Page header

Page header (1) reports information contained in the PDB entry (PDB ID, resolution) as well as in the corresponding UniProt record (ID, Organism, protein length). We also report basic structural information in terms of secondary structure content and ECOD class. In our case, the protein contains two different ECOD architectures: one with the prevalence of β-sheets and one containing both α-helices and β-sheets as secondary structure motifs. The overall content in β-sheets is 39%.

The user can access a more detailed description of the protein structural annotations by clicking on the “More” button (2). We report protein domain delimitation according to ECOD, CATH and SCOPe.

Finally, we also report general parameters computed from the molecular dynamics (MD) trajectories in the “Dynamics properties” section. The source data used to calculate the parameters and to produce plots on the page can be downloaded in a .zip archive using the Download button (3).

General properties

The “General properties” section allows the user to have an overview of the main protein properties and its average flexibility profile.

Along the sequence, one can visualise the secondary structure (assigned on the 1st MD frame) as well as 4 protein domain delineations (ECOD, CATH, SCOPe and SWORD2). Users can also visualise the experimental B-factor values extracted from the initial PDB file, and the flexibility profiles averaged over the 3 MD replicates (RMSF and Neq: see About for the details).

This change results from the structure extension since the gyration radius increases for the corresponding trajectory.

Flexibility profiles are available in two types of representations (2):

• Normalised by protein (linear scale): for a global view of the protein.
• Normalised on the complete dataset (log2 scale): useful to compare flexibility profiles of different proteins.

To facilitate the visualisation, additional information is available on mouse hover such as value, author position (original numbering in the PDB file) and ATLAS residue numbering (starting from 1).

Replicates overview

In the “Replicates overview” section we provide flexibility profiles as well as global analysis of the protein conformational mobility during the simulation.

The user can visualise the diagrams for different replicates all together or one by one by clicking on the legend (2), and can zoom with a click and drag on the zone of interest. RMSD values indicate the divergence of the protein conformation from the initial structure during the simulation. During the simulation, our protein undergoes an important conformational change in the replicate 1 (blue curve), as we can clearly see on the RMSD plot.

This change results from the structure extension since the gyration radius increases for the corresponding trajectory.

The fluctuation of the protein residues from the reference conformation is reflected on the RMSF plot. In our case it seems that most pronounced fluctuations concern residues 180-276. Such delimitation corresponds to the second beta-sheet domain. Nevertheless, RMSF does not reflect local deformability of the backbone. To identify the hinge zone responsible for the conformational variability of protein structure in the trajectory, we can visualise Protein Block (PB) Neq values (3). According to this plot, the zones undergoing the most pronounced deformations in the region of interest are located around residues 173-184 and 235-240. The region 185-217 is, on the contrary, locally rather rigid.

Detailed analysis

To get into the details of the detected conformational changes, one can, for each replicate (1), visualise the structure and MD trajectory using the 3D Viewers, contact maps, Ramachandran plots and DSSP plot in the “Detailed analysis” section.

In the “Structure” 3D viewer, the protein can be colored by sequence position or by initial secondary structure (2). In our example, the second beta-sheet domain is then colored in reds.

The user can also visualise the flexibility descriptors on the protein (3), modifying both the colour and width of the structure. From the PB Neq representation of our example, we can clearly see the location of the deformable hinge positions in the protein loops and inter-domain region.

The users can also take a look at the trajectory itself by clicking on the “Dynamics” tab (4) and observe the corresponding movements in 3D.

Next to it, on the “Animated” contact map (5) we can observe formation and destruction of the inter-domain contacts along the trajectory. Ramachandran plots (6) ensure that most of the residues are adopting conformations characteristic for the corresponding secondary structure.