A decade ago genes dominated the thinking of many molecular biologists, but not that of Ram Sasisekharan. He looked further ahead--past DNA, past proteins--to sugars. Polysaccharides cover proteins and the surface of all cells, but biologists at that time considered sugars inert, about as important to biological function as a plastic aspirin bottle is to fighting a headache. Still, Sasisekharan followed a hunch. "I instinctively felt there was something important there," he says. He was right. Cultivating these sweet opportunities, though, demanded teamwork.
In the late 1980s Sasisekharan started his doctoral work in Robert Langer's laboratory in the department of chemical engineering at the Massachusetts Institute of Technology. The reputation of Langer's lab as an invention factory would have intimidated the average student. Not Sasisekharan. He asked Langer for a project that nobody else wanted. So Langer set Sasisekharan loose on cloning heparinase, a task that had stymied previous postdoctoral and graduate students. This enzyme cuts up sugars in the heparin family, which surround the outside of cells. Such cutting can release growth factors stored in the extracellular matrix, the connective tissue-like coating on cells. Physicians use heparin to prevent blood clots after surgery and to treat clots that cause heart attacks.
From the start, Sasisekharan planned to follow a basic approach: find a compound's sequence, use that sequence to help unravel the compound's structure and, finally, determine how the substance works. To really figure out heparinase, Sasisekharan needed a teammate. Unexpectedly, he found one on a tennis court. While Sasisekharan volleyed with Ganesh Venkataraman, who was pursuing his Ph.D. in chemical engineering with M.I.T. professors T. Alan Hatton and Karen K. Gleason, these two doctoral students talked proteins. More to the point, Sasisekharan tried to recruit Venkataraman for help with heparinase, and he succeeded. "I had him work on making recombinant heparinase first," Sasisekharan says, "and at the same time convinced him to study sugars." Soon Sasisekharan had unraveled the sequence of amino acids that make up the protein heparinase.
All along, though, Sasisekharan wanted to go beyond enzymes to explore the biological role of sugars. His work on heparinase led naturally to an interest in the sugar that it cuts up--heparin. Sasisekharan first needed to determine the sequence of building blocks that make up this sugar. Then he hoped to use that sequence to find heparin's three-dimensional shape. He started preparing for this work years before, when he listened to his biophysicist father, Viswanathan, describe the importance of molecular shape and interactions in proteins and DNA. "I am highly influenced by my father's thinking," Sasisekharan notes. So the younger biologist knew, like his father before him, that he must unravel a molecule's shape to figure out its function.
Venkataraman began looking at heparin's structure. "As I started digging deeper," he relates, "I found there was very little information on the sequence." He and Sasisekharan needed a fast and accurate way to find the building blocks that make up heparin and other large polysaccharides. Heparin's sequence seems simple--just a repeating disaccharide, or two simple sugars linked together. Each of the simple sugars, though, can be modified in four places, which generates 16 possible versions. Consequently, the two simple sugars combined can come in 32 different "flavors." Human genes come with only four basic building blocks, and proteins use 20, so sugars looked considerably more complicated from the outset.
After completing their doctoral degrees, Sasisekharan and Venkataraman rejoined forces at M.I.T., as an associate professor and a research associate, respectively. They planned to develop a set of tools to sequence sugars. First they needed to name the different possible sugars. With 32 possible versions for a single disaccharide, even short chains skyrocket the permutations to a million or more. Venkataraman's engineering background pointed to numbers. "This was a problem that truly required a meeting of the minds," he asserts. "In hindsight, it was crucial that Ram used a biochemical approach and I used an engineering one." Sasisekharan saw the potential value of sequencing complex sugars, and Venkataraman devised a way to convert the complicated chemistry into a string of large numbers.
This article was originally published with the title Adding Sugar to Bioscience.