1. Molecular visualization
Tuomas Hätinen

2. Overview Introduction Visualisation styles Chime Swiss PDB Viewer
Online tutorial – basic features
Exercises
Swiss PDB Viewer
Demo – basic features
Exercises – Chris Wilton assisting

3. Context – Central Dogma
Gene
→ mRNA
→ Protein primary structure
→ Tertiary structure
→ Quaternary structure
→ Protein function
→ Phenotype

4. Introduction Structure determines function
Structural analysis provides basis for
Understanding molecular function
Prediction of function
Experimental design to test predictions

5. Structure data – textual representation
Structure data is stored in PDB file format in ATOM fields

6. Structure data – visualisation
A structure file contains large amount of data
Too much for the human mind to grasp

7. Structure data – informative views
Informative views higlighting important features
First image:
Fold of the myoglobin molecule and it’s prosthetic group
Second image:
residues within 3 Å of the heme group

8. Visual styles - Wireframe
Example: Cysteine
Stick/Wireframe: shows individual bonds and corresponding angles
Without hydrogen atoms With hydrogen atoms

9. Visual styles - Spacefill
Spacefilling:
Spheres represent the electron cloud around nuclei of atoms
Relative sizes of atoms and groups show up clearly
Merged spheres represent share electrons (covalent bond)
Without hydrogen atoms With hydrogen atoms

10. Visual styles – Ball and stick
Allows structure to be seen
shows atomic position and bonds, and a portion of volume – small spheres are centred at the nuclei of atoms
Without hydrogen atoms With hydrogen atoms

11. Visual styles – Backbone
Four amino acids shown (Lys, Ala, Ile, Thr from top to bottom)
Green line is a backbone trace: all side chains removed, rods connect alpha carbon positions (or phosphate atoms)
Backbone does not follow any actual bonds
Right image shows backbone superimposed on tetrapeptide
Used e.g. for structural superimpositions

12. Visual styles - Ribbon Ribbon Colour schemes shown
Smooth ribbon drawn through peptide units – may either be solid (‘ribbons’) or parallel wires (‘strands’)
Display the fold of a protein
Colour schemes shown
by secondary structure
by secondary structure succession
N-terminus blue
C-terminus red

13. Visual styles - Surface
Shows the surface accessible to water molecules
Most useful for studying the properties of the active sites
Molecular surface of lysozyme
Active site in a groove
Charged, hydrophilic surface

14. Colour schemes Colour by: Calculate molecular surface
secondary structure
secondary structure succession
B-factor (tells the quality of the model): red  least certain, blue
Accessibility to solvent
red: most accessible, violet: least accessible
Calculate molecular surface
color by: atom type (CPK), cavity or elcetrostatic potential

15. Visual styles – Ramachandran plot 1

16. Visual styles – Ramachandran plot 2
Peptide bond
Resonance in the peptide bonds
partial double bond nature
planar structure
Bond angles
ω (omega) bond angle
0° angle is defined as cis position of the main chain atoms preceding and following the bond
The picture is showing 180° angles
φ (phi) bond angle
Cα – NH bond
Ψ (psi) bond angle
Cα – CO bond

17. Ramachandran plot 3 Main chain conformation displayed
Steric hindrances restrict possible bond angles
Exceptions:
Glycine
Proline
Allowed areas shown
Used for checking the quality of experimentally solved structures
Tool for understanding the main chain conformation

18. Chime demo A web browser plugin For quick viewing Instructions:
Install Chime plugin from courses folder
Go to tutorial
Do Chime exercises

19. Swiss PDB Viewer demo Also called DeepView
Allows analysis of several proteins at same time
Extremely versatile
Linked to Swiss-Model (an automated homology modelling server – covered later in this course)

20. DeepView – import Enter PDB id Press here to import the file
from DeepView PDB server

21. DeepView
Accesses all the other window controls

22. DeepView: Main control windows

23. DeepView: Layers information

24. DeepView: Main controls (toolbar view – first part)
center
translation tool
zoom tool
rotation tool:
left:rotate right: translate both: zoom
world / local coordinates
Instructions!
read PDB file

25. DeepView: Main controls (toolbar – second part)
distance angle dihedral angles provenance
display centre fit mutation torsion

26. DeepView: Main controls (complete view)
Accesses all the other window controls
center
distance angle dihedral angles provenance
translation tool
zoom tool
rotation tool:
left:rotate right: translate both: zoom
display centre fit mutation torsion
read PDB file
world / local coordinates
Instructions!

27. DeepView: Control Panel
Current protein
Chain
Secondary structure type
Residue

28. Useful functions Analysis of parts of protein
Active site
Oligomerization surface
Superimposition of structures
Magic Fit

29. Stereo viewing View the protein in 3D
More information can be analyzed at once
To toggle: Display > Stereo View (Shift+T)
Recommended tutorial:

30. DeepView: Links DeepView homepage DeepView tutorial
DeepView tutorial
Klotho - Small molecules in PDB format: