Enzymes (biological catalysts) are generally "globular" as opposed to "fibrous" and they often work together in the form of multi-enzyme complexes. This means that both intramolecular self-assembly and intermolecular self-assembly must take place in order for the enzyme to reach the conformation that allows it to do its job. Intramolecular self-assembly means that the newly synthesized protein chain must fold into a functional state. Most often this is accomplished by the aggregation of hydrophobic residues in the center of the protein, thus forcing hydrophilic residues to the surface of the protein. Once a single protein chain is adequately folded, it will often begin intermolecular self-assembly. In order to assemble a molecular machine known as a "multienzyme complex," the numerous subunits (or proteins) contact one another in ways that cause new surfaces to appear, thus allowing further subunit components to bind. Since all the information for this self-assembly is often contained within the protein sequence, it is often possible to reproduce this assembly in a test tube. For instance, the molecular machine that builds proteins in E. Coli (the ribosome) can be taken apart into 58 isolated protein chains (as well as a few RNA molecules. If these components are mixed back together with the appropriate timing then functional ribosomes can be reassembled.

Membrane bound proteins are incorporated into the cellular membranes that surround cells and their compartments. In order for these proteins to perform their numerous functions (signal transduction, ion balance maintenance, molecular transport, electron transport, structure, etc.), they must be appropriately oriented and organized within the membrane. Determining their structure within the membrane is not an easy task for biochemists, since the membranes are often destroyed during purification. However, membrane bound proteins often have a common structural characteristic that suggests a mechanism for their assembly. That is, several hydrophobic residues exposed on a certain area of the protein. Since the center of the membrane is hydrophobic, it can be expected that these hydrophobic residues stick to the inside of the membrane. Again, the hydrophobic effect is most effective for this purpose. Finally, once the molecule is incorporated into the membrane, changes in the membranes constitution as well as interactions with neighboring membrane bound proteins govern the organization of these proteins.

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Keywords: protein self-assembly enzymes globular multienzyme complex intermolecular intramolecular ribosome membrane bound purification ion channels proton pumps hydrophobic barrier nanotechnology