PDB Focus: Molecule of the Month

The Molecule of the Month series is a wonderful collection of short columns featuring a new PDB structure of interest each month. They describe the functions and significance of the selected biological macromolecules for a general audience, providing a basic understanding of structural interactions. Written and illustrated by Dr. David S. Goodsell of the Scripps Research Institute, this feature adds a unique aesthetic quality and informative educational resource to the PDB Web site. You can access the Molecule of the Month installations at http://www.rcsb.org/pdb/molecules/molecule_list.html.

Below is a sample of the information that was presented in this feature during the past quarter:

Actin: Dynamic Molecular Infrastructure

PDB ID: 1atn

W. Kabsch, H.G. Mannherz, D. Suck, E.F. Pai, K.C. Holmes (1990): Atomic structure of the actin:DNase I complex. Nature 347, p. 37.

July, 2001 -- The complex ultrastructure of cells--their shape and internal structure--and the many motions of cells are largely supported by filaments of actin. A tangle of cross-linked actin filaments fills the cytoplasm of animal, plant and fungal cells, forming a "cytoskeleton" that gives the cell shape and form and provides a scaffold for organization. Tightly bundled actin filaments provide a sturdy backbone to extrude structures from the cell surface, such as the pseudopods used by amoebas for crawling and the finger-like microvilli of intestinal cells, which extend into the digestive tract and absorb nutrients. Actin also forms the ladder on which myosin climbs, providing the infrastructure for muscle contraction and creating the motion that we experience in our daily lives. Actin is plentiful throughout the body as it performs these basic structural tasks: it may comprise 5 percent of the protein in a typical cell, or up to one fifth of the protein in special cases, such as muscle cells.

Actin has a rare combination of strength and sensitivity. Actin filaments are used in many of the most strenuous structural tasks, but at the same time, actin filaments are easily and continually disassembled. One of the great hallmarks of actin is its dynamic character. Actin filaments are continually built and broken down as the needs of the cell change from moment to moment. In special cases, such as muscle actin or the actin bundles in microvilli, a collection of specialized actin-binding proteins stabilize the filament, forming a more permanent structure. But the bulk of actin in typical cells is in constant flux, constantly forming filaments and breaking down for each new task.

The dynamic character of actin is controlled by a molecule of ATP bound to each actin monomer. The state of this ATP determines the stability of the actin filament. Free actin typically holds an ATP molecule and binds tightly to growing filaments. After attaching, the ATP is broken and the actin subtly changes shape. This new form, with ADP bound, is not as stable in the filament and dissociates more easily. One of the unusual consequences of this behavior is "treadmilling." An actin filament will be continually building at one end, where new actin-ATP complexes are forming strong new connections, and at the same time slowly falling apart at the opposite end, where the actin-ADP form has weakened connections. Imagine the filament growing at one end and dissolving at the other, so that the whole structure slowly steps through the cell but never gets any longer or shorter.

Of course, cells cannot have actin filaments growing uncontrollably all over the cytoplasm. The poison phalloidin, from the death cap mushroom, demonstrates what would happen. It promotes the growth of actin and ultimately clogs the cell with rigid actin filaments, causing fatal liver and kidney damage in unwary mushroom lovers. In cells, a variety of actin-severing proteins control the growth of actin, ensuring that the filaments grow only when needed. Two of these actin watchdogs are gelsolin and profilin. Gelsolin, from PDB entry 1yvn, breaks actin filaments into short lengths when the level of calcium rises. Then, it remains bound to the end, blocking additional growth. Profilin, from PDB entry 1hlu, binds to free actin and keeps it from adding to filaments, also inhibiting growth. Both bind to the actin monomer at a similar location, blocking part of the site that binds to neighboring actin molecules in a filament.

Large helical protein assemblies, such as actin filaments, are notoriously difficult to study by crystallography, because the filaments do not form perfect crystals. The structures of actin in the PDB all have something bound to them, blocking formation of a filament, so the structures contain only a single actin molecule, not an entire actin filament. PDB entry 1atn, contains a DNA-cutting enzyme that just happens to bind to actin. Actin is a U-shaped molecule with ATP bound deep in the groove between the two arms. PDB entry 1alm, presents a model of one myosin motor bound to a short actin filament formed of five molecules, based on data from electron microscopy. The file contains only alpha carbon positions for the proteins, so you'll need to use backbone diagrams when you look at it.

A list of all actin structures in the PDB as of July, 2001, is available at http://www.rcsb.org/pdb/molecules/pdb19_report.html. For more information about actin, see http://www.rcsb.org/pdb/molecules/pdb19_4.html.

Poliovirus and Rhinovirus: Little RNA Viruses

PDB ID: 4rhv

E. Arnold, M.G. Rossmann (1988): The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. Acta Crystallogr A 44, p. 270.

August, 2001 -- Viruses are biological hijackers. They attack a living cell and force it to make many new viruses, often destroying the cell in the process. Picornaviruses, or "little RNA viruses," are among the most simple viruses. They are composed of a modular protein shell, which seeks out and binds to a target cell surface, surrounding a short piece of RNA, which contains all of the information needed to co-opt the cell's machinery and direct the construction of new viruses. In spite of their simplicity, or perhaps because of it, the picornaviruses are also among the most important viruses for human health and welfare. Three familiar examples are: poliovirus (PDB entry 2plv), rhinovirus (PDB entry 4rhv), and the virus that causes foot and mouth disease in livestock (PDB entry 1bbt).

Poliovirus and rhinovirus have specialized to attack primarily human beings, but they use two different approaches. Poliovirus, which is found in three similar forms, is designed to attack a given person only once. It makes its offspring and then is off to the next person. In most cases, poliovirus causes a simple flu-like disease as it attacks cells in the digestive system. This infection is rapidly cleared up by the immune system. But in about 1 in 100 cases, the virus spreads to the nerve cells that control muscle motion, causing paralysis--polio myelitis--as the nerve cells are infected.

Rhinovirus, on the other hand, is found in many different forms that attack a given person many times during their life. Each time you get a cold, a different form of rhinovirus (or occasionally, a different type of virus) is attacking. Your body learns how to fight it off, but you are still susceptible to the next form. On average, a person will have a new cold once every two years, so most of us are quite familiar with the symptoms of rhinovirus infection in our nose and respiratory tract. Because they are so simple, picornaviruses can be very stable. Rhinovirus can last for days on your hands and still be infectious. And because the virus is shed from infected people all through the period with symptoms and even for days after, it spreads effectively through contact from person to person.

Antibodies are our major defense against these small, efficient viruses. Vaccines prime the immune system with antibodies, making it ready to fight an infection. In the case of poliovirus, there are two types of vaccines. One is a killed version of the virus, which is slowly killed with formaldehyde over the course of several days so that it is inactivated, but still keeps its proper shape. The second is a weakened, but still live, strain of the virus that has been artificially bred to stimulate the immune system without causing disease. The immune system responds by making antibodies to fight these weakened viruses, leaving it ready to fight the real thing when it comes along.

The polio vaccines are one of the triumphs of modern medicine, but many people would say that the lack of a cure for the common cold is one of the great failings. The difficulty of creating a vaccine for the common cold lies in the diversity of rhinovirus. Over one hundred types of rhinovirus have been discovered as they strike people around the world, and new strains appear continually. Rhinovirus is a moving target that is not effectively combated with a single vaccine. Antiviral drugs, however, are a possible solution.

Many viruses, including the picornaviruses and bacteriophage phiX174 (discussed in an earlier Molecule of the Month), are icosahedral in shape. They are composed of 60 identical pieces that form a perfectly symmetrical shell, termed a capsid, around the viral genome. In the case of poliovirus and rhinovirus, the shell is composed of 60 copies of four different proteins for a total of 240 protein chains in all. These proteins are carefully designed to be stable, but not too stable. They must be fairly sturdy to allow the virus to pass from host to host through the hostile environment. But at the same time, they must be able to fall apart when they enter the cell, releasing the RNA inside. A carefully orchestrated set of structural changes occur as the virus attaches to the surface of the cell and is drawn inside, allowing the virus to deliver its RNA into the unwitting host.

The RNA protected inside the capsid is seen only as a blurry tangle in these crystallographic structures. It is not as perfectly symmetrical as the many proteins in the shell. The rhinovirus genome, when analyzed by sequencing techniques, contains just enough information to direct the construction of eleven proteins. These include the four separate proteins for its capsid, another four proteins that replicate its RNA, two proteins to clip each of these proteins into the proper shape, and one additional protein with as-yet obscure function.

Antibodies bind to the surface of picornaviruses and stop them from attacking cells. Rhinovirus binds to a receptor protein on the cell surface. The receptor protein is gripped within a groove that encircles the five-fold symmetrical arrangement of proteins (known as the canyon in the picornavirus literature). Antibodies bind to the surface of rhinovirus and poliovirus in this same position and block their attachment to the surfaces of cells. PDB entry 1rvf shows fragments of antibodies bound to rhinovirus. The intact antibodies are much larger than the small fragments seen here, so seven to ten antibodies are enough to form a bulky barrier on each virus to block attachment and infection.

Many structures of rhinovirus with antiviral drugs are available at the PDB, including the drug pleconaril, currently in clinical testing, (PDB entry 1c8m). Most drugs act by blocking protein binding sites or destabilizing a key interaction. These drugs, on the other hand, may act differently. They actually stabilize the virus structure so that it cannot release its cargo of RNA. The drugs bind in a little pocket under the deep groove that grabs onto the cellular receptor. Normally, the binding of virus to receptor shifts the structure of the virus, ultimately allowing the virus to release RNA. The drug, however, glues the virus shut.

A list of all picornaviruses in the PDB as of August, 2001 is available at http://www.rcsb.org/pdb/molecules/pdb20_report.html. For more information on picornaviruses, see http://www.rcsb.org/pdb/molecules/pdb20_5.html.

Antibodies: Molecular Watchdogs

PDB ID: 1igt

L.J. Harris, S.B. Larson, K.W. Hasel, A. McPherson (1997): Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 36, p. 1581.

September, 2001 -- Antibodies are our molecular watchdogs, waiting and watching for viruses, bacteria and other unwelcome visitors. Antibodies circulate in the blood, scrutinizing every object that they touch. When they find an unfamiliar, foreign object, they bind tightly to its surface. In the case of viruses, like rhinovirus or poliovirus presented last month in the Molecule of the Month, a coating of bound antibodies may be enough to block infection. Antibodies alone, however, are no match for bacteria. When antibodies bind to a bacterial surface, they act as markers alerting the other powerful defensive mechanisms available in the immune system.

Antibodies, and many of the other molecules used in the immune system, have a distinctive shape. Typically, they are composed of several flexible arms with binding sites at the end of each one. This makes perfect sense: since antibodies do not know in advance what attackers they might be fighting, they keep their options open. The flexible arms allow the binding sites to work together, grabbing with both arms onto targets with different overall shapes. The antibody in PDB entry 1igt has two binding sites, at the tips of the two arms extending right and left at the top. Notice the thin, flexible chains that connect these arms to the central domain at the bottom. Some antibodies have longer flexible linkers connecting the arms together, allowing them even more latitude when finding purchase on a surface. Other antibodies have four or ten binding sites, so each contact can be weaker and still allow the whole antibody to bind firmly.

Your blood contains upwards of 1,000,000,000,000,000 different types of antibodies. Each type binds to a different target molecule. Remarkably, all of these antibodies are created before they ever see a virus or bacterium. You don't make a special antibody when a virus or bacterium infects your body. Instead, all of your antibodies are pre-fabricated, lying in wait until a virus or bacterium attacks. There are so many different kinds of antibodies that one or two are bound to be the right ones to fight the infection.

This amazingly huge collection of antibodies is created by the recombination of genes in lymphocytes, the blood cells that make antibodies. Each lymphocyte creates a different type of antibody, based on how it has recombined its antibody genes. When an antibody encounters a virus or bacterium, the appropriate lymphocytes will multiply, flooding the blood with the particular antibodies needed to battle the invader. These lymphocytes may also make small adjustments on the antibodies they produce, tailoring their antibodies to bind more tightly and more specifically.

Antibodies are composed of four chains, two long heavy chains and two shorter light chains. The specific binding site is found at the tips of the two arms, in a pocket formed between the light and heavy chain. The binding site is composed of several loops in the protein chain that have very different lengths and amino acid composition. Differences in these "hypervariable loops" form the many types of pockets in different antibodies, each of which bind specifically to a different target. The rest of the antibody--the rest of the arms and the large constant domain that ties the two arms together--is relatively uniform in structure, providing a convenient handle when antibodies interact with the rest of the immune system.

When a foreign molecule is found in the blood, many different antibodies may bind to it, attacking at different angles. Three different antibodies that bind to the protein lysozyme can be found in PDB entries 1fdl, 3hfl, and 3hfm. These entries each include only one arm of the antibody (termed "Fab" for "antigen-binding fragment"), which has been separated from the antibody for ease in study. The antibodies pick entirely different binding sites on the small lysozyme molecule.

Researchers have used the incredible functional diversity of the immune system in a clever way: to design new enzymes. Enzymes work by easing molecules through a difficult chemical change. For instance, take the Diels-Alder reaction. Two molecules come together, forming an unstable intermediate. Then, the intermediate falls apart, releasing sulfur dioxide and forming the desired product. Enzymes act by stabilizing the intermediate, smoothing the path from start to finish.

To make an antibody into an enzyme, we need to find an antibody that stabilizes this intermediate transition state in a similar way. Researchers have done this by finding antibodies that bind to a molecule that mimics the transition state. These antibody-enzymes are termed catalytic antibodies. The catalytic antibody shown in PDB entry 1c1e performs the Diels-Alder condensation reaction. This is significant because this type of reaction is not performed by any natural enzymes. Antibodies that perform a number of other cleavage and condensation reactions, including reactions that are impossible any other way, may be found in the PDB.

Antibodies are very flexible, making it difficult to study an intact antibody. Most of the hundreds of antibody structures available at the PDB are fragments of antibodies, typically of just the Fab arm with the specific binding pocket. Three examples of intact antibodies are found in PDB entries 1igt, 1igy, and 1hzh. All are nice examples for exploration. These entries show how antibodies are able to twist into different shapes, forced by packing into the different crystal lattices. This will give you some idea of the range of motion that these molecules are capable of as they bind to their targets.

A list of all antibodies in the PDB as of September, 2001 is available at http://www.rcsb.org/pdb/molecules/pdb21_report.html. For suggestions for further reading about antibodies, see http://www.rcsb.org/pdb/molecules/pdb21_5.html.