Contributions of the N-terminal intrinsically disordered region of the severe acute respiratory syndrome coronavirus 2 nucleocapsid protein to RNA-induced phase separation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein is an essential structural component of mature virions, encapsulating the genomic RNA and modulating RNA transcription and replication. Several of its activities might be associated with the protein's ability to undergo liquid–liquid phase separation. NSARS-CoV-2 contains an intrinsically disordered region at its N-terminus (NTE) that can be phosphorylated and is affected by mutations found in human COVID-19 infections, including in the Omicron variant of concern. Here, we show that NTE deletion decreases the range of RNA concentrations that can induce phase separation of NSARS-CoV-2. In addition, deletion of the prion-like NTE allows NSARS-CoV-2 droplets to retain their liquid-like nature during incubation. We further demonstrate that RNA-binding engages multiple parts of the NTE and changes NTE's structural properties. The results form the foundation to characterize the impact of N-terminal mutations and post-translational modifications on the molecular properties of the SARS-CoV-2 nucleocapsid protein

Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics

Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and alpha-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior

The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling

Cellular RNA polymerases RNAPs can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. In Bacillus subtilis, the RNAP amp; 948; subunit and NTPase HelD have been implicated in RNAP recycling. We structurally analyzed Bacillus subtilis RNAP amp; 948; HelD complexes. HelD has two long arms a Gre cleavage factor like coiled coil inserts deep into the RNAP secondary channel, dismantling the active site and displacing RNA, while a unique helical protrusion inserts into the main channel, prying the amp; 946; and amp; 946; amp; 8242; subunits apart and, aided by amp; 948;, dislodging DNA. RNAP is recycled when, after releasing trapped nucleic acids, HelD dissociates from the enzyme in an ATP dependent manner. HelD abundance during slow growth and a dimeric RNAP amp; 948; HelD 2 structure that resembles hibernating eukaryotic RNAP I suggest that HelD might also modulate active enzyme pools in response to cellular cue

Conformational Dynamics and Antigenicity in the Disordered Malaria Antigen Merozoite Surface Protein 2

Merozoite surface protein 2 (MSP2) of Plasmodium falciparum is an abundant, intrinsically disordered protein that is GPI-anchored to the surface of the invasive blood stage of the malaria parasite. Recombinant MSP2 has been trialled as a component of a malaria vaccine, and is one of several disordered proteins that are candidates for inclusion in vaccines for malaria and other diseases. Nonetheless, little is known about the implications of protein disorder for the development of an effective antibody response. We have therefore undertaken a detailed analysis of the conformational dynamics of the two allelic forms of MSP2 (3D7 and FC27) using NMR spectroscopy. Chemical shifts and NMR relaxation data indicate that conformational and dynamic properties of the N- and C-terminal conserved regions in the two forms of MSP2 are essentially identical, but significant variation exists between and within the central variable regions. We observe a strong relationship between the conformational dynamics and the antigenicity of MSP2, as assessed with antisera to recombinant MSP2. Regions of increased conformational order in MSP2, including those in the conserved regions, are more strongly antigenic, while the most flexible regions are minimally antigenic. This suggests that modifications that increase conformational order may offer a means to tune the antigenicity of MSP2 and other disordered antigens, with implications for vaccine design

Surprising absence of strong homonuclear coupling at low magnetic field explored by two-field nuclear magnetic resonance spectroscopy

Strong coupling of nuclear spins, which is achieved when their scalar coupling 2πJ is greater than or comparable to the difference Δω in their Larmor precession frequencies in an external magnetic field, gives rise to efficient coherent longitudinal polarization transfer. The strong coupling regime can be achieved when the external magnetic field is sufficiently low, as Δω is reduced proportional to the field strength. In the present work, however, we demonstrate that in heteronuclear spin systems these simple arguments may not hold, since heteronuclear spin–spin interactions alter the Δω value. The experimental method that we use is two-field nuclear magnetic resonance (NMR), exploiting sample shuttling between the high field, at which NMR spectra are acquired, and the low field, where strong couplings are expected and at which NMR pulses can be applied to affect the spin dynamics. By using this technique, we generate zero-quantum spin coherences by means of a nonadiabatic passage through a level anticrossing and study their evolution at the low field. Such zero-quantum coherences mediate the polarization transfer under strong coupling conditions. Experiments performed with a 13C-labeled amino acid clearly show that the coherent polarization transfer at the low field is pronounced in the 13C spin subsystem under proton decoupling. However, in the absence of proton decoupling, polarization transfer by coherent processes is dramatically reduced, demonstrating that heteronuclear spin–spin interactions suppress the strong coupling regime, even when the external field is low. A theoretical model is presented, which can model the reported experimental results.</p

Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana

Multistep phosphorelay MSP cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ INDEPENDENT 1 CKI1RD from Arabidopsis thaliana. We observed that the crystal structures of free, Mg2 bound, and beryllofluoridated CKI1RD a stable analogue of the labile phosphorylated form were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2 binding and beryllofluoridation alter the conformational equilibrium of the amp; 946;3 amp; 945;3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the amp; 946;3 amp; 945;3 loop while keeping the active site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the amp; 946;3 amp; 945;3 loop directly interacts with the ATP binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the amp; 946;3 amp; 945;3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic amp; 946;3 amp; 945;3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain ETR1RD exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MS