Atomic insights into the genesis of cellular filaments by globular proteins

McPartland, Laura; Heller, Danielle; Eisenberg, David S.; Hochschild, Ann; Sawaya, M.R.

doi:10.1038/s41594-018-0096-7

Cited by 5 publications

(7 citation statements)

References 61 publications

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“…Here the reason for Asn1 filamentation may be similar. A new protein-protein interface may be induced by the D330V mutation, either through a stacking or bridging and stacking mechanism [ 23 ]. The Asn1 protein level in ASN1 D330V -GFP ASN2 KO cells is higher than that in ASN1 WT -GFP ASN2 KO, ASN1 R354E -GFP ASN2 KO and ASN1 E48K -GFP ASN2 KO cells.…”

Section: Discussionmentioning

confidence: 99%

Filamentation of asparagine synthetase in Saccharomyces cerevisiae

et al. 2018

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Asparagine synthetase (ASNS) and CTP synthase (CTPS) are two metabolic enzymes crucial for glutamine homeostasis. A genome-wide screening in Saccharomyces cerevisiae reveal that both ASNS and CTPS form filamentous structures termed cytoophidia. Although CTPS cytoophidia were well documented in recent years, the filamentation of ASNS is less studied. Using the budding yeast as a model system, here we confirm that two ASNS proteins, Asn1 and Asn2, are capable of forming cytoophidia in diauxic and stationary phases. We find that glucose deprivation induces ASNS filament formation. Although ASNS and CTPS form distinct cytoophidia with different lengths, both structures locate adjacently to each other in most cells. Moreover, we demonstrate that the Asn1 cytoophidia colocalize with the Asn2 cytoophidia, while Asn2 filament assembly is largely dependent on Asn1. In addition, we are able to alter Asn1 filamentation by mutagenizing key sites on the dimer interface. Finally, we show that ASN1D330V promotes filamentation. The ASN1D330V mutation impedes cell growth in an ASN2 knockout background, while growing normally in an ASN2 wild-type background. Together, this study reveals a connection between ASNS and CTPS cytoophidia and the differential filament-forming capability between two ASNS paralogs.

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Section: Discussionmentioning

confidence: 99%

Filamentation of asparagine synthetase in Saccharomyces cerevisiae

et al. 2018

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“…To date, the only possibility for RNase A to undergo fibrillation is to overpass the super-saturation barrier, as recently reported by Noji and co-workers [ 25 ]. In our case, the “open” conformation [ 4 ] of the 16–22 hinge loop, which represents a crucial portion of the open interface [ 4 ] stabilizing all RNase A N-swapped oligomers [ 3 , 5 ], might favor part of the oligomers’ population to undergo massive aggregation but without the formation of fibrils.…”

Section: Discussionmentioning

confidence: 99%

“…The events governing protein self-association can favor the formation of amyloid fibrils and are among the most studied life science topics of the last 20–25 years [ 1 , 2 , 3 ]. In particular, the three-dimensional domain swapping (3D-DS) mechanism associated with protein oligomerization, in some cases related to massive supramolecular aggregation [ 4 , 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Slow Evolution toward “Super-Aggregation” of the Oligomers Formed through the Swapping of RNase A N-Termini: A Wish for Amyloidosis?

Gotte

Butturini

Bettin

et al. 2022

IJMS

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Natively monomeric RNase A can oligomerize upon lyophilization from 40% acetic acid solutions or when it is heated at high concentrations in various solvents. In this way, it produces many dimeric or oligomeric conformers through the three-dimensional domain swapping (3D-DS) mechanism involving both RNase A N- or/and C-termini. Here, we found many of these oligomers evolving toward not negligible amounts of large derivatives after being stored for up to 15 months at 4 °C in phosphate buffer. We call these species super-aggregates (SAs). Notably, SAs do not originate from native RNase A monomer or from oligomers characterized by the exclusive presence of the C-terminus swapping of the enzyme subunits as well. Instead, the swapping of at least two subunits’ N-termini is mandatory to produce them. Through immunoblotting, SAs are confirmed to derive from RNase A even if they retain only low ribonucleolytic activity. Then, their interaction registered with Thioflavin-T (ThT), in addition to TEM analyses, indicate SAs are large and circular but not “amyloid-like” derivatives. This confirms that RNase A acts as an “auto-chaperone”, although it displays many amyloid-prone short segments, including the 16–22 loop included in its N-terminus. Therefore, we hypothesize the opening of RNase A N-terminus, and hence its oligomerization through 3D-DS, may represent a preliminary step favoring massive RNase A aggregation. Interestingly, this process is slow and requires low temperatures to limit the concomitant oligomers’ dissociation to the native monomer. These data and the hypothesis proposed are discussed in the light of protein aggregation in general, and of possible future applications to contrast amyloidosis.

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“…104,422−430 Runaway domain swapping and end-to-end domain stacking are the two main structural mechanisms leading to the emergence of protein filaments that have been categorized in nature. 431 In the context of protein assembly engineering, domain swapping, discussed in section 3.1.1 in the context of protein dimer design, is also relevant to the development of protein materials formed by fibrilization. 432 Genetic protein fusion is another strategy that relies on existing protein interfaces for assembly design (sections 2.2.1 and 3.2.3).…”

Section: Extended 1d Assembliesmentioning

confidence: 99%

Protein Assembly by Design

et al. 2021

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Proteins are nature’s primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

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Atomic insights into the genesis of cellular filaments by globular proteins

Cited by 5 publications

References 61 publications

Filamentation of asparagine synthetase in Saccharomyces cerevisiae

Filamentation of asparagine synthetase in Saccharomyces cerevisiae

Slow Evolution toward “Super-Aggregation” of the Oligomers Formed through the Swapping of RNase A N-Termini: A Wish for Amyloidosis?

Protein Assembly by Design

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