Explore protein conformation with an interactive 3D model.
We developed, together with Parallel Graphics Inc., a software tool called Charged Strings, designed to enhance student understanding of the most pivotal idea in molecular biology: the way the interaction between different radicals in a hetero-polymer string, such as protein, affects the 3-D structure of the polymer.
Download Charged Strings
If you have Internet Explorer and a PC, you can download the software. First download the Cortona player from http://www.parallelgraphics.com
and then download the Charged Strings as an executable file from ftp://concord.org/pub/homs/cortvrml.zip. It will appear on your computer as "cortvrml.zip".How to Use Charged Strings
In Charged Strings, users can manipulate a string comprised of ten elements, each representing an amino acid that can be charged positively or negatively, and has more than one negative or positive charge. By clicking on the charge buttons the user can set the charge of every element from minus five to plus five in steps of one. Students can predict how every change in charge will effect the overall 3-D shape of the string. The application then calculates the minimum energy of the new system based on an algorithm that computed the minimum of energy. The resulting representation can be rotated to view the molecule in 3-D using a VRML browser, saved, and compared with new sequences.
But why would anyone care ? Worldwide scientists are using computer models to uncover the 3-D shape of many important protein molecules. This approach has already helped scientists understand the cause of Sickle Cell Anemia. They hope it will help them to find a cure for AIDS and other diseases. When medical researchers know the 3D structure of a protein, and how it might be changed in a malfunctioning cell, they can then design ways to lessen the effect of that "wrong" protein.
Try a Charged String activity.
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