Molecules of the Quarter: Myoglobin, Bacteriophage phiX174, and DNA Polymerase
April 4, 2000 -- The PDB has initiated a new feature for its Web site called "Molecule of the Month." Written and drawn by David S. Goodsell, an assistant professor of molecular biology at The Scripps Research Institute in La Jolla, California, these features provide an overview of significant milestones in the growth of the PDB's macromolecular structure data for a diverse audience.
Myoglobin: The First Protein Structure
January 2000 -- Any discussion of protein structure must necessarily begin with myoglobin, because myoglobin is where the science of protein structure really began. After years of arduous work, John Kendrew and his coworkers determined the atomic structure of myoglobin, laying the foundation for an era of biological understanding. That first glimpse at protein structure is available at the PDB, under the accession code 1mbn. Take a closer look at this molecule, or look directly at the PDB information for 1mbn. You will be amazed, just like the world was in 1960, at the beautiful intricacy of this protein.
Myoglobin is a small, bright red protein. It is very common in muscle cells, and gives meat much of its red color. Its job is to store oxygen, for use when muscles are hard at work. If you look at John Kendrew's PDB file, you will notice that the myoglobin that he used was taken from sperm whale muscles. As you can imagine, marine whales and dolphins have a great need for myoglobin, so that they can store extra oxygen for use in their deep dives undersea.
Bacteriophage phiX174: A Milestone at the PDB
February 2000 -- The 10,000th entry in the Protein Data Bank, the bacteriophage phiX174, is a perfect example of how the science of protein structure has progressed in four decades. In 1960, the world got its first look at the structure of a protein. That first structure was the small protein myoglobin, composed of one protein chain and one heme group--about 1260 atoms in all. By contrast, the 10,000th entry in the PDB contains 420 protein chains and over half a million atoms. Enormous structures like this are not uncommon in the Protein Data Bank. The stakes have risen dramatically since the structure of myoglobin was first revealed.
A bacteriophage is a virus that attacks bacteria. The phiX174 bacteriophage attacks the common human bacteria Escherichia coli, infecting the cell and forcing it to make new viruses. Do you think that viruses are living organisms? PhiX174 is composed of a single circle of DNA surrounded by a shell of proteins. That's all. It can inject its DNA into a bacterial cell, then force the cell to create many new viruses. These viruses then burst out of the cell, and go on to hijack more bacteria. By itself, it is like an inert rock. But given the proper bacterial host, it is a powerful reproducing machine. What do you think? Is it alive?
DNA Polymerase: The Secret of Life
March 2000 -- DNA polymerase plays the central role in the processes of life. It carries the weighty responsibility of duplicating our genetic information. Each time a cell divides, DNA polymerase duplicates all of its DNA, and the cell passes one copy to each daughter cell. In this way, genetic information is passed from generation to generation. Our inheritance of DNA creates a living link from each of our own cells back through trillions of generations to the first primordial cells on Earth. The information contained in our DNA, modified and improved over millennia, is our most precious possession, given to us by our parents at birth and passed to our children.
DNA polymerase is the most accurate enzyme. It creates an exact copy of your DNA each time, making less than one mistake in a billion bases. This is far better than information in our own world: imagine reading a thousand novels, and finding only one mistake. The excellent match of cytosine to guanine and adenine to thymine, the language of DNA, provides much of the specificity needed for this high accuracy. But DNA polymerase adds an extra step. After it copies each base, it proofreads it and cuts it out if the base is wrong.