Protein Factory Reveals Its Secrets (Part 1)

Last year, the Nobel Prize in Chemistry heralded work on DNA transcription, a cornerstone process in molecular biology in which a cell synthesizes a messenger RNA (mRNA) version of genomic DNA. For some time, many research teams have been studying the other side of molecular biology's central dogma—the translation of mRNA into protein. That translation occurs on one of nature's most versatile molecular synthesizers: the ribosome.
Harry NollerView Enlarged Image
Complexity Ribosome structure reveals the system's molecular complexity. A tRNA (orange) is shown base pairing with part of mRNA (gold) on left and extending into the ribosome's peptidyltransferase center on right.
If genomic DNA is the cell's planning authority, then the ribosome is its factory, churning out the proteins of life.
It's a huge complex of protein and RNA with a practical and life-affirming purpose-catalyzing protein synthesis. Bacterial cells typically contain tens of thousands of ribosomes, and eukaryotic cells can contain hundreds of thousands or even a few million of them. The ribosome found in the bacterium Escherichia coli is made up of three RNA components and more than 50 proteins. It weighs about 2.5 million daltons. Eukaryotic versions have four RNAs and about 80 proteins and weigh about 4 MDa.
These dozens of components are all squeezed into two RNA-protein subunits, one small and one large. The ribosome's active site—where proteins are created by the one-at-a-time addition of amino acids to a growing peptide chain—is located in the large subunit. The active site may make protein, but it contains very little protein of its own, with only one of the ribosome's many protein components contributing to the mostly RNA architecture of the active site. Because RNA is so predominant in the active site, the ribosome is widely believed to be an RNA catalyst, or ribozyme—and, in fact, is thought to be the largest known ribozyme.
Understanding how the ribosome works is of fundamental interest, but such knowledge also could prove useful. For example, many antibiotics target bacterial ribosomes, so ribosome research could lead to new types of antibacterial agents. Researchers at the New Haven, Conn., start-up Rib-X Pharmaceuticals are riding on that hope. They have been using structure-based design in their efforts to discover novel ribosome-targeted antibiotics.
In the past decade or so, the ribosome has gone from being a biomolecule whose very structure was largely a mystery to one whose architecture is known at an atomic level and whose detailed workings are beginning to be better understood. Scientists have determined dozens of ribosome structures. They are conducting extensive mutational studies and are assessing the catalytic role of specific ribosome residues. They also have been carrying out theoretical modeling to aid understanding of the ribosome's detailed mechanism of action.
"The current model of [ribosomal] peptide bond formation is based on many different experiments, which sometimes did not seem to agree at first glance but little by little filled in the picture," says professor of physical biochemistry Marina Rodnina of Witten/Herdecke University, Witten, Germany.
Many basic facts about ribosome-catalyzed protein synthesis have long been known. The ribosome reads mRNA's genomic message and translates it into protein. When the ribosome factory is open for business, an mRNA binds to its small subunit, and amino acids corresponding to the mRNA's sequence are delivered one by one to the ribosome by aminoacyl transfer RNAs (tRNAs). Each tRNA molecule carries an anticodon, a three-nucleotide code that corresponds to the amino acid it's carrying. These anticodons must be matched up with corresponding codons (complementary three-nucleotide codes on mRNA), to enable a protein chain to be built to order.
The ribosome complex has three tRNA binding sites-A (aminoacyl), P (peptidyl), and E (exit). When peptide bond formation occurs, the amine from a new amino acid on the tRNA bound at the A site attacks a carbonyl at the end of the growing peptide chain, which is attached to the tRNA bound at the P site. The reaction lengthens the peptide by one amino acid unit.