Explore protein structure fast and easy. In the lectures on Hemoglobin (and later in the Protein structure lab), you saw the 3-dimensional structure of proteins. This allowed you to see a protein in its full 3-dimensional form and to make hypotheses about the interactions between various side chains. However,
you were not able to test your hypotheses because the program did not allow you to make changes to the protein sequence and observe their effects on the protein's structure and function.

In this lab, you will get an opportunity to interactively explore protein structure and function in a simplified system. This is a highly-simplified model of protein folding. It is not intended to predict the correct structures of any proteins; it is designed to illustrate the major principles involved in that process. The important features of proteins that this software retains are as follows:
1. Amino acids have side-chains of varying hydrophobicity, charge, and hydrogen bonding capacity.
2. The amino acids a reconnected in an un-branched chain that can bend.
3. Hydrophobic amino acids will tend to avoid the water that surrounds the protein; hydrophilic amino acids will bind to the water.
4. Amino acids that can form hydrogen bonds will tend to form hydrogen bonds if they can.
5. Positively-charged amino acids will tend to form ionic bonds with negatively-charged amino acids if they can.
6. Like-charged amino acids will repel each other if they can.
7. Ionic interactions are stronger than hydrogen bonds, which are stronger than hydrophobic interactions.
8. Proteins can be folded under oxidizing (Disulfide Bonds ON) or reducing (Disulfide Bonds OFF) conditions.

Even though this software provides some important insights into protein folding, you should always keep in mind that this is an approximation. The most important "gotcha's" to be aware of are:
1. This program folds proteins in 2-dimensions only.
2. This program treats all amino acids as equal-sized circles.
3. This program folds the protein based on the interactions between the side chains only.
4. This program does not model secondary or quaternary structure.
5. This program assumes that all side chains with hydrogen bonding capability can bond with each other.

These simplifications are necessary for two reasons. The first is technical: it turns out to be extremely difficult to predict the full 3-d folded structure of a protein given only its amino acid sequence. As of the writing of this lab manual, it takes a super-computer several days to predict the fully-folded shape of even a small protein like lysozyme. Even then, the predictions don't always match known structures. Given the computers we have in the Bio 111 labs, it might take years.

The second reason is educational. As you saw in the lysozyme lab, proteins are complex 3-dimensional molecules. It can be hard to find your way around when inside one. Likewise, it would be very difficult to visually compare two protein molecules to observe the effects of changes to their amino acid sequence. It would be easy to miss the forest (the forces that control protein structure) for the trees (the tiny details of the structures).

For these reasons, we will use this simplification. It retains the properties of amino acids that are important in Bio 111 while being simple and fast.

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.