Shelnutt's discovery was made possible by a computer program developed about three years ago by his then postdoctoral student Walter Jentzen. The program, the only one of its kind, uses a mathematical procedure for characterizing the structure of hemes in terms of normal coordinates. When heme proteins are put into a solution and the water slowly evaporates, they emerge in a crystalline form. Protein X-ray crystallographers then determine the positions of the atoms in these very large molecules and deposit this structural information in the Brookhaven Protein Data Bank. The structures can then be put into the computer program, which quantifies the heme's nonplanar structure. Shelnutt also uses a light-scattering method, called resonance Raman spectroscopy, to detect the structure of proteins in solution.
So far Shelnutt has used the program to study more than 400 existing protein crystal structures. And while he has identified some 70 different heme shape variations (called distortions), he has determined that only six are important for hemes in proteins -- including saddling, ruffling, doming, propellering, and two types of waving. Each was named according to how the heme appears. Only a small amount of energy causes distortion for these six shapes.
He has also determined that distortions are specific to functions and can be found in proteins from both similar and different species that perform similar tasks, making certain shapes "conserved." "Conserved heme structures within the proteins tell us that the heme's shape plays an important role in determining the function of the protein," Shelnutt says. "We can see that different proteins may perform similar functions from the shape of the heme."
He adds that some 800 hemes have been identified in the Protein Data Bank.
However, before his research, "people didn't realize that the shapes of the
Contact: Chris Burroughs
DOE/Sandia National Laboratories