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A Closer Look at RIPK1-RIPK3 Core Amyloids | Science Trends

A Closer Look at RIPK1-RIPK3 Core Amyloids

Amyloids are fibrillar proteinaceous assemblies whose accumulation is a hallmark of several human diseases. Formation of amyloid fibrils occurs when protein monomers change their structure and clump together. This kind of irreversible polymerization can lead to the accumulation and propagation of toxic oligomeric seeds. Such accumulation of amyloid fibrils takes place in more than 20 distinct diseases, including Alzheimer’s disease and type II diabetes.

Conversely, the last decade has witnessed the discovery of a second class of amyloids that are key to sustain life; these are the so-called functional amyloids and, in contrast to pathological amyloids, these fibrils readily disassemble after carrying out their functions.

Among the emerging number of functional amyloids uncovered to date, perhaps the RIPK1-RIPK3 necrosome core is the most perplexing. This is the first example of a human signaling complex of amyloidal nature. More precisely, the association of these two proteins RIPK1 and RIPK3 through their so-called RIP homotypic interaction regions (RHIMs), enables the formation of a functional amyloid fibril that serves to signal in a programmed cell death known as necroptosis. In contrast to all amyloid fibrils reported to date, the RIPK1-RIPK3 necrosome amyloid fibrils build on the assembly of two distinct proteins, instead of one protein. That is, this is the first example of a hybrid amyloid. By this unique feature, the RIPK1-RIPK3 necrosome has revolutionized the amyloid paradigm. Therefore, it is crucial to understand how the incorporation of two distinct proteins is favored over the homo-oligomerization process of protein self-stacking during amyloid formation.

The development of new solid-state Nuclear Magnetic Resonance (ssNMR) method has proven a powerful tool to elucidate amyloid structures. Therefore, the authors used ssNMR to unravel the enigmatic structure of the necrosome core formed by RIPK1 and RIPK3 at atomic resolution. The samples used for the structural study were obtained using molecular biology tools. Briefly, the strategy consists of feeding E. coli bacteria with 13C- and 15N-isotopically labeled material as the carbon and nitrogen sources for cell growth. By this method, it is possible to force bacteria cells to produce the proteins of interest (RIPK1 and RIPK3) in large amounts. Carbon and nitrogen atoms in these proteins will be enriched in 13C- and 15N isotopes, which are visible to the NMR technique. Proceeding this way, the authors isolated hybrid amyloid fibrils formed by RIPK1 (amino acid residues 496-583) and RIPK3 (residues 388-518) that were subjected to ssNMR analysis.

The interpretation of the solid-state NMR data is like solving a puzzle. Just like puzzle pieces need to come together to the right place to provide the right picture, the NMR data affords a large number of distances between a pair of atoms. There is only one way in which all such distances simultaneously fit a structural representation. In the case of the RIPK1-RIPK3 amyloid fibrils, the authors were able to obtain a number of distances below 8 Å between amino acid residues in the two proteins, which ultimately yielded the 3D structure of the amyloid complex at high resolution.

The structure of the RIPK1-RIPK3 illustrates for the first time the basis for hetero- over homo-oligomeric assembly, or how distinct proteins preferentially stack with each other rather than with themselves. It is interesting that among the ~90 and ~130 residues contributed by RIPK1 and RIPK3, respectively, only a restricted number is required for hetero-amyloid assembly or hybrid amyloid formation. Figure 1 illustrates how the two amyloidal, core sequences of both proteins align to allow protein alternation.

Figure 1: Illustrating how few amino acid residues in RIPK3(blue) and RIPK1 (green) drive homo-amyloid formation incorrect activation with analogous architecture to those of the more favorable hetero-amyloid determined by ssNMR. Republished with permission from Elsevier from https://doi.org/10.1016/j.cell.2018.03.032.

The striking feature of the core structure is how stacking with essentially identical conformations can form hybrid amyloid fibrils despite differences in amino acid composition. Whereas peptides bearing the core RHIM sequences can each form homo-amyloids themselves with the same architecture observed in the RIPK1-RIPK3 hetero-amyloid (Figure 1), the ssNMR structure of this hybrid amyloid provides a potential explanation for this preference; namely, the protein monomers in the fibrils are more tightly bound by alternately stacking RIPK1, RIPK3, RIPK1, RIPK3, etc. with respect to both the homo-RIPK1 and homo-RIPK3 counterparts.

This work is significant and has broad implications in the structural and human biology of cell death and beyond. The RIPK1-RIPK3 core is the first detailed structural study of a hetero-amyloid at atomic resolution, therefore providing a structural basis for understanding the mechanisms of signal transduction and hetero-amyloid formation in broader contexts. The first step towards rational drug design strictly requires the determination of the 3D structure of the target protein. Elucidating the key structure of the RIPK1-RIPK3 core could pave the way for the development of inhibitors of the necrosome core, whose incorrect activation is involved in some complex pathologies.

These findings are described in the article entitled The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex, recently published in the journal CellThis work was conducted by Miguel Mompeán, Wenbo Li, Jixi Li, Ségolène Laage, Ansgar B. Siemer, Gunes Bozkurt, Hao Wu, and Ann E. McDermott from Columbia University, Harvard Medical School, and Boston Children’s Hospital.

About The Author

Hao Wu

Hao Wu is a Chinese American biochemist and crystallographer and the Asa and Patricia Springer Professor of Structural Biology in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School.[1] Her work focuses on molecular mechanisms of signal transduction in cell death and inflammation. She is the discoverer of signalosomes, which are large macromolecular complexes involved in cell death and in innate and adaptive immune pathways. She has established a new paradigm for signal transduction that involves higher-order protein assemblies. She has received the Pew Scholar Award, the Rita Allen Scholar Award, the Margaret Dayhoff Memorial Award, the NYC Mayor's Award for Excellence in Science and Technology, NIH MERIT and Pioneer Awards, and the Purdue University Distinguished Science Alumni Award. She was elected AAAS fellow in 2013 and to the National Academy of Sciences in 2015

Gunes Bozkurt

I'm an experienced protein biochemist with a demonstrated history of working in the life sciences and translational medicine fields. I am a self-motivated, proactive team player with analytical skills who shows initiative with a scientific mindset. I am passionate to apply my life sciences expertise to the art of investing and business development because I want to make an impact by integration of innovations into our lives.

Ann E. McDermott

Ann McDermott's research group studies the mechanisms of several enzymes, principally through solid-state NMR spectroscopy. She has studied the opening of the active site flexible loop of the glycolytic enzyme, Triosephosphate isomerase, and its coupling to the appearance of product, using a range of biophysical probes. The compressed "non-bonded" interactions of the pre-reactive substrate on the active site of this enzyme, and the conformational dynamics, have been experimentally probed at high resolution. Analogous studies are underway for bacterial Cytochrome P450, where conformational flexibility impacts the range of chemistry carried out by the enzyme. These studies involve recent advances in high-resolution solid-state NMR spectra of uniformly or selectively isotopically enriched proteins wherein site-specific assignments allow for efficient structural, dynamic and mechanistic studies. She also studies the photosynthetic reaction center, and demonstrated for the first time a coherent, quantum mechanical photochemical mechanism for enhancement of NMR detection sensitivity by three orders of magnitude involving the primary players of electron transfer.

Miguel Mompeán

Miguel is a research scientist at the Spanish National Research Council, Institute of Physical Chemistry "Rocasolano".