Many proteins form rigid structures, and the structure is often assumed to directly relate to that protein’s specific biological function. However, there are also “floppy” intrinsically disordered proteins (IDPs) that are functional despite lacking a stable tertiary structure. As much as 30% of all eukaryotic proteins are believed to be IDPs, and much still remains unknown about the details of their structures. Using innovative X-ray methods, a University of Notre Dame team is now a step closer to unraveling how these mysterious proteins work.
"We have excellent methods available for determining the structures of proteins that fold into one rigid structure, but a significant fraction of all proteins are too flexible to be studied using these methods. Even worse, results from two of the most commonly used methods to study IDPs disagree with each other," said Patricia Clark, a biophysicist at Notre Dame and co-author of the study. "So we developed a novel analysis procedure to help resolve this."
The procedure utilizes a technique called small-angle X-ray scattering (SAXS). With SAXS, an X-ray beam passes through the protein, scattering light in patterns that contain information on the protein's size and shape. The new method analyzes a broader range of the X-ray scattering pattern than previous SAXS methods. It then fits these patterns to IDP structures with different degrees of disorder as generated by computer simulations.
The team’s findings suggest that when IDPs begin to fold in the presence of water, they actually expand rather than collapse. This is contrary to previous data suggested by another protein analysis technique, fluorescence resonance energy transfer (FRET). The team notes that the floppy structures of IDPs may more closely resemble what would be expected for a truly random structure. This randomness may actually have an evolutionary basis to help prevent IDPs from misfolding and accidentally interacting with other proteins.
Intriguingly, a number of IDPs are implicated in human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Proteins such as α-synuclein, tau protein, p53, and BRCA1 have large intrinsically unstructured regions that are responsible for mediating many protein-protein interactions. The study authors note that the advancements made in this work will enable detailed study of folding and misfolding mechanisms. "While this work is a fundamental, basic research demonstration of protein behavior, the implications are really broad," Clark said.
The team's findings were published yesterday in Science.