In between the size of an atom and a drop of water, objects the size of living cells would be expected to vibrate mechanically at intermediate frequencies (10,000-500, 000 Hz).

But also consider that other oscillations besides mechanical shaking are of interest in cells, including the rate of protein folding and unfolding, the rate at which nutrients enter and leave a cell, the rate at which life processes take place, and many others.

Researchers at Northwestern University have offered a clue that may get to the core of the cell death question and establish a common mechanism in these diseases.

In a study, published in the journal Science, the research team showed that polyglutamine ( the toxic component of the protein responsible for Huntington's disease ) is so demanding on the cell's system that it changes the environment within the cell, causing other metastable, or partially folded, proteins to crash and lose function. Over time, this can cause the organism to die.

" Our results suggest that these disease-associated, aggregation-prone proteins may exert their destabilizing effects by interfering generally with other proteins that are having difficulty folding," said Richard I. Morimoto, who led the study.

Now, a discovery by Weill Cornell Medical College researchers is changing decades-old conventional wisdom on the "coiled coil," a common protein structural motif scientists thought they knew well.

The finding, recently published in the journal Structure, marks an incremental but important advance in understanding the complex, three-dimensional interactions between these building blocks of life.

"A deeper knowledge of these types of relationships is crucial, because it gets us a tiny step closer to recreating them artificially -- using 'designer proteins' to treat and even cure disease," explains senior author Dr. Min Lu, Associate Professor of Biochemistry at Weill Medical College of Cornell University, New York City.

While the sequencing of the human genome was justly hailed as a milestone, it may prove to be just a stop on the way to a much bigger prize -- protein engineering.

"Remember, genes are simply the code that cells use to make proteins," Dr. Lu explains.

Every day, the body creates tens of thousands of different proteins that fold together in complex, three-dimensional ways to perform specific functions.

"Understanding, fixing, and even reproducing these interrelationships is really the next scientific frontier, with infinite possibilities for the health sciences and beyond. Right now, however, we know very little about the way proteins fold," he says.

Using plants, it is technically possible to grow, harvest, and process pharmaceutical proteins on a large scale. The genetically modified crop containing edible vaccine, for instance, can be consumed raw or partially processed. By targeting protein expression into specific organs of the plant such as grains, one creates a stable storage system. By targeting the recombinant protein to subcellular regions of the cells, such as the endoplasmic reticulum, a favorable environment is created for its appropriate folding and assembly, thus increasing the amount of recombinant proteins produced. Additionally, targeting the recombinant protein to the membrane concentrates the product. As a consequence, the cost of downstream purification is minimized. Finally, using plants for the production of drugs reduces the risk of contamination with human or animal pathogens, unlike production via animal or human sources.

So far, pharmaceutical proteins produced in plants can be classified into three groups: human biopharmaceutical proteins, including growth hormone, human serum albumin, β-interferon, and erythropoietin; recombinant antibodies such as IgG1 and IgM; and recombinant subunit vaccines, from the hepatitis B envelope proteins and the rabies virus glycoproteins to the cholera toxin B subunit.

In the past couple of decades, a slough of studies has looked at the benefits of vitamin E and other antioxidants. While a considerable amount of this research touts the advantages of consuming antioxidants, some of the studies have found that in certain cases, antioxidants, including vitamin E, may actually increase the potential for developing heart disease, cancer and a host of other health problems.

This study provides clues as to why this could happen, say Jiyan Ma, an assistant professor of molecular and cellular biochemistry, and his colleague David Cornwell, an emeritus professor of molecular and cellular biochemistry, both at Ohio State.

"We deleted each hydrogen bond and then measured how relaxed the protein was afterwards," Fitzgerald said. "It turns out we destabilized the structure in each case. So the relaxed state was not so relaxed any more. The proteins were more stable with those hydrogen bonds.

"Those bonds seemed to clearly play a role in protein folding. And what we were able to uncover in this work is that this role may be highly conserved in a protein fold."

With Wang as the first author, the three chemists described their results in a paper published online on Friday, Feb. 10, 2006 in the journal Proceedings of the National Academy of Sciences. Their research was funded by the National Institutes of Health.

Their paper reported that deletions at each position on one folded protein, known as Arc, had the identical effect at the analogous position on the other protein, called CopG. "Remarkably, the five paired analogs with...mutations at structurally equivalent positions were destabilized to exactly the same degree," the authors wrote.

“Science,” as we use the word in everyday language, is a field that consists of hundreds of years of tested ideas that describe how the world works. Science, in a more formal context, is a method, an approach.

The goals of science are to build on what’s known, through new discoveries and correction or clarification of old information. While it’s true that ID theory uses facts of science to support its claims, it has nothing new to report. It only seeks to prove itself. Science doesn’t seek to prove itself, but rather to describe the behavior and character of the universe.

ID is a single belief or idea: “an intelligent force had a hand in building and organizing life.” To equate the two by pitting them against one another is ridiculous. It’s like stating a very broad idea, such as, “Fruits and vegetables are nutritious,” and comparing it to the comment, “I like steak.” The latter is a single preference. The former is an evaluative statement with a broader scope.

I see no problem with a scientist holding the belief that an overarching intelligent force influenced life. But that belief is personal. It’s for the scientist’s own mind.

When the scientist is testing wastewater for chemical compounds, or studying how bees interact with pollinators or even looking at the genetic code of fruit flies, that belief doesn’t factor in.

How big a role hydrogen bonds actually play in protein folding has been a controversial scientific question, according to Duke associate chemistry professor Michael Fitzgerald. "There's been an ongoing debate about the exact role of those hydrogen bonds," he said in an interview. "Are they really super-important, or are they really negligible?"

Fitzgerald, his graduate student Min Wang and his former graduate student Thomas Wales helped address that question in an effort that took years of work.

One by one, they slightly "mutated" the normal arrangement of atoms in proteins to effectively delete hydrogen bonds at five analogous positions along the structural "backbones" of two different protein molecules that fold in the same pattern. Then they analyzed how each deletion affected the stability of the protein. "Stability" means how low energy, or "relaxed," the protein was.

Protein-based therapeutics is the newest class of chemical compounds being developed by the drug industry, and it is estimated that about 900 to 1,200 clinical candidate proteins and/or peptides are currently being investigated. In addition, 140 therapeutic proteins have been approved and 500 are in clinical trials, and it is expected that at least 50 biotherapeutics will come on to the market over the next few years.

Many of these biotherapeutics are produced using technologically advanced cell biosystems. These include microbial and mammalian systems, as well as transgenic plants and animals. These cell-based protein manufacturing technologies offer certain advantages, but they present a number of challenges as well. The use of microbes for human applications is decades old, but the advent of genetic engineering provided the means to produce recombinant proteins in bacteria and yeast, making them productive bioreactors.

In the study of proteins, researchers have not quite figured out what causes a protein to go from a folded to unfolded state.

But Laurence said the recent study sheds some light on the mystery.

The structure in the energy landscape is what encourages it to fold or not to fold,” he said. “You want to see what protein is doing in an unfolded state and why it folds. Then you can understand why the folding sometimes goes wrong.”

Laurence said protein folding gone awry can provide some keys to as to why certain people are prone to Alzheimer’s or other neurodegenerative diseases. In addition, understanding how and why protein folds can help scientists design proteins to perform specific tasks.