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Protein Ribbon
May 01, 2003

image: Lawrence Berkeley National Laboratory
As someone once said, "form follows function", meaning that the shape of an object is at least partially determined by its function. This idiom seems to hold true for proteins, so by doing the opposite—looking at a protein’s shape—we can take an educated guess at its function.

But what does a protein look like? Let’s say, for example, you have 20 different kinds of beads, each of different sizes and shapes and each with characteristics that make it attract or repel other beads—perhaps with magnets in specific spots on the beads. Depending on where and how the magnets are placed and on the size and shapes of the beads, the beads will either attract or repel one another. Now thread these beads in a specific sequence and in a specific orientation on some flat lace, so the beads can't spin on the lace. Jiggle the lace around on the floor. Your "beads on a string" will fold into a three-dimensional shape that is largely determined by the sequence of the beads. If you change the sequence, the shape will change.

Although overly simplified, this describes what happens in nature with proteins. Individual proteins are very large molecules that are made up of a series of amino acids—about 300 in a typical protein—that are linked one to another to form a chain, similar to the beads on a string. There are 20 different amino acids, each with its own unique properties. That is, some are large, some are small, some attract others, some repel others and some are more or less indifferent to others. The sequence of these amino acids determines the protein’s shape—and also its function.

The picture above represents the shape of a single protein. Just as in this picture, each protein can be represented as a ribbon-like structure, similar to the beads on a string, but without you seeing the individual beads. Each protein has a specific shape. For example, some are coiled, some are folded, while still others are coiled and folded. On top of that, several proteins can intertwine to form a complex of proteins, called an aggregate. Living cells are constructed and driven by aggregates of proteins, which function like a bunch of interdependent machines. These aggregates not only initiate and control almost every chemical process in a cell, but also form the framework that molds the size and shape of different cells and form much of the linkages that enable cells to come together into tissues and organs.

How do you find out what a protein looks like? Presently, the workhorse technique for imaging proteins is x-ray crystallography. In brief, a purified sample of protein is crystallized and then x-rays are passed through it. The atoms in the crystal cause the x-rays to scatter, creating a pattern that is specific for each protein and that is translated by computer into 3-D images like the ones shown above. Fortunately, recent technological advances have made the process of x-ray crystallography much easier and faster. In the past, the x-rays for this technique were generated by x-ray tubes, which were not very "bright", and the analysis of one protein sample could take months or even years. Now, synchrotrons—large, circular tunnels that are used to accelerate electrons, like Berkeley Lab’s Advanced Light Source (ALS)—are used to generate much brighter x-ray beams. With this advance, the amount of time needed to collect the data for a single protein crystal is a matter of weeks, days or even hours.

For more information, visit Berkeley Lab Research Review

produced by Donna Vaughan

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