Posted on behalf of Retread

Well of course they don’t, but the proteins we know the most about (because they can be crystallized and their structure determined by X-ray diffraction) do have a shape. Sperm whale myoglobin, the first protein to have its 3-dimensional structure determined, showed that this couldn’t be the whole story. Sperm whales (air breathing mammals after all) use their myoglobin to carry oxygen during their hour-long dives down to 1000 meters. Kendrew and Perutz’s crystal structure showed no way for oxygen to find its way in to the embedded porphyrin ring. Amazingly, the 153 amino acids of myoglobin must themselves breathe to let the oxygen in.

All it takes to denature (seriously change its tertiary structure so it is no longer functional) a protein of 100 amino acids is 10 kcal/mole (Voet & Voet – Biochemistry 3rd Edition p. 258). That’s two hydrogen bonds – not much.

Sight your eye at the alpha carbon of one of the amino acids of this protein, looking toward the carbonyl carbon. There are three conformational energy minima the carbonyl can adopt. That’s potentially 3^99 = 10^48 conformations (clearly an overestimate because of self intersection, but still, a huge number). Yet to be crystallizable, this protein must choose just one of them, and it must be lower in energy by 2 hydrogen bonds than all the rest.

In addition, to get to this single structure, the protein can’t possibly sample all the conformations available to it. The rotation barrier of ethane is 12 kJ/mole and a barrier of 73 kJ/mole allows a rotation rate of 1 per second, and every 6 kJ changes the barrier by a factor of 10 at 25 deg C (Clayden et al. Organic Chemistry pp. 450-1). So the maximum rate of rotation of ethane is 10^11 per second (at a body temperature of around 37 deg C) rather than 10^10 at 25 deg C. This is clearly an upper bound on the rotation rate as the mass attached to the alpha carbons of a protein will make the rotation far slower, but let it pass (that’s why I chose ethane in the first place). That’s 10^37 seconds to sample the conformations available, far longer than the age of the universe. This is the Levinthal paradox.

So for the crystallizable proteins (all of biological interest so far) one conformation out of all those available must be more stable (but only by two hydrogen bonds) than all the rest, and the particular conformation must be findable quickly (or we’d all be dead).

How likely is this for a ‘random’ sequence of amino acids. We’ll probably never know (but we might if we’re lucky). This is the subject of the next post…

A Joslin researcher is moving his work into the clinic to test whether anti-inflammatory drugs can help combat diabetes.

Courtney Humphries

Diabetes. Obesity. Cardiovascular disease. Increasingly, these once-separate afflictions are being seen as manifestations of a common problem. Over the past few years, a surprising common denominator has emerged: the immune system. Scientists have found that inflammation plays a key role in a set of disorders that include type II diabetes, obesity, and heart disease—collectively called the metabolic syndrome.

Steve Shoelson, a professor of medicine at Harvard Medical School and a researcher at Joslin Diabetes Center, is investigating the link between an overactive immune system and modern-day metabolic problems. He’s now working with clinical researchers at Joslin to move some of his findings in type II diabetes into a clinical trial to see if anti-inflammatory drugs can lower blood sugar levels.

Steve Shoelson of the Joslin Diabetes Center is studying the link between inflammation and diabetes. (Credit: Joslin)

If further trials confirm that these drugs benefit diabetics, anti-inflammtory drugs could be used to prevent disease in those at risk of metabolic disease, as well as help to treat it. “It’s very similar to hypertension and cholesterol,” Shoelson says, which are risk factors for heart disease that can be managed preventively. “You would decrease risk if you can suppress inflammation.”

Revisting an old idea

Inflammation itself has been well studied by immunologists: after an infection, a host of different types of immune cells are deployed to the infection site to control the infection.

But Shoelson says that the situation is different in patients with metabolic diseases: the same markers of an immune response are present, but they persist chronically at a low level instead of following the dramatic rise and fall in an infection. Patients destined to develop diabetes or suffer from heart attacks, for instance, have higher white blood cell counts. Although this chronic, low-grade inflammation has been observed in metabolic disease, it has been trickier to determine whether it’s a cause or an effect.

Several years ago, Shoelson’s team was studying mechanisms underlying insulin resistance—the failure of the body to respond to its own insulin, a condition that raises blood sugar and can lead to diabetes. They found reports from more than a century ago that high doses of anti-inflammatory medications called salicylates lowered the blood sugar levels of patients with diabetes.

Shoelson’s team has since shown that salicylates, which are related to aspirin, could reverse insulin resistance in mice by targeting a molecular pathway involved in inflammation. Further studies from Shoelson’s lab (including this one) and others have suggested that switching on this and other inflammatory pathways can cause insulin resistance.

Because salicylates are commonly used to treat inflammation and arthritis, Shoelson has been able to quickly translate his scientific findings into clinical trials. He and Allison Goldfine, director of clinical research at the Joslin, are leading a national, multicenter Phase II/III trial to investigate whether one of these drugs, called salsalate, can reduce blood sugar levels in people with diabetes. The trial began in January 2007 and is expected to yield results this summer.

Another smaller study headed by Goldfine recently reported that salsalate treatment lowered inflammation and blood sugar levels in 20 obese teens.

Other research has implicated inflammation in the development of heart disease, so a Boston-based study, also led by Goldfine, is being launched to investigate how well salsalate can slow the progression of cardiovascular disease.

Not just drugs

Meanwhile, Shoelson’s lab is working to understand the links between inflammation and metabolism. “What instigates the inflammation and how the inflammation works are areas of intense investigation,” he says. “We don’t know a lot of the details.”

Anthony Ferrante, assistant professor of medicine at Columbia University, says that Shoelson has helped to turn isolated observations about anti-inflammatory agents and diabetes and into a framework for thinking about how the two are connected, providing a rationale for pursuing anti-inflammatory treatments. “Going forward in the next 10 years, his observations will have a big effect on how diabetes will be treated,” Ferrante says.

Although his research has led to trials testing drugs for metabolic disease, Shoelson believes that we already know the ultimate prevention and cure: diet and exercise. “These are the cures for the entire epidemic,” he says. “We need to return ourselves to the exercise levels and diet that people had centuries ago.” But given the daunting task of changing society’s behavior, Shoelson says drugs can work in concert with lifestyle changes to help prevent disease.