Molecular Anatomy: X-Ray Crystallography Helps Solve the Mystery of Protein Structure

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A protein may have more twists and bends than a bagful of pretzels...While most objects--shirts, sheets, newspapers, camping equipment--are inoperative until unfolded, scientists agree that only when a protein folds is it able to act.footnote 1

The typical mammalian cell can synthesize some 10,000 different proteins. These are large molecules made up of a sequence of molecular units called amino acids. But it is their intricately folded, three-dimensional shapes that give proteins their very specialized and powerful biochemical capabilities.

They are the work-horses of life. Proteins carry out a great variety of tasks, from providing the structural scaffolding for our cells, tissues, muscles, and bones, to serving as hormonal messengers and enzymes, regulating biochemical processes, and relaying genetic information, among other duties.

Deciphering the structure of proteins has been the quest of scientists for decades. The pioneering work of UW chemist Lyle Jensen in x-ray crystallography, begun in the 1940s, helped to provide the scientific community with a powerful tool for picturing the complex, 3-D structure of these ubiquitous biomolecules. Jensen pioneered computational techniques in crystallography, not only to determine the positions of hydrogen atoms in small molecules, but also to determine the atomic positions in proteins with higher accuracy than previously thought possible.

X-ray crystallography begins with growing a pure crystal of the material whose structure is to be determined. A beam of x-rays--very short-wavelength, high-energy light waves--is then passed through the crystal. The regular and repeating arrangement of atoms in the crystal gives rise to a complex pattern of spots, which originally were recorded on film. Encoded in the pattern is information about the positions of the atoms in the crystal. With a considerable amount of mathematical computation it is possible to calculate a map of electron densities, displayed as contour maps resembling topographic maps in geography. The peaks in the electron density map correspond to the atomic positions in the molecule. From that map, a 3-D model of the molecule can be constructed.

Jensen completed his doctoral thesis on the technique of x-ray crystallography at the UW in 1943, working with chemistry professor Edward Lingafelter, who had just set up a lab to conduct structural studies based on x-ray diffraction data. After a series of research positions in the midwest, Jensen returned to the UW for what originally was supposed to be a temporary stay. But in 1949 a tenure-track faculty position opened in the Department of Anatomy in the newly established medical school, and Jensen's expertise happened to match the interests of H.Stanley Bennett, then chairman of the anatomy department.

Bennett was a Harvard-trained MD with extraordinary vision. He believed that the study of anatomy should go beyond the gross and microscopic anatomical features to include the submicroscopic realm. It was a view of anatomy that was radical, even verging on heresy, for the time.footnote 2 Bennett charged Jensen with the mission of creating a facility to probe biologically and medically important structures at the molecular level. The anatomist's arsenal of tools was expanded beyond the optical microscope to include the electron microscope and x-ray crystallography. Bennett's vision seems all the more extraordinary, considering that x-ray crystallography was still in its infancy and could only determine the structure of relatively small molecules at that time.

It was extremely labor-intensive work to solve even a small structure in the days before the advent of modern computers. Jensen reflects that "research results from the new x-ray equipment were slow in coming because of the time required to set up the equipment and carry through the calculations Nevertheless, Dr. Bennett understood and never put me under any pressure to 'publish or perish.'"

Jensen recalls that in the '50s, "calculations by hand to locate 12 atoms in a small molecule required more than 2,000 hours." He began in 1949 with the new antitubercular drug isonicotinic acid hydrazine (C5H4NCONHNH2), using a single crystal from a sample supplied by Squibb Pharmaceutical. Computing was done by crude means ("mechanical desk calculator, trig tables") and results were published in 1954.footnote 3

In the mid-fifties, progress accelerated rapidly for the UW group and for others around the world. These were heady times for x-ray crystallographers, as advances in computing made it possible to tackle more complex structures. In 1953, Watson and Crick deduced the double helical structure of DNA. By 1954, Dorothy Hodgkin at Oxford had solved the structure of vitamin B12. In 1958 and 1959, researchers at Cambridge had obtained the first electron density maps of proteins myoglobin and oxyhemoglobin, spurring Jensen and colleagues at the UW to study the small metalloproteins--a class of proteins that contain one or more metal atoms. In July of 1968, one of those--called rubredoxin--was solved by the UW group. In the early 1970s, Jensen and colleagues showed that computational techniques could refine the structure of proteins derived from x-ray diffraction data with unprecedented accuracy. These techniques developed by Jensen have become standard in the field of crystallography today.

Jensen's former UW colleague M. Roy Schwarz, now senior vice president of the American Medical Association, reflects upon the biophysical cytology class that he taught with Jensen in 1958: "Stan Bennett and you were years ahead of the rest of the world but right on track. We did move to the molecular level of structure and function."footnote 3 Bennett's anticipation of the importance of the molecular basis of biological structures, and Jensen's achievements to visualize them, have stood the test of time.

  1. "Super-Fast Computer Program Helps to Predict Protein Structure," Sandia National Laboratories News Release, Albuquerque, N.M., Sept. 1, 1995.
  2. "Anatomy/Biological Structure at the University of Washington: A Historical Perspective," from the History of the UW Medical School, Manuscripts and Archives Division, UW Libraries.
  3. Lyle Jensen, personal communication.
  4. Assistance provided by Lyle Jensen is greatly appreciated.

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