Proteins that bind with each other typically stick to the straight and narrow—well-defined and highly structured binding sites. This convention is usually respected even by unstructured proteins, which commonly interact with well-structured binding sites on other molecules. Now, however, another kind of protein interaction has been observed, one that may transform our view of protein binding.
Two intrinsically disordered proteins have been found to form a high-affinity complex that is itself unstructured. This discovery, made by scientists based at the University of Zurich, is more than a curiosity. It may add to our understanding of molecular communications, which has, to date, been built on our recognition of lock-and-key protein-binding mechanisms.
The new discovery may also advance the development of new kinds of therapies, specifically, drugs that can bind to unstructured proteins. Such proteins are largely unresponsive to traditional drugs, which bind to specific structures on a target protein’s surface.
The new kind of protein interaction was observed to occur between histone H1, a DNA-packaging protein in chromatin, and prothymosin α, which acts as a kind of shuttle that deposits and removes the histone from DNA. Additional details about the interaction appeared February 21 in the journal Nature, in an article entitled “Extreme Disorder in an Ultrahigh-Affinity Protein Complex.”
The two unstructured proteins, the article’s authors indicated, “associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character.” Both proteins are involved in several regulatory processes in the body, such as cell division and proliferation, and therefore also play a role in several including cancer.
“On the basis of closely integrated experiments and molecular simulations,” they continued, “we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues.”
“The interesting thing about these proteins is that they're completely unstructured—like boiled noodles in water,” noted Ben Schuler, Ph.D., professor of biochemistry at the University of Zurich and head of the research project described in the Nature article. In this project, single-molecule fluorescence and nuclear magnetic resonance spectroscopy were used to determine the arrangement of the proteins.
Observed in isolation, the proteins show extended unstructured protein chains. The chains become more compact as soon as both binding partners come together and form a complex. The strong interaction is caused by the strong electrostatic attraction, since histone H1 is highly positively charged while prothymosin α is highly negatively charged.
To investigate the shape of the protein complex, the researchers labeled both proteins with fluorescent probes, which they then added to selected sites on the proteins. Together with computer simulations, this molecular map yielded the following results: H1 interacts with prothymosin α, preferably in its central region, which is the region with the highest charge density.
Moreover, it emerged that the complex is highly dynamic. The proteins' position in the complex changes extremely quickly—in a matter of about 100 nanoseconds.
The new interaction mechanism, the article’s authors noted, may occur fairly commonly. This suggestion is based on proteome-wide sequence analyses, which suggests that this kind of interaction mechanism may be abundant in eukaryotes.
Living beings have many proteins that contain highly charged sequences and may be able to form such protein complexes. There are hundreds of such proteins in the human body alone. “It's likely,” Schuler asserted, “that the interaction between disordered highly charged proteins is a basic mechanism for how cells function and organize themselves.”