Transcript Protein-visualization

Protein visualization - History
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Before modern desktop computers because available, crystallographers built 3D structural models by
hand
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The earliest models such as that of myoglobin (Kendrew et al., 1958), were built from masses of rods, wires
and spheres, so complex that molecule was lost in the web of the supporting metal framework
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As with many other areas of science, macromolecular structure determination took off with the
advent of electronic computing and graphics technologies and thus macromolecular visualisation.
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The earliest attempts at electron representations of macromolecular model used a computer
controlled oscilloscope to display the rotating image of a protein structure (Levinthal et al., 1968).
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One of the earliest and most widely used programs for constructing and manipulation molecular
structures was FRODO (Jones, 1978). FRODO provided high-quality, interactive, colour images of
electron density maps and structures. Gave the use the ability to fit a model into displayed density by
moving fragments of the model or even invidual atoms.
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1980s-1990s: visualization becomes cheaper with the start of Silicon Graphics and their graphics
workstations -- owning an SGI workstation is still not cheap or routine
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FRODO remained in widespread use throughout the 1980s before eventually being superceded by O
(Jones et al., 1991).
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RasMol developed by Roger Sayles as part of his graduate work in the early 1990s.
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Late 1990s-present: high quality graphics available on desktop PCs; software developers play catchup
Visualization Objectives
Structure
– Backbone; secondary, tertiary & quaternary
Side chain groups
– Hydrophobic, charged, polar, acidic/base, etc.
Cross-links
– Hydrogen bonds, disulfide bonds
Surfaces
– VanderWaals, solvent-accessible
Charge distributions, distances & angles, etc.
Common visualization styles
To visualise a whole molecule for the purpose of showing its shape, a solid surface
can be used
C, N, S, H
Helix
Loop
Sheet
Rainbow
Common visualization styles
Jane Richardson pioneered a style of prepresenting alpha helices as simple cylinders or broad,
spiral ribbons, and beta-starnds as broas, flat ribbons (Richardson, 1985). This remains one of the
most enduring and appealing ways of representing protein secondary structure.
C, N, S, H
Helix
Loop
Sheet
Rainbow
Common visualization styles
To visualize a whole molecule for the purpose of showing the position of each atom, a
wireframe diagram can be used
C, N, S, H
Helix
Loop
Sheet
Rainbow
Visualisation strategies
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To focus attention on particular amino acids or atoms: display the protein backbone as a
ribbon or cartoon, then select the atoms of interest and color them to contrast, or display
them as sticks or spheres
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To show features of a protein surface (location of charges, etc) display the protein as a
solid with the desired surface facing forward; color the surface by electrostatic potential
or atom type
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To choose a good view for presentation, display the molecule in a non- display-intensive
format (like ribbons or sticks) choose an orientation, and then add the more graphicsintensive elements such as surfaces and cartoons
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Good views for presentation clearly show the relationship of the feature you’re
emphasizing to the structure as a whole, and are as uncluttered as possible while still
showing detail of the feature
Software types
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Crystallographic model building: program allows interactive manipulation of
structure model to fit to electron density
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Structure query: program provides clickable distance monitors, contact maps,
Ramachandran maps, and other information about the molecule in addition to
an interactive visualization
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Presentation: program provides high-resolution color or black and white
graphics with or without an interactive visualization
Visualisation styles and software
•RasMol: Structure interrogation, ppresentation. Lightweight but very powerful interactive
structure viewer. The Swiss-Army knife of macromolecular visualisation.
•PyMOL: Powerful python-based visualisation program. Input is via both a graphical user
interface and a python-based command language.
•VMD: Structure analysis and presentation, with an emphasis on molecular dynamics. Includes
numerous tools for dealing with molecular dynamics, trajectories and models.General-purpose
interactive visualisation.
•Chimera: Basic model building, model query, presentation. A modular package for all aspects
of molecular visualisation, from simple model building through production of high-quality
images
•Swiss PDB viewer: Structure interrogation, ppresentation and bbasic modelling. SwissPdbViewer is an application that provides a user friendly interface allowing to analyse several
proteins at the same time.
•Xfit: Electron density map interpretation, mmodel building and presentation. Part of XtalView
crystallography package. Sports a comprehensive set of model building tools, most notably the
ability to generate electron density from structure factors on the fly.
•O: Electron density map interpretation and mmodel bbuilding. Extremely powerful, if somewhat
unintuitive, model-building package. One of the most widely used model-building packages,
certainly in academia.
Tutorials
• Pymol
Early next week
• Swiss Prot
• VMD (Michelle)