Molecular visualization
Tuomas Hätinen
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Overview
Introduction Visualisation styles Chime
Online tutorial – basic features
Exercises
Swiss PDB Viewer Demo – basic features
Exercises – Chris Wilton assisting
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Context – Central Dogma
Gene→ mRNA
→ Protein primary structure → Tertiary structure
→ Quaternary structure→ Protein function
→ Phenotype
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Introduction
Structure determines function Structural analysis provides basis for
Understanding molecular function
Prediction of function
Experimental design to test predictions
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Structure data – textual representation
Structure data is stored in
PDB file format in ATOM
fields
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Structure data – visualisation
A structure file contains large amount
of data
Too much for the human mind to
grasp
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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
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Visual styles - Wireframe
Example: Cysteine
Stick/Wireframe: shows individual bonds and corresponding
angles
Without hydrogen atoms With hydrogen atoms
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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
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Visual styles – Ball and stick
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
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Visual styles – Backbone
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
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Visual styles - Ribbon
Ribbon 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
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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
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Colour schemes
Colour by:
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
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Visual styles – Ramachandran plot 1
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Visual styles – Ramachandran plot 2
Peptide bond Resonance in the peptide bonds
- partial double bond nature- planar structure
Bond angles ω (omega) bond angle
- Peptide bond
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
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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
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Chime demo
A web browser plugin For quick viewing
Instructions:
1. Install Chime plugin from courses folder
2. Go to tutorial
http://c4.cabrillo.cc.ca.us/projects/chime_tutorial/html/index.htm
3. Do Chime exercises
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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)
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DeepView – import
Enter PDB id
Press here to import the filefrom DeepView PDB server
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DeepView
Accesses all the other window controls
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DeepView: Main control windows
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DeepView: Layers information
24read PDB file
DeepView: Main controls
(toolbar view – first part)
world / local coordinates
center translation tool zoom tool
rotation tool:
left:rotate right: translate both: zoom
Instructions!
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DeepView: Main controls
(toolbar – second part)
display centre fit mutation torsion
distance angle dihedral angles provenance
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read PDB file
DeepView: Main controls
(complete view)
Accesses all the other window controls
world / local coordinates
center translation toolzoom tool
rotation tool:
left:rotate right: translate both: zoom display
centre fit mutation torsion
distance angle dihedral angles provenance
Instructions!
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DeepView: Control Panel
Secondary structure type
Chain
Residue
Current protein
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Useful functions
Analysis of parts of protein Active site
Oligomerization surface
Superimposition of structures Magic Fit
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Stereo viewing
View the protein in 3D
More information can be analyzed at once
To toggle: Display > Stereo View (Shift+T)
Recommended tutorial: http://www.usm.maine.edu/~rhodes/0Help/StereoView.html
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DeepView: Links
DeepView homepage http://au.expasy.org/spdbv/
DeepView tutorial http://www.usm.maine.edu/~rhodes/SPVTut/
Klotho - Small molecules in PDB format: http://www.biocheminfo.org/klotho/
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