Designer Protein: Largest Protein Ever Created from Scratch Reported

Scientists have been trying to accurately synthesize molecules with shapes that mimic biological molecules, specifically proteins that drive important biochemical pathways in humans. While this field has enjoyed some success in the redesign of natural proteins to incorporate novel functions, so far attempts to synthesize large proteins with predictable structures have not borne fruit. Now, researchers at the University of Pennsylvania Medical Center (Philadelphia) have created the largest protein from scratch, as reported in the May 11 issue of the Proceeding of the National Academy of Sciences.

"The ability to do this really takes us out of the realm of tinkering with existing proteins to engineering entirely new proteins and polymers," says senior author William F. DeGrado, professor of biochemistry and biophysics. "We have shown that it is now possible to design a protein with a well-defined three-dimensional structure."

In this work, which was a collaboration between scientists at the Fox Chase Cancer Center at the University of Pennsylvania Medical Center and Bristol-Myers Squibb Co. (Princeton, NJ), a 73 amino acid protein, called alpha-3D, was synthesized de novo in a bacterial expression system and subjected to extensive analysis by NMR spectroscopy. This protein, which is three times larger than previously synthesized proteins, is a bundle of three counterclockwise-coiling helices, inspired by the IgG binding protein of Staphyloccocus aureus. The NMR analysis of alpha-3D revealed that it had thermodynamic and spectroscopic properties typical of native proteins, but differs from most biological proteins in that the helices coil counterclockwise rather than clockwise. However, it was found to be more stable than most designed proteins described to date.

According to Scott Walsh, a doctoral student in DeGrado's laboratory who designed, produced, and characterized alpha-3D, the next step will be to build a specific function into the protein's structure. Currently, he is retooling the surface of alpha-3D to cause it to bind to a variety of hormonal receptors. Natural proteins that do this are expensive to produce and suffer from limited shelf lives. Novel mimics of these proteins may have enhanced stability and potency.

DeGrado notes that implications of this advance in protein design could be as broad as those for natural proteins—from manufacturing entirely new polymers for industrial catalysts to creating new pharmaceuticals.

This work was conducted in the Johnson Research Foundation, a funding and research organization within Penn's Department of Biochemistry and Biophysics that concentrates on the study of physics as it applies to medicine.

For more information: William F. DeGrado, Professor of Biochemistry and Biophysics, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104-6059. Tel: 215-898-4590. Fax: 215-573-7229. Email: wdegrado@mail.med.upenn.edu.