint set (which you might remember corresponds to one fixed/frozen assignment state so that you always know what you actually restrained even if assignments on the peaks change.
View the generated restraints by going to M: Structure: Restraints & Violations, {Restraints} - ensuring the restraint set matches the one you put the calculation results into and the "Restraint List:" is set to "1:Dihedral:DANGLE...". Note that if you have a structural model for your protein you can see how the model's angles match with the DANGLE prediction. You can do this by either pressing [Calculate Violations] (load a structure first), or in the DANGLE popup itself you can select a structure from which the PHI/PSI angles are superimposed on the angle plot.
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