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/