Protein Structure Visualization

By using Chime – a browser plugin

Yuying Tian

Information Visualization (Instructor: Dr. Chris North)

Protein Architecture

Primary structure: amino acid sequence

There are four basic levels of structure in protein architecture

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.

- A tool for understanding and discovery

Visualizing Protein Structure

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.

• 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