Protein Structure Visualization

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Protein Structure Visualization
By using Chime a browser plugin
Yuying Tian Information Visualization
(Instructor Dr. Chris North)
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Protein Architecture
There are four basic levels of structure in
protein architecture
Primary structure amino acid sequence
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Secondary structure spatial arrangement of amino
acid residues
?-sheet
?-helix
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Tertiary structure spatial arrangement of amino
acid residues that are far apart in the linear
sequence
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Quaternary structure spatial arrangement of
subunits. One subunit is one chain of amino acid
sequence.
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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
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Visualizing Protein Structure
- A tool for communication and teaching
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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.
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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.
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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. 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