Abstract Attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy of proteins in aqueous solution is often limited by water absorption and other optical artifacts. To overcome these limitations, we evaluated the structural features and hydrogen-deuterium exchange (HDX) kinetics of the α -helical protein GCN4 in both hydrated (wet) and vacuum-dried (dry) states. While solvent heavily mask the second-derivative spectra of wet samples, vacuum drying yielded a thin, protein-rich film on the ATR crystal, significantly enhancing the signal-to-noise ratio and resolving the protein features without altering the native structure. Dry-state analysis clearly resolved the Amide I, Amide II, and deuterium-shifted Amide II’ (1450 cm −1 ) bands. Notably, second-derivative analysis of the dry spectra of the HDX samples revealed a bimodal Amide I distribution consisting of a stationary band at 1653 cm −1 from the solvent-inaccessible regions and an isotopically sensitive band shifting from 1648 cm −1 to 1644 cm −1 from solvent-accessible regions. These results demonstrate that vacuum-dried ATR-FTIR spectroscopy effectively eliminates solvent masking, providing the spectral clarity required to resolve discrete α -helical sub-populations after deuteration.

Abstract DNA topology is a key regulator of chromatin structure and transcription, yet its direct role in transcription factor recognition remains unclear. Here, we investigate how distinct DNA topological states modulate binding of the Saccharomyces cerevisiae bZIP transcription factor GCN4 using topologically defined plasmids. By combining, complementary biochemical approaches, including Bio-Layer Interferometry applied here for the first time to topology-dependent protein–DNA interactions, we show that DNA supercoiling directly reshapes GCN4–DNA recognition. Positively supercoiled DNA forms more stable and persistent complexes, whereas negatively supercoiled DNA retains greater conformational heterogeneity. To interpret these effects, we performed multiscale molecular simulations. Coarse-grained simulations of plasmids recapitulate the global topology-dependent trends observed experimentally, while matched minicircle models reproduce the same behaviour at the local scale. In strong agreement with experimental data, simulations reveal that DNA topology modulates the conformational ensemble of the GCN4 basic region. Overall, positively supercoiled DNA promotes a more ordered binding mode and localized protein distribution, whereas negatively supercoiled DNA supports increased structural plasticity. These findings identify DNA topology as an active determinant of transcription factor recognition and provide a multiscale framework linking global DNA mechanics to local protein–DNA interactions. Graphical Abstract

This chapter is dedicated to analysing how biological nuclear magnetic resonance (NMR) has evolved in the more than 70 years from its discovery and to discussing some of the applications of this technique to biological systems. To restrict a vast field, we treat liquid-state NMR leaving out solid-state applications that, although very important, are less consolidated and still fast evolving. We focus in particular on studies in complex environments, such as in-cell and/or crowded environments, that is a subject in which NMR can give its very best. We provide examples of various applications and hopefully show how versatile the technique is. We also briefly discuss how NMR can be coupled with other techniques to expand its horizons, increasing the intrinsic potentialities of this powerful technique.

Liquid-liquid phase separation is widely invoked in transcriptional regulation, yet prevailing models attribute condensate formation primarily to intrinsically disordered activation domains rather than structured DNA-binding motifs. Here, we overturn this view by demonstrating that the isolated basic leucine zipper (bZIP) domain of the yeast transcription factor Gcn4 undergoes robust DNA-induced phase separation in the complete absence of its activation domain. Using small-angle X-ray scattering in combination with all-atom molecular dynamics simulations and ensemble optimization, we directly resolve the conformational landscape of the Gcn4 bZIP–DNA complex across coexisting dilute and condensed phases. Beyond the canonical uninterrupted helical conformation captured in crystal structures, we identify a previously unrecognized minor population featuring a pronounced helical kink at the basic region–leucine zipper junction. These findings establish DNA binding as a sufficient physical driver of bZIP phase separation and demonstrate that small-angle scattering can quantitatively interrogate protein conformational ensembles within biomolecular condensates, opening new avenues for the structural chemistry of phase-separated systems. ### Competing Interest Statement The authors have declared no competing interest. European Innovation Council, https://ror.org/05cx8cy07, 101046920 Swedish Research Council, https://ror.org/03zttf063, 2022-06725

Cognitive and behavioural symptoms associated with amyotrophic lateral sclerosis and frontotemporal spectrum disorders (ALS-FTSD) are thought to be driven, at least in part, by the pathological accumulation of TDP-43. Here we examine post-mortem tissue from six brain regions associated with cognitive and behavioural symptoms in a cohort of 30 people with sporadic ALS (sALS), a proportion (12/30) of which underwent standardized neuropsychological behavioural assessment as part of the Edinburgh Cognitive ALS Screen (ECAS). Overall, the behavioural screen performed as part of the ECAS predicted accumulation of pathological phosphorylated TDP-43 (pTDP-43) with 100% specificity and 86% sensitivity in behaviour-associated brain regions. Notably, of these regions, pathology in the amygdala was the most predictive correlate of behavioural dysfunction in sALS. In the amygdala of sALS patients, we show variation in morphology, cell-type predominance and severity of pTDP-43 pathology. Further, we demonstrate that the presence and severity of intra-neuronal pTDP-43 pathology, but not astroglial pathology, or phosphorylated Tau pathology, is associated with behavioural dysfunction. Cases were also evaluated using a TDP-43 aptamer (TDP-43APT), which revealed that pathology was not only associated with behavioural symptoms, but also with ferritin levels, a measure of brain iron. Intra-neuronal pTDP-43 and cytoplasmic TDP-43APT pathology in the amygdala is associated with behavioural symptoms in sALS. TDP-43APT staining intensity is also associated with increased ferritin, regardless of behavioural phenotype, suggesting that ferritin increases may occur upstream of clinical manifestation, in line with early TDP-43APT pathology, representing a potential region-specific imaging biomarker (e.g. volumetric or susceptibility-weighted MR imaging) of early disease in ALS.

Molecular crowding refers to the excluded volume restriction of the space available to molecules in a solution due to the high concentration of other molecules, particularly macromolecules like proteins and nucleic acids. This restriction of space, or excluded volume effect, leads to changes in the behavior and properties of the crowded molecules. In this chapter, we discuss how RNA affects crowding and is affected by it and describe techniques that allow us to study these phenomena. We also discuss methods to extract granules that can then be used to understand their components.

Neurodegeneration has traditionally been largely attributed to protein aggregation, yet ribonucleic acid (RNA) has emerged as an active driver of pathology. Expanded repeat RNAs, misregulated RNA-binding proteins, and aberrant RNA-protein interactions can directly or indirectly trigger neuronal dysfunction, although the distinction between the two mechanisms might, in some cases, be loose. RNA modulates prion-like aggregation, scaffolds liquid-liquid phase separation, and either promotes or inhibits protein assembly, depending on RNA sequence and structure. The aim of this review is to discuss our current understanding of RNA's dual role-as a facilitator of aggregation or as a potential therapeutic target- revealing new mechanistic insights into diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and spinocerebellar ataxias. We highlight RNA metabolism as a central determinant of neuronal vulnerability.

The conformational transition related to protein unfolding is often considered as the transition between the folded conformation and one unfolded form. However, there are many aspects that hint at a much richer and more complex unfolded state made of a conformational ensemble not only for the unfolded species but also during the unfolding process. Proteins often sample intermediate conformations that may retain elements of secondary structure, preserve part of the hydrophobic core, or display localized unfolding restricted to specific regions. During the unfolding pathway, there are often minor transitions involving local secondary-structure regions outside the hydrophobic core. Many researchers have also hypothesized the existence of one or more intermediates, albeit usually invisible because they are low populated. In the present Mini-Review, we re-examine critically crucial aspects of this fascinating problem starting from our own experience in protein stability and unfolding and revise the limitations and implications of the two-state model.

Annexins are a protein family well known to bind to phospholipids in a calcium-dependent way. They are involved in several different crucial cellular processes such as cell division, calcium signaling, membrane repair, vesicle trafficking, and apoptosis. Although RNA binding for some members of the family was reported long ago, it was only recently that it was shown that a common feature of the family is also the ability to bind RNA, a discovery that has added significantly to our perception of the cellular role of these proteins. In the present review, we discuss the properties of annexins under an updated light and the current knowledge on the RNA binding properties of annexins. We then focus specifically on annexin A11, because this is a less characterized member of the family but, at the same time, a potentially important component of the mRNA transport machinery in neurons. We hope to offer to the reader a more complete picture of the annexins' binding properties and new tools to evaluate the multifaceted functions of this important protein family.

The present work proposes an explanation for a recent observation that has conclusively proven that heavy water, that is, water containing the non-radioactive isotope of hydrogen deuterium, is mildly sweet, at variance with the tasteless common water. No firm explanation was proposed for this unexpected behavior. Yet, the subject is far from being an irrelevant curiosity, as the explanation of yet unidentified properties of the sweet receptor can help us to understand the molecular bases of food appreciation that have direct repercussions on pathologies such as diabetes and obesity. Here, a simple but convincing structural explanation of the taste of heavy water is proposed that is based on the influence of heavy water on the conformation of the active form of the receptor. The explanation requires the concept of "constitutive receptor activity", that is, a notion well accepted in many areas of pharmacology but clearly neglected in reference to taste receptors. We discuss how constitutive activity also explains other properties such as the recognition of sweet proteins that are several thousand times sweeter than small carbohydrates.

Yeast frataxin (Yfh1) is a small natural protein from yeast that has the unusual property of undergoing cold denaturation at temperatures above the freezing point of water when under conditions of low ionic strength. This peculiarity, together with remarkable resilience, allows the determination, for the whole protein as well as for individual residues, of the stability curve, that is the temperature dependence of the free energy difference between the unfolded and folded forms. The ease of measuring stability curves without the need to add denaturants or introduce ad hoc destabilizing mutations makes this protein an ideal 'tool' for investigating the influence of many environmental factors on protein stability. The present review aims at recapitulating all the open questions that Yfh1 has helped to address, including understanding the differences and commonalities of the cold, heat and pressure unfolded states. This protein thus offers a unique tool for studying aspects of protein stability so far been considered difficult to assess and provides important guidelines that could allow the identification of other similar systems.

TDP-43 protein is an RNA-binding protein linked to amyotrophic lateral sclerosis, frontotemporal dementia, and Alzheimer disease. While normally a protein that shuttles between the nucleus and cytoplasm, TDP-43 has recently been found also in extracellular vesicles. These are an important medium for cell-cell communication that allows the transfer of lipids, proteins, and genetic material among cells. An increasing concern in neurodegenerative diseases, however, is the possibility that extracellular vesicles can also provide an effective way to spread misfolded proteins that could "infect" other cells according to a "prion-like" mechanism. To characterize the interaction of TDP-43 with lipid membranes, we carried out a systematic biophysical study using a TDP-43 fragment lacking the first 84 N-terminal residues, called M85, and synthetic model phospholipid membranes. We utilized standard techniques, such as fluorescence and microscopy, complemented by neutron reflectivity measurements. Our results show that lipid charge affects the modality by which M85 interacts with membranes: a higher negative charge induces the protein to bind to the bilayer surface, promoting protein aggregation and decreasing lipid bilayer damage that this interaction causes. Thus, we speculate that the M85-lipid membrane interaction could play an important and previously undefined role in TDP-43-related neurodegenerative diseases.

Cytochrome c (Cyt-c), encoded by the CYCS gene, is crucial for electron transport, peroxidase activity, and apoptosis. Mutations in CYCS cause thrombocytopenia 4 (THC4), a disorder with low platelet counts. We have, for instance, recently described six Italian families with five different heterozygous missense CYCS variants. These mutations likely enhance peroxidase and apoptotic activities, yet the mechanisms causing reduced platelet production and increased apoptosis are unclear. This study investigates clinically-related Cyt-c variants using an integrated bioinformatics approach. Our findings reveal that all variants are at evolutionarily conserved sites, potentially disrupting Cyt-c function and contributing to disease phenotypes. Specific variants are predicted to affect phosphorylation (T20I, V21G, Y49H), and ubiquitination (G42S, A52T, A52V, T103I). Molecular dynamics simulations (500 ns) revealed significant structural deviations from the wild-type protein, with mutants showing reduced stability and increased unfolding and flexibility, particularly in the Ω-loops. These changes result in the displacement of the Ω-loops away from the heme iron, weakening critical hydrogen bonds and consequently opening the heme active site. This open conformation may enhance accessibility to small molecules such as H₂O₂, thereby promoting peroxidase activity, which may enhance apoptosis and likely impact megakaryopoiesis and platelet homeostasis in THC4.

Spinocerebellar ataxia type 3 (SCA3) is a rare inherited neurodegenerative disease caused by the expansion of a polyglutamine repeat in the protease ataxin-3 (Atx3). Despite extensive knowledge of the downstream pathophysiology, no disease-modifying therapies are currently available to halt disease progression. The accumulation of protein inclusions enriched in the polyQ-expanded Atx3 in neurons suggests that inhibiting its self-assembly may yield targeted therapeutic approaches. Here it is shown that a supramolecular tweezer, CLR01, binds to a lysine residue on a positively charged surface patch of the Atx3 catalytic Josephin domain. At this site, the binding of CLR01 decreases the conformational fluctuations of the distal flexible hairpin. This results in reduced exposure of the nearby aggregation-prone region, which overlaps with the substrate ubiquitin binding site and primes Atx3 self-assembly, ultimately delaying Atx3 amyloid fibril formation and reducing the secondary nucleation rate, a process linked to fibril proliferation and toxicity. These effects translate into the reversal of synapse loss in a SCA3 cultured cortical neuron model, an improved locomotor function in a C. elegans SCA3 model, and a delay in disease onset, accompanied by reduced severity of motor symptoms in a SCA3 mouse model. This study provides critical insights into Atx3 self-assembly, revealing a novel allosteric site for designing CLR01-inspired therapies targeting pathological aggregation pathways while sparing essential functional sites. These findings emphasize that targeting allosteric sites in amyloid-forming proteins may offer unique opportunities to develop safe therapeutic strategies for various protein misfolding disorders.

Annexins are a family of calcium-dependent phospholipid-binding proteins involved in crucial cellular processes such as cell division, calcium signaling, vesicle trafficking, membrane repair, and apoptosis. In addition to these properties, Annexins have also been shown to bind RNA, although this function is not universally recognized. In the attempt to clarify this important issue, we employed an integrated combination of experimental and computational approaches. Using the catRAPID algorithm, we accurately predicted known RNA-binding partners of Annexins, supported by experimental validation. We then constructed a virtual library of potential mRNA partners for Annexin A2, identifying regions within its structure directly involved in RNA binding. Beyond RNA interaction, some Annexins, notably AnxA7 and AnxA11, exhibit strong phase separation tendencies driven by their N-termini. These biophysical properties likely play roles in RNA trafficking and localization particularly in neurons, where they may influence processes such as synaptic plasticity, learning, and memory. Our predictions contribute to a deeper understanding of the Annexin function, emphasizing their potential impact on RNA regulation and cellular compartmentalization through phase separation and propose a powerful computational tool for the prediction of RNA-binding properties.

Proteins unfold under different environmental insults, among which are heat, cold, high pressure, and chaotropic agents. Understanding the mechanisms that determine unfolding under each of these conditions is an important problem that directly relates to the physical forces that determine the three-dimensional structure of a protein. Here, we studied a residue-specific description of the unfolding transitions of marginally stable yeast protein Yfh1 using high-pressure nuclear magnetic resonance. We compared the cold, heat, and pressure unfolded states and demonstrated what has up to now been only a hypothesis: the pressure-unfolded spectrum at room temperature shares features in common with that at low but not at high temperature and room pressure, suggesting a tighter similarity of the mechanisms and a similar role of hydration in these two processes. By exploring the phase diagram of the protein and mapping unfolding onto the three-dimensional structure of the protein, we also show that the pressure-induced unfolding pathways at low and high temperatures differ, suggesting a synergic mechanism between pressure- and temperature-induced denaturation. Our observations help us to reconstruct the structural events determining unfolding and distinguish the mechanisms that rule the different processes of unfolding.

Spinocerebellar ataxia type 3 (SCA3) is a rare neurodegenerative disorder caused by the expansion of a polyglutamine (polyQ) repeat in ataxin-3 (Atx3) for which no disease-modifying therapies are available. The presence of protein inclusions enriched in polyQ-expanded Atx3 in neurons suggests that inhibiting its self-assembly may provide targeted therapies. Here, it is demonstrated that the supramolecular tweezer CLR01 binds to a lysine residue on a positively charged patch of the Atx3 catalytic Josephin domain, decreasing conformational fluctuations of the distal helical hairpin, without altering its ubiquitin hydrolase activity. This reduces exposure of the aggregation-prone region that initiates Atx3 self-assembly, ultimately delaying Atx3 amyloid fibril formation and reducing the secondary nucleation rate, a process linked to fibril proliferation and toxicity. CLR01's effects translate into the reversal of synapse loss in SCA3 cultured cortical neuron model, improve locomotor function in a Caenorhabditis elegans SCA3 model, and delay disease onset with reduced severity of motor symptoms in a SCA3 mouse model. These insights reveal a novel allosteric site for developing CLR01-inspired therapies targeting pathological aggregation while preserving essential functional sites. They also highlight that targeting allosteric sites in amyloid-forming proteins may provide new opportunities for safe therapeutic strategies for various protein misfolding disorders.