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Taming a molecular mustang

Horse taming does not generally come to mind in connection with molecular biophysics, where one studyies the shape, structure and dynamics of proteins and DNA. However, scientists from the National Centre for Biological Sciences (NCBS) in India and the National Cancer Institute (NCI), USA, have found two enzymes that interact with each other in a manner somewhat like a trainer taming a wild mustang.

The enzymes function in human cells in a pathway that tags proteins – including one that suppresses the spread of cancer – for degradation. Understanding the dynamics of how these enzymes work could be useful in designing drugs to prevent the spread of cancer.

Damaged or unnecessary proteins in the cell are tagged for destruction with a small protein called ubiquitin through a process called ubiquitination. This tagging mechanism occurs in three steps with three classes of enzymes E1, E2 and E3. Ubiquitin is activated by E1, then transferred to E2, which then interacts with E3 and the protein to be tagged, also called a substrate protein, in the last step of the process. In human cells, the E3 enzyme gp78 interacts with the E2 enzyme Ube2g2 during ubiquitination.

Previous studies with other E2 proteins have shown that E2s can be very dynamic, which means that they can assume various shapes or conformations. But, to transfer ubiquitin onto a substrate protein, E2s must adopt a specific conformation when bound to E3s. Although it was known that E3s could induce E2s to adopt such a conformation, the mechanism of how this happened remained a mystery until now.

In a new publication in the journal Structure, scientists from NCBS and NCI have shown that a part of the E3 enzyme gp78 can ‘tame’ the dynamic E2 enzyme Ube2g2, to facilitate binding to a second area of gp78 during the last step of the ubiquitin-transfer process.

“Our work shows that it is not simply the static docking (or binding) of two proteins together that drives a reaction or signals the next step in a cascade. Rather, it reveals that biomolecular recognition can be both exquisitely subtle and complex. In this study, we observe that partner proteins match dynamics and select the proper state to effect a signal for the next stage of a reaction,” says Andrew Byrd from NCI.

The E3 enzyme, gp78, has two areas or domains called G2BR and RING that bind to Ube2g2. Using Nuclear Magnetic Resonance (NMR) spectroscopy and molecular dynamics (MD) simulations, the researchers have demonstrated that when the G2BR domain of gp78 latches onto Ube2g2, it arrests Ube2g2’s molecular gyrations. The abated Ube2g2 dynamics allows the RING domain to bind so that ubiquitin transfer to the substrate protein can occur efficiently.

“This kind of brings to my mind, the analogy of a trainer taming a wild horse. The G2BR domain rides on the dynamic Ube2g2 and tames it down for the RING domain,” says Ranabir Das from NCBS. “For the first time, we have experimental evidence that E2s, in this case Ube2g2, are inherently dynamic and that the E3s can modulate the E2 dynamics for function,” he adds.

The two proteins gp78 and Ube2g2 used in this study are well-known to be involved in the degradation of the protein Kai-1, which is a metastasis suppressor that hinders the spread of cancer. Since Ube2g2 and gp78 are involved in promoting the spread of cancer, the knowledge of how these two partner enzymes interact and function in a coordinated fashion, is expected to be useful in designing drugs against the spread of cancer.

“For many years, structural biology has provided views of the ‘ground state’ of proteins and other molecules. However, it is the ‘excited states’ or ‘dynamic states’ that can drive the molecular recognition. The methods to reveal these dynamic states have been developed in the past 10-15 years, and now with improved instrumentation and methods, we can apply these concepts to biologically significant events,” says Byrd. “By understanding the specifics of signalling and recognition events in key biological processes, we hope to develop selective modulation techniques for new therapeutic interventions,” he adds.


About the work:

The work described in the article above has been published in a publication titled “Conformational dynamics and allostery in E2:E3interactions drive ubiquitination: gp78 and Ube2g2" in the journal Structure in May 2017.

Image credits: Pixabay