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Protein Structure Visualization
By using Chime – a browser plugin
Yuying Tian
Information Visualization (Instructor: Dr. Chris North)
Protein Architecture
There are four basic levels of structure in protein architecture
Primary structure:
amino acid sequence
Secondary structure: spatial arrangement of amino acid residues
-helix
-sheet
Tertiary structure: spatial arrangement of amino acid residues
that are far apart in the linear sequence
Quaternary structure: spatial arrangement of subunits. One
subunit is one chain of amino acid sequence.
Visualizing Protein Structure
- A tool for understanding and discovery
Interpreting the mechanism of protein function
Prediction of structures of closely-related proteins
Drug design to produce molecules that will bind and
inactivate pathogens
Visualizing Protein Structure
- A tool for communication and teaching
Visualizing Protein Structure
- A tool for communication and teaching
The information conveyed into color image undergoes a qualitative
change because it brings the eye-brain system into play in a way
that is impossible for purely numbers, symbols, and text.
Sickle Cell Disease
Hemoglobin protein is responsible for oxygen storage
and transportation in red blood cell.
Single amino acid mutation alters the 3-D structure of
the protein, which results in a distortion of the shape of
the red blood cell (sickle shape) and the loss of ability to
transport oxygen.
Chime
•
Chime is freely available as a browser plugin.
•
Chime displays protein structure in an interactive way.
The user can select an appropriate view and can change
modes and color schemes.
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Chime also has a lot of options for structure analysis,
which helps to reveal structure – function relationship
of protein.
Please come to class to see demo of Chime