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The cell is a crowded environment where a relevant fraction of the available space is occupied by proteins, nucleic acids, and metabolites. Here we discuss recent advancements in the understanding of crowding effects on intrinsically disordered proteins. Differently from their structured counterparts, these proteins do not adopt a stable three‐dimensional structure and remain flexible and dynamic in solution. The physics of polymers and colloids provides a framework to interpret how crowding modulates conformations, dynamics, and interactions of disordered proteins. Flory‐Huggins models enable rationalizing the different degree of compaction induced by crowding agents in terms of depletion interactions. The same interactions modulate the diffusion of the disordered proteins in a crowded milieu and the association and dissociation rates when interacting with a ligand. Altogether, this theoretical framework provides new insights into the interpretation of the effects of the cellular environment on disordered proteins. [ABSTRACT FROM AUTHOR]

The structure of a hydrogel network determines its ability to dissipate stress upon deformation, as well as its ability to swell in water. By designing systems with cross-linkable thiol groups in the monomers, radical thiol–ene chemistry was used to form controlled networks for acrylamide monomers. The use of radical thiol–ene chemistry effectively suppressed homo-polymerization of the bis(acrylamide) monomer and resulted in networks of alternating thiol and acrylamide monomers. Additionally, if the stoichiometry between the monomers is controlled, the network should approach that of ideality. In the case of bis(acrylamide) monomers, the incorporation of hydrogen-bond donors into the network creates a single network hydrogel with the benefits of high strength and ductility from the simultaneous incorporation of chemical and physical cross-links. Additionally, this strategy suppresses the formation of homo-polymerization in the acrylamide monomer to achieve an alternating network, which is supported with NMR characterization of base-digested fragments. For three different monomer compositions, the resulting gels had high compressive strength (up to 40 MPa) and tunable mechanical properties. The high mechanical strength of the 1 : 1, thiol : ene gel composition is due to the uniform distribution of cross-links, which creates defect-free networks for efficient stress transfer. The present one-pot synthetic strategy toward controlled gel networks affords monomer versatility and synthetic ease, as well as the potential for mechanically robust materials. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 Nucleocapsid protein (N) performs several functions during the viral lifecycle, including transcription regulation and viral genome encapsulation. We hypothesized that N toggles between these functions via phosphorylation-induced conformational change, thereby altering N interactions with membranes and RNA. We found that phosphorylation changes how biomolecular condensates composed of N and RNA interact with membranes: phosphorylated N (pN) condensates form thin films, while condensates with unmodified N are engulfed. This partly results from changes in material properties, with pN forming less viscous and elastic condensates. The weakening of protein-RNA interaction in condensates upon phosphorylation is driven by a decrease in binding between pN and unstructured RNA. We show that phosphorylation induces a conformational change in the serine/arginine-rich region of N that increases interaction between pN monomers and decreases nonspecific interaction with RNA. These findings connect the conformation, material properties, and membrane-associated states of N, with potential implications for COVID-19 treatment., Competing Interests: Declaration of Interests The authors declare no competing interests.

The cardiac troponin complex, composed of troponins I, T, and C, plays a central role in regulating the calcium-dependent interactions between myosin and the thin filament. Mutations in troponin can cause cardiomyopathies; however, it is still a major challenge to connect how changes in sequence affect troponin's function. Recent high-resolution structures of the thin filament revealed critical insights into the structure-function relationship of troponin, but there remain large, unresolved segments of troponin, including the troponin-T linker region that is a hotspot for cardiomyopathy mutations. This linker region is predicted to be intrinsically disordered, with behaviors that are not well described by traditional structural approaches; however, this proposal has not been experimentally verified. Here, we used a combination of single-molecule Förster resonance energy transfer (FRET), molecular dynamics simulations, and functional reconstitution assays to investigate the troponin-T linker region. We show that in the context of both isolated troponin and the fully regulated troponin complex, the linker behaves as a dynamic, intrinsically disordered region. This region undergoes polyampholyte expansion in the presence of high salt and distinct conformational changes during the assembly of the troponin complex. We also examine the ΔE160 hypertrophic cardiomyopathy mutation in the linker and demonstrate that it does not affect the conformational dynamics of the linker, rather it allosterically affects interactions with other troponin complex subunits, leading to increased molecular contractility. Taken together, our data clearly demonstrate the importance of disorder within the troponin-T linker and provide new insights into the molecular mechanisms driving the pathogenesis of cardiomyopathies., Competing Interests: CONFLICT OF INTEREST STATEMENT All experiments were conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest. M.J.G. acknowledges research support from Edgewise Therapeutics unrelated to this project.

The SARS-CoV-2 Nucleocapsid (N) is a 419 amino acids protein that drives the compaction and packaging of the viral genome. This compaction is aided not only by protein-RNA interactions, but also by protein-protein interactions that contribute to increasing the valence of the nucleocapsid protein. Here, we focused on quantifying the mechanisms that control dimer formation. Single-molecule Förster Resonance Energy Transfer enabled us to investigate the conformations of the dimerization domain in the context of the full-length protein as well as the energetics associated with dimerization. Under monomeric conditions, we observed significantly expanded configurations of the dimerization domain (compared to the folded dimer structure), which are consistent with a dynamic conformational ensemble. The addition of unlabeled protein stabilizes a folded dimer configuration with a high mean transfer efficiency, in agreement with predictions based on known structures. Dimerization is characterized by a dissociation constant of ~ 12 nM at 23 °C and is driven by strong enthalpic interactions between the two protein subunits, which originate from the coupled folding and binding. Interestingly, the dimer structure retains some of the conformational heterogeneity of the monomeric units, and the addition of denaturant reveals that the dimer domain can significantly expand before being completely destabilized. Our findings suggest that the inherent flexibility of the monomer form is required to adopt the specific fold of the dimer domain, where the two subunits interlock with one another. We proposed that the retained flexibility of the dimer form may favor the capture and interactions with RNA, and that the temperature dependence of dimerization may explain some of the previous observations regarding the phase separation propensity of the N protein.

The ε4-allele variant of apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimer's disease, although it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of pathogenicity remain undetermined due to limited structural information. Previous studies have led to conflicting models of the C-terminal region positioning with respect to the N-terminal domain across isoforms largely because the data are potentially confounded by the presence of heterogeneous oligomers. Here, we apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically detailed model of monomeric ApoE4 and probe the effect of lipid association. Importantly, our approach overcomes previous limitations by allowing us to work at picomolar concentrations where only the monomer is present. Our data reveal that ApoE4 is far more disordered and extended than previously thought and retains significant conformational heterogeneity after binding lipids. Comparing the proximity of the N- and C-terminal domains across the three major isoforms (ApoE4, ApoE3, and ApoE2) suggests that all maintain heterogeneous conformations in their monomeric form, with ApoE2 adopting a slightly more compact ensemble. Overall, these data provide a foundation for understanding how ApoE4 differs from nonpathogenic and protective variants of the protein.