Transcript Slide 1

Molecular visualization
Tuomas Hätinen
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
 Prediction
molecular function
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
 by
secondary structure
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 file
from 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
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DeepView: Main controls
(toolbar view – first part)
center
translation tool
zoom tool
rotation tool:
left:rotate
right: translate
both: zoom
world / local
coordinates
read PDB file
Instructions!
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DeepView: Main controls
(toolbar – second part)
distance
angle
dihedral angles
provenance
display
centre
fit
mutation
torsion
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DeepView: Main controls
(complete view)
Accesses all the other window controls
center translation tool
zoom tool
distance
angle
dihedral angles
provenance
rotation tool:
left:rotate
right: translate
both: zoom
read PDB file
world / local
coordinates
Instructions!
display
centre
fit
mutation
torsion
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DeepView: Control Panel
Current
protein
Chain
Secondary structure
type
Residue
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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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