Examples

Here you can find a set of pre-computed results to explore Heligeom outputs, taken from the Heligeom webserver paper. Each example can be explored by clicking on the Examples menu on the Run page.

2GLS: an oligomeric ring assembly.

Link to the results
In this structure, two successive chains (here A and B) provide a pitch of 0 and 6 monomers per turn. This information allows (re-)constructing a regular cyclic hexamer.

4ESV and core regions.

Link to the results
The proteins making up helicase DNAse B in the 4ESV structure have two domains. In the different monomers of the crystallized molecule, the N-terminal domain is seen to have multiple orientations relative to the C-terminal domain. This example highlights Heligeom server's capacity to compare two oligomeric forms, showcasing the importance of defining a core region in the case of flexible monomers.

For the 1st oligomeric form, the complete chains B and C are specified. In the 2nd oligomeric form the same two chains are specified, but a quasi-rigid "core" region is defined that excludes the mobile N-terminal domain.

One sees that Heligeom produces different results according to the presence or absence of the N-terminal domain in the analysis.
When the complete monomers are used for the helical analysis (first oligomeric definition), the different relative orientations of the N-terminal domains contribute to a large rmsd after superposition, which affects the calculated screw transformation.
Limiting the analysis to the stable core regions, as in the second oligomeric definition, results in a smaller rmsd and more meaningful helical parameters.

3ICE and alternative interfaces.

Link to the results
This example focuses on different interfaces within the same structure - here an hexameric ring structure of the Rho helicase transcription termination factor.
Depending of which pairs of chains are chosen for analysis, the fNAT values characterizing the interfaces differ: here 0.43 for interface AB vs EF and 0.85 for AB vs BC.

4ESV ring flattening.

Link to the results
The DNAse B molecule in 4ESV is organized as a shallow helix wih a pitch of less than 40 A. Suggested mechanisms for this enzyme's function involve a transition from this helical form to a ring conformation.
Here we will show how Heligeom server can be used to explore possible ring geometries close to the helical crystal structure:

As in the "4ESV and core regions" example, residues 184-365 of chains B and C have been defined as the core regions, which excludes the mobile N-terminal domains and results in a core-assembly pitch of 38.1 A and 6.04 monomers per turn.

For the present example you may obtain a ring assembly having exactly 6 monomers and a pitch of 0, by constructing an assembly while requesting "flattening" of the starting helix.
This launches a Monte Carlo procedure to adjust the monomer core packing in order to attain the closest integral number of monomers per turn, as described on the About page.

Concretely, you enter 6 for the number of monomers and check the box "Flatten the oligomer". We also recommend aligning the axis of the assembly to the Z-axis by checking the appropriate box.
For this example we also pre-defined each monomer to include a few N-terminal domain residues as well as the core region, in order to better visualize where the flexible N-terminal domain is joined to the core.

However, because the construction is made by assembling identical copies of the first monomer, no N-terminal variability will be present in the resulting assembly.