The team, led by Marios G. Krokidis, combined AlphaFold-based structure prediction, the disorder-focused FuzPred algorithm, and HADDOCK molecular docking simulations to compare wild-type FUS with three mutant variants: G156E, R234L, and R521C. Each mutation sits in a different functional region of the 526-residue protein, which is largely built from intrinsically disordered regions — stretches that never settle into one rigid shape but instead constantly sample many conformations. FUS uses this flexibility to bind RNA, regulate transcription, participate in DNA damage repair, and shuttle between the nucleus and cytoplasm.

The structural comparison revealed that none of the mutations causes a dramatic collapse of the protein’s folded domains. Global backbone deviations, measured on high-confidence residues, ranged from about 5.5 angstroms for R234L to roughly 15.4 angstroms for R521C, but these values mostly reflect changes in how the intact folded domains — such as the RNA recognition motif and zinc finger — are oriented relative to one another through flexible linkers, not classical misfolding. The mutations themselves all fall in regions that AlphaFold flags as low-confidence, consistent with their intrinsically disordered character.

More telling were the local measurements. Solvent-accessible surface area calculations showed that all three mutants expose additional surface to the aqueous environment, with G156E and R521C producing the largest increases — 104.24 and 108.44 square angstroms respectively — and strongly negative hydrophobicity-weighted values, indicating that hydrophobic patches are being pushed into contact with water. The authors suggest this creates a thermodynamic drive to bury those patches through aberrant intermolecular aggregation, a route that could push FUS away from its native dynamic state and toward pathological solid-like phase transitions.

The FuzPred analysis sharpened the picture. For each residue, the algorithm estimates the probability of a disorder-to-order transition upon binding (pDO), the probability of remaining disordered (pDD), and the multiplicity of binding modes (MBM), which captures how many different interaction geometries a region can explore. When the researchers subtracted the wild-type profile from each mutant’s, the global differences were tiny — but the local changes within ten residues of each mutation site were clearly visible. All three mutations reduced local pDD and increased local MBM, suggesting a loss of the protein’s healthy, fuzzy binding behavior and a drift toward less coordinated, more promiscuous interaction patterns.

The docking simulations then connected these local disorder changes to concrete functional consequences. For R521C, which sits in the C-terminal proline-tyrosine nuclear localization signal, the team docked the NLS peptide against Transportin-1, the nuclear import receptor that normally carries FUS into the nucleus. The wild-type peptide bound with a HADDOCK score of −87.8 ± 3.4 kcal/mol, while the R521C mutant scored −79.5 ± 3.6 — weaker, despite actually presenting a slightly larger buried surface area. The energy breakdown showed the mutant’s electrostatic contribution dropped sharply, from −382.9 to −264.5 kcal/mol, indicating that replacing a positively charged arginine with cysteine undermines the charge complementarity that drives recognition. This aligns with earlier experimental and computational work showing that R521C reduces Transportin-1 affinity and causes FUS to accumulate in the cytoplasm, a major pathogenic step in ALS.

For G156E, which lies just upstream of the RGG1 RNA-binding domain, the team docked a 60-residue peptide against a 23-nucleotide RNA fragment. The wild-type complex achieved a HADDOCK score of −74.7 ± 1.6 kcal/mol with a buried surface of roughly 1,736 square angstroms, reflecting the multivalent contacts typical of RGG-mediated RNA recognition. The G156E mutant scored −61.6 ± 5.7, with a smaller interface of about 1,401 square angstroms. The authors attribute this to the added glutamate’s negative charge sitting close to the RNA phosphate backbone, increasing electrostatic repulsion and weakening the interaction. Because RGG domains help drive RNA-dependent phase separation and the formation of ribonucleoprotein granules, weakening these contacts could destabilize normal condensates and promote the misregulated RNA metabolism seen in ALS.

R234L, located in the intrinsically disordered RGG2 domain, could not be docked in the conventional sense because no experimentally determined FUS–RNA complex involving that region exists, and standard docking platforms require well-defined structural templates. Instead, the researchers interpreted its effects through the disorder analysis, which showed a local reduction in pDD — a loss of the native, functional flexibility that RGG domains rely on for multivalent RNA recognition. Removing an arginine from this positively charged motif would be expected to diminish both electrostatic attraction and cation–π interactions with RNA, consistent with the mutation’s association with disrupted RNA metabolism.

Taken together, the findings support a view of FUS-related ALS in which pathogenicity arises not from wholesale misfolding but from localized rearrangements in intrinsic disorder, binding versatility, and molecular recognition. Each mutation prunes a different functional modality — R521C compromises nuclear import, G156E weakens RNA binding, R234L erodes RGG2-mediated interactions — yet all three converge on the same cellular outcome: impaired nucleocytoplasmic distribution, altered stress granule behavior, and a tendency toward pathological aggregation. The authors caution that AlphaFold-derived models of intrinsically disordered regions should be treated as plausible conformational hypotheses rather than definitive structures, and they propose extending the approach with molecular dynamics simulations, multiple RNA sequence contexts, and integration with experimental data from NMR, cross-linking, and cellular localization assays. The same computational framework could also be applied to other disordered ALS proteins such as TDP-43 and hnRNPA1, offering a route toward therapies that restore protein localization and RNA homeostasis rather than simply blocking aggregation.

Subject of Research: Computational analysis of how ALS-associated FUS mutations alter conformational dynamics, intrinsic disorder, and molecular interactions

Article Title: ALS-associated FUS mutations induce site-specific alterations in conformational dynamics and molecular interactions

Article References: Amourgianos, C., Exarchos, T. P., Vlamos, P., & Krokidis, M. G. (2026). ALS-associated FUS mutations induce site-specific alterations in conformational dynamics and molecular interactions. Frontiers in Chemical Biology, 5, Article 1851848. https://doi.org/10.3389/fchbi.2026.1851848

Image Credits: AI Generated

DOI: 10.3389/fchbi.2026.1851848

Keywords: ALS, FUS, intrinsically disordered proteins, AlphaFold, FuzPred, HADDOCK, molecular docking, RNA binding, nuclear import, Transportin-1, phase separation, neurodegeneration

The signal recognition particle, or SRP, is one of biology’s most conserved devices. In its eukaryotic form it is a ribonucleoprotein complex built from six proteins and a single SRP RNA, and its day job is to escort nascent secretory and membrane proteins to the endoplasmic reticulum, pausing translation just long enough to hand each growing polypeptide to its proper translocation channel. Since Walter and Blobel first purified the complex from dog pancreas more than four decades ago, SRP has served as a textbook example of coordinated protein and RNA function. Yet a curious feature of its life cycle has long intrigued cell biologists: unlike most cytoplasmic machines, the eukaryotic SRP assembles inside the nucleus, specifically within the nucleolus, where its RNA and protein components must converge before the finished particle is exported back out to the cytoplasm.

That nuclear assembly step creates an obvious logistical problem. SRP proteins are synthesized on cytoplasmic ribosomes, so each one must be imported back into the nucleus before it can join the particle. In baker’s yeast, genetic and cell biological work showed that SRP biogenesis involves import of the SRP proteins into the nucleolus, assembly with the SRP RNA, and export mediated by the exportin Xpo1p. In mammalian cells, SRP19 has been shown to enter the nucleus with the help of importin 8 and transportin. But while indirect studies pointed to import receptors as the gatekeepers for SRP protein traffic, no one had demonstrated a direct physical interaction between an import receptor and an SRP protein in a reconstituted biochemical system. The new paper closes that gap, and it does so in an organism where the stakes are measured in hundreds of thousands of lives a year.

Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, depends on a functional SRP to build the exported and membrane proteins it needs to remodel its host red blood cell. Previous work by some of the same authors had characterized the parasite’s SRP components and showed that ivermectin, an antiparasitic drug known to block importin α/β-mediated nuclear import, disrupts the nucleocytoplasmic shuttling of the parasite’s SRP and kills the cultured parasites. Follow-up studies from collaborating groups demonstrated that importin α inhibitors act against differentiated stages of both P. falciparum and the related apicomplexan Toxoplasma gondii. What remained missing was the molecular handhold: proof that a specific SRP protein docks directly onto the parasite’s importin α, the way classical nuclear localization signal-containing cargoes do.

To obtain that proof, the researchers took a deliberately reductionist approach. They cultivated P. falciparum 3D7 parasites in continuous in vitro culture, then amplified the coding sequence of SRP 14 from synthesized complementary DNA and the coding sequence of importin α from genomic DNA. The amplified genes were cloned into bacterial expression vectors and the recombinant proteins were produced in Escherichia coli and purified. Importin α was tagged with glutathione S-transferase and immobilized on glutathione-agarose resin, providing a solid-phase platform onto which increasing concentrations of SRP 14 could be presented. Binding was then assessed across a concentration series, an experimental design that allows the strength and saturability of the interaction to be judged rather than merely its presence or absence.

The result was unambiguous. SRP 14 bound to immobilized importin α in a concentration-dependent manner, establishing for the first time a direct interaction between an import receptor and a eukaryotic SRP protein. This matters because binding assays conducted with purified components eliminate the ambiguity that shadows cell-based observations, where a cargo might reach the nucleus through indirect associations, bridging proteins, or parallel import pathways. By showing that the two purified parasite proteins recognize each other on their own, the study elevates SRP 14 to the status of a bona fide importin α cargo candidate and implies that the classical import pathway, rather than a specialized route, likely delivers this SRP subunit to the site of particle assembly in the parasite.

The technical details of the interaction are consistent with what is known about importin α biology. Importin α recognizes cargoes bearing classical nuclear localization signals, short stretches of basic amino acids that come in monopartite and bipartite flavors, and structural work has revealed six distinct classes of such signals that occupy different binding grooves on the receptor. Whether the importin α-binding determinant of P. falciparum SRP 14 conforms to one of these canonical classes, or instead exploits an unusual sequence feature, remains to be mapped, and the paper does not resolve that question. Similarly, the identity of the adaptor that would complete the full import cycle, namely importin β and the Ran GTPase system that releases cargo inside the nucleus, lies beyond the scope of the present experiments. What the study establishes is the anchor point of the pathway: the cargo-receptor contact itself.

Beyond the biological conclusion, the authors contribute a methodological advance that may prove broadly useful. In parallel with the glutathione-agarose format, they developed a binding assay in a standard 96-well plate, with importin α immobilized in the wells and SRP 14 titrated across them. The format converts a bench-scale binding experiment into something approaching a screening platform, requiring modest amounts of protein and no specialized detection instrumentation beyond standard plate readers and protein quantification by methods such as the linearized Bradford assay. Because the authors describe it as cost-effective and designed to study the binding of importin α cargoes generally, it could be adapted to hunt for small molecules that disrupt cargo-receptor contacts, a strategy already validated by AlphaScreen-based high-throughput assays for nuclear import inhibitors developed in other systems.

That screening angle connects directly to a therapeutic opportunity. Importin α/β-mediated nuclear import has emerged as a validated drug target in pathogens as diverse as HIV-1 and dengue virus, and ivermectin’s ability to inhibit this pathway has been linked to antiparasitic effects against P. falciparum. If SRP assembly in the parasite genuinely depends on importin α ferrying SRP 14 into the nucleus, then molecules that selectively block the SRP 14-importin α interface would strike at a step that is essential for the parasite’s protein-targeting capacity while having no equivalent target in the human red blood cell, which lacks a nucleus altogether. The plate-based assay reported here offers a concrete starting point for identifying such inhibitors.

Caveats remain, and the authors are careful about them. The study reports binding, not nuclear import in living parasites, and it does not demonstrate that disrupting the interaction kills the parasite or that SRP 14 carries a functional nuclear localization signal in vivo. Confirming the physiological relevance will require cellular studies, ideally genetic disruption of the interaction interface followed by readouts of SRP assembly, protein export, and parasite viability. Still, the conceptual contribution is clear and cleanly made: the missing molecular link between the malaria parasite’s protein-targeting machine and its nuclear transport apparatus has now been forged in vitro. For a field that has spent decades dissecting SRP in yeast and mammalian cells, watching the same story play out in one of humanity’s oldest adversaries is a reminder that even the most conserved corners of cell biology can yield new leverage against disease.

Subject of Research: Direct binding between signal recognition particle 14 and importin α in Plasmodium falciparum and its implications for nuclear import of SRP proteins

Article Title: Signal recognition particle 14 binds to importin α in Plasmodium falciparum

Article References: Vikash, A., Sonsy, & Panchal, M. (2026). Signal recognition particle 14 binds to importin α in Plasmodium falciparum. Molecular Biology Reports, 53(1), Article 1553. https://doi.org/10.1007/s11033-026-12676-z

Image Credits: AI Generated

DOI: 10.1007/s11033-026-12676-z

Keywords: Plasmodium falciparum, signal recognition particle 14, importin alpha, nuclear import, nucleocytoplasmic transport, malaria, SRP biogenesis, binding assay, protein trafficking, nuclear localization signal, ivermectin, molecular biology

Phase separation is the physical phenomenon by which a well-mixed solution splits into distinct phases, the way oil separates from vinegar in a shaken bottle of salad dressing. In cells, proteins containing intrinsically disordered, low-complexity domains can drive the formation of membraneless compartments called condensates, which concentrate specific molecules without any enclosing lipid membrane. Nucleoli, stress granules and nuclear speckles all form this way. The key property of healthy condensates is dynamism: molecules diffuse in and out, and the entire assembly can dissolve within seconds or minutes once conditions change. This liquid-like behavior depends on weak, multivalent interactions among the low-complexity domains, which constantly break and reform.

The trouble begins when those weak interactions stop being weak and transient. The review describes how, in ALS, condensates formed by RNA-binding proteins such as FUS and TDP-43 progressively lose their reversibility, maturing from liquid droplets into gel-like states and eventually into solid fibrillar aggregates that are hallmarks of the diseased motor neuron. This liquid-to-solid transition, sometimes called pathological hardening, is driven by the same low-complexity domains that make condensates form in the first place. Given time, the transient beta-sheet-like contacts within these domains can lock into stable structures, converting a dynamic organelle into an irreversible inclusion that the cell cannot dismantle.

What makes the new review distinctive is its emphasis on the layers of cellular regulation that normally prevent this maturation. The authors assemble evidence that molecular chaperones, best known for helping newly made proteins fold, also patrol condensates. Heat shock protein 70 family members, for example, can bind exposed hydrophobic stretches within condensates, remodel their internal organization and keep the assemblies fluid. Chaperone activity thereby extends the window in which a condensate remains reversible, buying the cell time to dissolve it before aggregation becomes permanent. When chaperone capacity is overwhelmed or declines, as it does with age and stress, that window narrows.

Nuclear import receptors form a second, perhaps more surprising, line of defense. Karyopherin-beta2, the receptor that ferries FUS into the nucleus, does more than transport. It binds directly to the proline-tyrosine nuclear localization signal within FUS and, in doing so, physically shields the low-complexity domain from engaging in the multivalent contacts that drive phase separation and fibrillization. In effect, the import receptor acts as a portable anti-aggregation chaperone, keeping FUS soluble during its journeys through the cytoplasm. The review highlights how this mechanism illustrates a broader principle: compact folded domains can modulate the behavior of disordered regions they are physically linked to or bound against.

The proteostasis network supplies a third layer of regulation. Enzymatic components such as protein disulfide isomerase and peptidyl-prolyl cis-trans isomerase A can alter the conformational state of proteins inside or near condensates, while ubiquilin-like protein 2, an ALS-linked protein, helps shuttle ubiquitinated cargo between condensates and the protein degradation machinery. Optineurin, another ALS-associated factor, participates in autophagic clearance of aggregates. Together these systems form a quality-control pipeline that continuously remodels and removes material from condensates, limiting the residence time of any given molecule and thereby reducing the probability that transient contacts will ripen into stable aggregates.

The review then turns to one of the most devastating genetic insults in ALS: the hexanucleotide repeat expansion in the C9ORF72 gene, the most common known cause of familial disease. This expansion produces arginine-rich dipeptide repeat proteins, and these short, highly basic peptides are potent modifiers of phase behavior. They can seed the condensation of RNA-binding proteins and, critically, impair nuclear import pathways, including the transport receptors that keep FUS in check. The result is a double hit: more condensation is promoted at the same time as the systems that would normally reverse it are disabled. The authors present this as a mechanistic explanation for why C9ORF72 pathology so closely resembles the FUS and TDP-43 proteinopathies seen across the ALS spectrum.

Perhaps the most forward-looking section of the review concerns zinc finger domains. Recent structural and biophysical studies suggest that these small, compact, folded modules can recognize specific polymer states of low-complexity domains and constrain their growth. Rather than dissolving condensates outright, zinc finger domains appear to cap or crosslink the polymers in ways that limit further elongation and material transition. This supports what the authors describe as a model in which structured domains act as modulators of higher-order assemblies, reading the physical state of a condensate and restraining its maturation. If confirmed across multiple ALS-associated proteins, this recognition mechanism could represent an entirely new regulatory vocabulary that cells use to manage their liquid organelles.

The therapeutic implications are considerable. Most ALS drug development has targeted downstream events, such as oxidative stress, excitotoxicity or the aggregates themselves. The framework laid out by the Nara Medical University team suggests an upstream strategy: preserve or restore condensate homeostasis. Enhancing chaperone activity, boosting nuclear import, supporting proteostasis components or mimicking the polymer-capping behavior of zinc finger domains could all, in principle, keep pathological proteins in their reversible, harmless state before fibrils ever form. Because the same regulatory principles appear to govern TDP-43, FUS and C9ORF72-related pathology, a therapy aimed at condensate homeostasis might cut across the genetic subtypes of the disease rather than addressing them one by one.

Cautious optimism is warranted. The review is a synthesis of mechanistic studies rather than a demonstration of efficacy in patients, and the authors themselves frame their conclusions as a model to be tested: clarifying how chaperones, import receptors, proteostasis enzymes and structured domains operate across ALS-associated proteins remains the task ahead. Yet the conceptual shift is hard to overstate. ALS, on this view, is not merely a disease of misfolded proteins but a disease of lost reversibility, in which the cell’s capacity to keep its own internal liquids liquid has been eroded. Understanding and reinforcing that capacity may prove to be one of the most promising directions in the search for effective treatments.

Subject of Research: Regulation of biological phase separation by molecular chaperones and related factors in amyotrophic lateral sclerosis

Article Title: Regulation of biological phase separation by molecular chaperones and related factors in amyotrophic lateral sclerosis

Article References: Iguchi, N., Isozumi, N., Sugie, K., & Mori, E. (2026). Regulation of biological phase separation by molecular chaperones and related factors in amyotrophic lateral sclerosis. BMC Medicine. https://doi.org/10.1186/s12916-026-05261-5

Image Credits: AI Generated

DOI: 10.1186/s12916-026-05261-5

Keywords: amyotrophic lateral sclerosis, phase separation, molecular chaperones, TDP-43, FUS, C9ORF72, nuclear import, proteostasis, protein aggregation, RNA-binding proteins, zinc finger domains, condensates