Academic journal article The American Biology Teacher

Visual Technologies

Academic journal article The American Biology Teacher

Visual Technologies

Article excerpt

[ILLUSTRATION OMITTED]

Georgina Ferry (2007) recently published a biography of Max Perutz in which she chronicles the many difficulties he faced in his over 20-year effort to work out the structure of hemoglobin. Among the problems he encountered was dealing with the massive mathematical calculations involved in relating the spots on the x-rays of protein crystals to the position of atoms in the hemoglobin molecule. He began his work when computers were still essentially a thing of the future. While it's easy for us to see how computers would have eased his work, actually finding a role for electronic calculating devices was not as straightforward as it might now seem. In an early foray into the world of computers, Perutz paid a significant sum to have data cards punched in order to mechanize some calculations; the results turned out to be almost useless. In the later stages of his work, he did have significant electronic assistance that aided his eventual publication of the hemoglobin structure in 1960. However, for many years he and his colleagues faced mathematical hurdles, and Perutz always left computer work to others, he had no enthusiasm for it.

Reading a historical work such as Ferry's is a good way to put today's research into perspective. Now many protein structures can be worked out in a matter of weeks or even less using desktop computers; nor do researchers have to spend hours, with machine shop help, in the construction of three-dimensional models. These can be made virtually using freely available software such as Jmol and RasMol. Then biology teachers and students can manipulate the resulting images (http://molvis.sdsc.edu/fgij/snaps/index.htm. Fortunately, Perutz lived until 2002, so he was able to see these advancements, in whose early stages he had played such a significant role.

Nuclear Pore Complex

But even since 2002, there has been a great deal of progress. Recently, a group of researchers at Oxford University published a model for the structure of the nuclear pore complex (NPC), the gatekeeper for the movement of molecules into and out of the nucleus (Alber et al., 2007a,b). Not surprisingly, this is a large, complicated structure that controls the movement of mRNA out of the nucleus and nuclear regulatory proteins into it. Trying to figure out a structure that had 456 protein molecules of 30 different kinds would seem to be as daunting even today as Perutz's research on hemoglobin seemed in the 1930s when he began. But as computers ultimately came to his aid, technology also assisted a large group of NPC collaborators at several different institutions. They used two major approaches. First they gathered as much structural and chemical information as possible on the protein components. Then they fed this data into a computer model using what was known about the size and symmetry of the NPC as a constraint on the possible configurations and placement of the proteins. Essentially, they began with a cloud of beads, each representing one of the proteins, and then ran thousands of trials, each attempting to localize the beads into the most likely position consistent with all the variables. The result was a plausible structure, consistent with the data: The NPC as a whole is composed of eight spokes arranged around a central transport channel or pore. Half the proteins form a scaffold or network that coats the membrane (Aitchison & Wozniak, 2007).

It can cause a dizzy feeling in people who love molecular structures to think about Perutz's work and then about this present-day extension of it. He labored for 20 years on one protein, while less than 50 years after he published the hemoglobin structure, researchers are coming up with a solution to the problem of how 456 proteins not only fit together but interact with the lipid of the nuclear membrane as well. We obviously have Perutz and many other early structural chemists to thank for today's advances. We also have technology to thank. …

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