Nature Structural Biology pp 653 - 657

A parasitic worm called Ascaris lumbricoides infects over 1 billion people, and its close relative Ascaris suum is a common internal parasite of pigs.

These worms live in the digestive system and as a result are exposed to many of the enzymes, called 'proteases', that digest food. If these worms did not have a defense mechanism, they could possibly be digested as well. But, fortunately, (or, rather, unfortunately for humans and pigs), these worms can defend themselves. They produce several proteins that inhibit their hosts' proteases, allowing them to survive in their harsh environment.

One of the proteases in the gut of animals is called pepsin, and consequently, one of the inhibitors from Ascaris suum has been named pepsin inhibitor-3, or PI-3 for short. Until now, the molecular details of how PI-3 prevents the action of pepsin have not been understood.

Michael James, of the University of Alberta in Canada, and his colleagues have now solved the structure of PI-3 bound to pepsin, by X-ray crystallography. They find that PI-3 inhibits the protease by a mechanism that has not yet been seen in any other protease-inhibitor complexes. PI-3 binds in a unique way to the protease's active site, physically preventing that region of the protein from touching and digesting potential substrates, such as food particles—or the surface of the infecting worm.

Hopefully, these results can be exploited in the design of drugs that would prevent the action of PI-3, leaving the worm more exposed to the hosts' proteases and therefore ridding the body of the infection.

Nature Structural Biology pp 687 - 692 and 693 - 699

Botulinum neurotoxins cause flaccid muscle paralysis and are among the deadliest poisons known to men—they are responsible for the food poisoning disease botulism, the symptoms of which include blurred vision and respiratory failure. They have also been developed into biological weapons—their toxicity is ~100,000 times that of sarin, the notorious nerve gas that was developed by the Nazi's during World War II and was used in the Tokyo subway attack in 1995. Currently, the predominant treatment for exposure to botulinum neurotoxins is the injection of antitoxin, which prevents the symptoms from worsening. However, it may take weeks to months to overcome the remaining toxic effects. Thus, effective antidotes are clearly needed.

Botulinum neurotoxins are secreted by strains of bacteria called Clostridium botulinum. They consist of two protein components that serve separate functions—one component, called the heavy (H) chain, is involved in targeting and transporting the other component, called the light (L) chain, which carries the actual toxic activity, into the neuronal cells. Once inside the cells, the L chains cleave proteins that participate in the release of neurotransmitters at the junctions between the neuronal and muscular cells, thereby causing muscle paralysis. Effective antidotes to botulinum neurotoxins could block any one of three steps—targeting, transporting or cleavage—essential for their toxicity. Designing such antidotes, however, requires a thorough understanding of the molecular mechanisms of these steps.

Two crystal structures of botulinum neurotoxin serotype B now provide insights into the targeting and the cleavage steps of the toxic activity of these deadly poisons. The structure of the L chain in complex with its substrate determined by Ray Stevens' group at the Scripps Research Institute, USA, provides information on how substrates are recognized and then cleaved, whereas the structure of the entire neurotoxin in complex with a mimic of a cell surface receptor, determined by Subramanyam Swaminathan's group at the Brookhaven National Laboratory, USA, reveals how the toxins might bind to the neuronal cell surface to gain entry. Bal Ram Singh, at the University of Massachusetts Dartmouth, USA, discusses the implications of these structures in an associated News and Views report.

Nature Structural Biology pp 644 - 647

While a picture is worth a thousand words, it captures only a single moment in time. A movie, on the other hand, strings these individual snap shots together to create a moving picture. Likewise, X-ray and nuclear magnetic resonance images of proteins provide a static picture. In order to understand how different molecules interact it is essential to have some way to monitor protein-protein interactions in real time.

Using the atomic force microscope (AFM), Viani and coworkers of the University of California at Santa Barbara, USA have been able to observe the interactions between individual protein molecules. The AFM uses a sharp probe that moves over the surface of a sample. The probe is a tip on the end of a cantilever that bends in response to the force between the tip and the sample. Thus, this sophisticated instrument is like a record player with the output being an image of the surface of the molecule rather than sound.

Recent advances using small cantilevers make it possible to make fast, real time measurements. Using the chaperonin system GroEL/GroES that assists protein folding in bacteria as a model system, Viani and colleagues could watch individual molecules of GroES bind and then dissociate from individual GroEL proteins. GroEL, a double-ring complex, binds unfolded proteins at the surface inside the ring where the folding reaction occurs. Binding of the cofactor GroES to the top of the GroEL cylinder results in an enclosed cage and prevents premature release of its content. Thus, determining how and when GroEL and GroES interact to bring about protein folding should further our understanding of this essential process within cells.