The Molecule of the Month series explores the functions and
significance of selected biological macromolecules for a general
audience. These features, written and illustrated by Dr. David
S. Goodsell of the Scripps Research Institute, are available at
A sample of the molecules featured during this past quarter are included below:
October, 2002 -- Dihydrofolate reductase is a small enzyme that plays a supporting role, but an essential role, in the
building of DNA and other processes. It manages the state of folate, a snaky organic molecule that shuttles carbon
atoms to enzymes that need them in their reactions. Of particular importance, the enzyme thymidylate synthase
uses these carbon atoms to build thymine bases, an essential component of DNA. After folate has released its
carbon atoms, it has to be recycled. This is the job performed by dihydrofolate reductase.
Dihydrofolate reductase, shown in PDB entry 7dfr,
juggles two relatively large molecules in its reaction. It has a long groove that binds to folate at one end, and to
NADPH at the other end. The protein wraps sidechains around the two molecules, positioning them tightly next
to one another. Then, the enzyme transfers hydrogen atoms from NADPH to the folate, converting folate to a useful
Enzymes with essential roles are sensitive targets for drug therapy. Dihydrofolate reductase was the first enzyme to
be targeted for cancer chemotherapy. The first drug used for cancer chemotherapy was aminopterin. It binds to
dihydrofolate reductase a thousand times more tightly than folate, blocking the action of the enzyme. Today,
methotrexate and other variations on aminopterin are used, because of their tighter binding and better clinical
characteristics. Since these drugs attack a key step in the production of DNA, they tend to kill cells that are actively
growing rather than cells that are not growing. Since cancer cells are often the most rapidly reproducing cells in a patient,
the drug will have the strongest effect on the cancer cells. The side effects of chemotherapy, however, are the result of the
drug on other normally-growing tissues, such as hair follicles and the lining of the stomach.
Further information about dihydrofolate reductase can be found at
Ferritin and Transferrin: Iron Storage and Transport
November, 2002 -- Iron is found everywhere on the Earth, so it is no surprise that living cells use iron ions in
many ways. We use iron throughout our body, for many tasks. Iron ions bind strongly and specifically to small
molecules such as oxygen, making it an essential tool for manipulating these elusive molecules. Iron ions also
cycle easily between the ferrous and ferric forms, providing a handy tool for manipulating individual electrons.
Iron ions, however, pose a great challenge in our modern biological environment. The water filling cells and the
oxygen in the air together conspire to convert iron ions to the ferric state, which is highly insoluble, forming
rust-like oxides. The cell must somehow shelter iron ions so that they may be stored and delivered in the
necessary quantities. This is the job of ferritin and transferrin.
Inside cells, extra iron ions are locked safely in the protein shell of ferritin, shown in PDB entry
1fha. Ferritin is composed of 24 identical protein subunits that
form a hollow shell. After entering the ferritin shell, iron ions are converted into the ferric state, where they form
small crystallites along with phosphate and hydroxide ions. There is room to pack about 4500 iron ions inside.
We have about 3.7 grams of iron in our body, painstakingly gathered from iron in our diet. About 2.5 grams are
locked inside the hemoglobin in our blood, where they assist in the transport of oxygen. This is a valuable and
essential resource, so special mechanisms for the recycling of this iron have been developed. Another few
tenths of a gram are found in myoglobin, which also assists in oxygen management. A remarkably small
amount--about 0.02 g--is distributed between the many different proteins that transfer electrons, such as the
proteins of the electron transport chain that create most of our cellular ATP supplies. The rest, about a gram,
is stored inside ferritin to fulfill future needs.
Iron ions are delivered in the blood by the protein transferrin, shown in PDB entry
1h76. Each transferrin molecule can carry two iron ions,
with each ion coupled with a carbonate ion. The protein contains an array of amino acids that are perfectly
arranged to form four bonds to the iron ion, which locks it in place. Once it finds its iron atoms, transferrin flows
through the blood until it finds a transferrin receptor on the surface of a cell. PDB entry
1cx8 contains coordinates for the part of the receptor that is
outside the cell. Transferrin binds tightly to the receptor and is drawn into the cell in a small vesicle. The cell
then acidifies the inside of this little pocket, which causes transferrin to release its iron. Then, the receptor
and empty transferrin are recycled back to the outside of the cell. Triggered by the neutral pH of the blood,
the receptor releases the empty transferrin, and it continues its job of gathering iron.
Further information about ferritin and transferrin can be found at
Cytochrome c: Delivering Electrons
December, 2002 -- Electricity is a common phenomenon in our modern world, powering everything from the lights in your
room to the computer in front of you. Electricity is the flow of electrons within a conductive material, such as metal wires.
These electrons flow in bulk, meandering from atom to atom along the wire. Cells also use electricity to power many
processes, but the electrons move in a very different way. The electrons do not flow smoothly along a cell-sized wire.
Instead, electrons are transported one at a time, jumping from protein to protein. In this way, the electrons may be
picked up from one particular place and delivered exactly where they are needed.
Cytochrome c, shown in PDB entry 3cyt, is a carrier of electrons.
Like many proteins that carry electrons, it contains a special prosthetic group that handles the slippery
electrons. Cytochrome c contains a heme group with an iron ion gripped tightly inside. The iron ion readily
accepts and releases an electron. The surrounding protein creates the perfect environment for the electron,
tuning how tightly it is held. The protein also determines where cytochrome c fits into the overall cellular
Cytochrome c is an ancient protein, developed early in the evolution of life. Since this essential protein
performs a key step in the production of cellular energy, it has changed little in millions of years. So, you
can look into yeast cells or plant cells or our own cells and find a very similar form of cytochrome c. If you
look around the PDB, however, you can find a diverse collection of other electron carrier molecules. There are
many variations on cytochrome c, which use heme and iron to carry electrons, but change the protein
surrounding them to perform different jobs. Other carriers use other prosthetic groups to carry electrons,
such as clusters of iron and sulfur (such as ferredoxin), brilliant blue copper ions (such as azurin and
plastocyanin) or more exotic metal ions. Like cytochrome c, each of these proteins is a single connection in
a cellular electronic circuit, transferring electrons from one point to another.
Further information about cytochrome c can be found at
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.