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III.C. Mol* Molecular Surface/Properties

Didem Vardar-Ulu and Shane Austin

Overview: This chapter describes the application of coloring to help display molecular properties.

Outcome: The user will be able to display the molecular surface of a structure, apply a chemical property-based coloring scheme, and change transparency.

Time to complete: 10 minutes

Modeling Skills

  • Display the Molecular Surface of Protein
    • Molecular with different colors
    • Electrostatic Potential
    • Hydrophobicity

About the Model

PDB ID: 1XWW

Protein: Low molecular weight protein tyrosine phosphatase

Activity:  hydrolyzes Tyr-OPO32-  phosphoester bond

Description:  single chain, bound SO42- competitive inhibitor, bound glycerol (nonspecific stabilizer)

Steps

Load the Structure:

  1. Go to rcsb.org
  2. In the search bar at the top, type: 1XWW and press Enter.
  3. On the landing page, click the “Structure” tab next to the highlighted “Structure Summary” tab to open the user interface and load the structure.

Show the Molecular Surface: (Figure 1)

Screenshot of a computer interface showing options to adjust molecular representations, including hiding components and adding surfaces.
Figure 1: Showing the molecular surface. See text for arrow descriptions.
                1. To hide components in the Structure Panel that you do not want to see in the 3D Canvas view, such as “Ligand”, “Water”, and “Ion”, click the “eye” icon next to them (Arrows 1).
                2. Click on the three dots next to the component you want to modify (E.g., Polymer) (Arrow 2).
                3. Click “Add representation” (Arrow 3) to activate the drop-down menu with available representations.
                  Green protein molecule depicted in molecular surface representation.
                  Figure 2: Molecular Surface Representation of 1XWW
                4. Click “Molecular Surface” to add it to the list of representations at the bottom of the panel for the component.
                5. Use the “eye icon” (Arrow 4) to hide the default “Cartoon Representation”.
                6. Collapse the dropdown menu by re-clicking “Add Representation” (Arrow 3).

Color the Molecular Surface (Figure 3)

Note: The default color theme is “Chain ID”. There are six color theme categories, each category has several preset coloring schemes that can be accessed by clicking the category name.

 

Computer screen displaying protein structure with labeled steps 1-4 for coloring the molecular surface.
Figure 3: Coloring the molecular surface
  1. Click “Molecular Surface Representation” to activate additional controls (Arrow 1).
  2. Click on the cell next to “Color Theme” to expand the menu (Arrow 2)
Coloring by hydrophobicity:
  1. Click “Residue property” to expand the menu. (Arrow 3)
  2. Click “Hydrophobicity.” (Arrow 4)
  3. Collapse the dropdown menu by re-clicking the cell next to “Color Theme” (Arrow 2)

 

Change the Transparency of the Molecular Surface (Figure 5)

Computer screen displaying steps 1-4 for changing molecular surface transparency.
Figure 4: Changing the transparency of the molecular surface
                  1. Click “Molecular Surface Representation” to activate additional controls (Arrow 1).
                  2. Click on the three dots to the right of “Type” to expand the menu (Arrow 2).
                  3. Use the slider bar to adjust the “Opacity” (E.g., 0.5)(Arrow 3)
                  4. Collapse the dropdown menu by re-clicking “Molecular Surface Representation” (Arrow 1)
3D image of a colorful molecule on a computer screen, showcasing changing molecular surface transparency.
Figure 5: Molecular Surface Representation of 1XWW colored by Hydrophobicity at 50% Transparency. Red indicates hydrophilic, yellow indicates neutral, while green indicates hydrophobic.

 

 

 

 

 

 

 

 

 

Note: You can access additional controls for adjusting the molecular surface’s appearance by clicking “Advanced Options.” (Figure 4, Arrow 1). E.g., increasing the “radius” to 2 will result in a smoother surface appearance.

Overlay the Molecular Surface on a Different Representation (Figure 7)

Show an overlay of multiple representations (E.g., A semitransparent surface colored by hydrophobicity overlaid on a cartoon representation colored by chain id)
3D view of the model with molecular surface overlay; arrows highlight the ‘eye icons’
Figure 6: Overlaying the molecular surface on a cartoon
                  1. Add desired representations
                  2. Color each representation
                  3. Adjust the transparency of each representation
                  4. Use the “eye icon” to show all the desired representations as an overlay.
Figure 7: Overlay of Molecular Surface and Cartoon Representation of 1XWW.

 

 

 

 

Jump to the next Mol* tutorial: IV.C. Biological vs. Asymmetric Units

License

Seeing the Invisible: Learning to Teach with Biomolecular Visualization Copyright © by The BioMolViz Working Group. All Rights Reserved.

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