GPCRmd

GPCR viewer

Video tuturial

General features

Mouse controls:

  • Left button hold and move: rotate camera around center.
  • Middle button hold and move: zoom camera in and out.
  • Middle button click: center camera on atom.
  • Right button hold and move: translate camera in screen plane.
  • Left button click: pick atom or distance.
    • When an atom is clicked, a label with information about it appears. Click at the background to deselect it, the label will disappear. To maintain a label, double-click on an atom. Double-click on a label to remove it.
    • To draw a distance line between two atoms just single-click one atom after the other. Distances can be removed by double-clicking on one of the atoms at the edges.
    • It is also possible to remove all the atom labels and distances at once, with the Clear dists. button.

If you wish to use more complex visualization options, you can open the structure and trajectories in MDsrv just by clicking at the button.

Selection tools

Quick selection

Quick-selection buttons allow to rapidly display the molecules present at the dynamics. Hover the buttons with your mouse to see the abbreviated name of these molecules, which can be used to create your own selections.

It is also possible to select the residues or molecules that are found within a certain distance of a ligand. It is only necessary to:

  1. Indicate what you want to visualize (residues or molecules found at the simulation).
  2. Input the wanted threshold distance (in angstroms).
  3. Indicate the molecule type around which the selection is made. Apart from predefined molecules, it is also possible to show the residues/molecules that are close to a personalized selection which, again, can include generic GPCR residue numbering.

If the selection is correct, a green checkmark () will appear at the left. More than one distance selection can be displayed at the same time. Selections made with this tool will appear in coral red, with atoms that are within the threshold distance shown opaque and the rest of atoms of the residue/ligand shown with transparency. The distance selection will be updated for each trajectory frame, as the disposition of the atoms may change.

Atom selection

Use the text input field to specify your personalized representations. You can choose a representation type (licorice, cartoon, etc.) and a coloring scheme (color by element, by chain, etc.).

Selections must be expressed using the NGL selection language. Moreover, to indicate protein residues it is also possible to use generic GPCR residue numbering: Ballesteros-Weinstein (ex. 1.50), GPCRdb structure-based numbering (ex. 1x50) or a combination of both (ex. 1.50x50).

For example, if you input 40-70:P or CLZ, residues numbered from 40 to 70 at the PDB belonging to chain P and Clozapine will be displayed. Another example, this time using a combination of different generic GPCR numbering styles, could be 1.50 - 2x48 or 3.35x35 or SOD.

Sequence selection

The GPCR viewer also provides the option to select a protein segment from its sequence. Set your selection by clicking at the desired range or ranges of residues, selected segments will appear at the sequence in green. To deselect a residue range from the sequence, just click on it. Finally, click at Confirm selection: the residue range(s) will be added to a text input field, which you can modify to adjust the selection to what you want to display. If you want to add new sequence selections, click at the button.

GPCR conserved positions

The GPCR conserved positions selection provides the possibility to rapidly select positions or domains conserved in the different GPCR family classes. In this section, the GPCR class of the protein being represented will appear in bold. It is also possible to visualize in your protein the positions that correspond to conserved positions from other GPCR classes. For example, if your protein belongs to class A, you can represent the residue that corresponds to class B 2.50 (2.50b). Hover the buttons with your mouse for more information about the conserved positions and motifs, if available. Class A positions are shown in blue, B in orange, C in yellow and F in pink.

Analysis tools

Distance within 2 atoms

This tool is used to calculate the distance between atom pairs across the different frames of a trajectory, and therefore across time. To calculate a distance, you need to indicate the pair or pairs of atoms you are interested in. This can be done in different ways:

  • Select a pair of atoms at the viewer screen by clicking on them and, afterwards, importing the created distances with the blue arrow button .
  • Indicate the desired atom pairs manually, by selecting "Compute distance between" atoms and inputting a pair of atom indices at the text input fields.
  • Indicate the desired atom pairs manually, by selecting "Compute distance between" residues and indicating the residue, chain and atom name you are interested in. The residue number and chain name must be indicated according to the NGL selection language (ex. 50:P), and the atom name selected from the droplist.

It is also necessary to select the trajectory that will be used for the calculation.
Finally, just click at Compute. Only atom pairs which are marked with a green checkmark () will be considered, since the absence of a checkmark indicates an error in the input (only numbers are allowed). The result will appear as a plot of distance by time or by frame, which can be downloaded as an image (). It is also possible to download the data obtained as a csv file (). Moreover, the distances calculated can be displayed at the viewer screen, in the colors indicated at the plot legend. Such distance representations can be deactivated by deselecting the "Display distance" checkbox.

RMSD

This tool computes the RMSD of all the conformations in a target trajectory to a reference conformation. It is necessary to indicate the trajectory to be used and the frames to be considered. Also, a reference frame of a given trajectory. It is possible to chose which atoms are going to be considered in the calculation: only alpha carbons, non-hydrogen protein atoms, protein C-alpha, etc. As in the case of distance analysis, the result will be shown in a plot (RMSD by time or by frame). It is possible to download the plot as an image () or all the obtained data as a csv file ().

Ligand-residue interaction frequency

This analysis tool calculates the frequency of interaction between the protein residues and a given ligand across a trajectory. When the distance between any of their atoms and the ligand is smaller than the threshold, it is considered to be an interaction. It is possible to chose which residue atoms will be considered (heavy atoms only or all atoms). The result is presented as table and a plot, which can be downloaded as an image (). The residues that are found to interact can be displayed at the viewer screen (shown in purple), which can be deactivated using the "Display interacting residues" checkbox. It is also possible to download the interaction data obtained ().

HBonds

This tool identifies Hydrogen Bonds formed in a simulation, splitting the results between protein-protein hydrogen bonds and protein-not protein bonds. We use the MDTraj module function called "wernet_wilson" , which basically stablishes a threshold distance of 3.3 Angstroms between the donor and acceptor atoms; more concretely, this threshold becomes progressively stricter as the angle formed by H-D-A increases (a perfect straight bond is 0 degrees, as the donor atom is central). You can select between a few options:

  1. Do not include Hbonds between neighbours: If selected, excludes hydrogen bonds among residues which are less than 5 residues apart. These are usually the hydrogen bonds stabilizing alpha helices.
  2. Include backbone Hydrogen Bonds: If selected, includes hydrogen bonds formed between backbone (BB) atoms or side chains (SC) atoms, in any combination (SC-SC,BB-BB,SC-BB).
  3. Only Side Chain Hydrogen Bonds: If selected, only includes hydrogen bonds formed between side chain atoms.

Finally, you can set a frequency threshold so only those hydrogen bonds which hold the cited condition in a proportion of the frames greater than the value you have set will appear in the results. You can also define an interval of frames into which perform the analysis.
Results have a "Show Hbond" button next to them which displays the bond in the viewer. At the end of the results table, you can find a "Show All" button, which displays all the bonds in that table at once.

Salt Bridges

This tool allows you to identify the salt bridges formed through a simulation. Salt bridges are defined as any combination between these two sets: {Arg-NH1, Arg-NH2, Lys-NZ, His-NE2, His-ND1} and {Glu-OE1, Glu-OE2, Asp-OD1, Asp-OD2} in which the participating atoms are closer than 4 Angstroms. Histidine atoms are only considered if the residue is protonated. As with hydrogen bond analysis, you can select a percentage threshold, and the results include a "Show Salt Bridge" button and a "Show All" button. Furthermore, you can select an interval of frames, instead of the whole trajectory.

SASA analysis

This tool allows you to compute the Solvent Accesible Surface Area(SASA) of a given set of atoms. We use the shrake_rupley function from MDTraj module. Once we have the SASA value for each atom at each frame, we sum the SASA of all the atoms belonging to each frame. Then, we plot the obtained value per frame, so you can see how the SASA of that set of atoms fluctuates through time. We have defined a few options to define the atoms that will be considered:

  1. All atoms: Includes all atoms in the simulation.
  2. Sequence Selection: Imports the selection you have defined in the Sequence Selection tool (remember to click "Confirm Selection" button).
  3. Receptor:Includes all GPCR atoms.
  4. Lower half of receptor: Includes atoms in the GPCR whose Z component is less than the mean Z component of P atoms in the lipid leaflets.
  5. Upper half of receptor: The opposite of option 4.
  6. Extracellular receptor: Includes all atoms in the GPCR whose Z component is greater than the mean Z component of the P atoms in the outter membrane leaflet.
  7. Intracelular receptor: Includes all atoms in the GPCR whose Z component is less than the mean Z component of the P atoms in the inner membrane leaflet.

Furthermore, you can select an interval of frames, instead of the whole trajectory.

Flare plots

If a flare plot is available for the simulation being displayed at the viewer, the option to obtain it will be available at the analysis section. Flare Plots are a tool for the study and representation of intra-protein interactions developed at the Stanford University by Dr. Fonseca and Dr Venkatakishnan. This approach makes it possible to obtain a highly visual depiction of complex data, such as the set of interactions formed between protein residues throughout MD simulations, in the form of circular interactive networks named Flare plots. Applied to the study of GPCRs, Flare plots are capable to generate networks which group protein residues according to the helix in which they belong and differentiate interactions between residues of the same helix from inter-helix interactions. For the moment, flare plots are available for the representation of hydrogen bonds formed between residues of the GPCR through a given simulation trajectory. Hydrogen bonds interactions are represented as lines connecting residue pairs.

Once the flare plot page is accessed, there are a series of control options available:

  • It is possible to summarize the interactions formed through all the trajectory frames. The frequency of each interaction is represented by the thickness of the lines connecting residues.
  • The Track HB freq. button indicates the frequency in which each residue takes part in an interaction. Such frequency is indicated by the height of a coloured box adjacent to each residue.
  • The Sort within helix button sorts the residues belonging to the same helix according to the frequency in which they take part in an interaction. Note that the "Track HB freq." option needs to be activated.

Hover or click a residue to highligh the lines representing the interactions in which it participates. Clicked interactions will appear at the GPCR representation displayed at the left of the flare plot.