Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA.

The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein.

Specific protein-RNA interactions are mostly preserved in biomolecular condensates.

Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS).

Relaxation-Assisted Magnetization Transfer Phenomena for a Sensitivity-Enhanced 2D NMR.

2D NOESY and TOCSY play central roles in contemporary NMR. We have recently discussed how solvent-driven exchanges can significantly enhance the sensitivity of such methods when attempting correlations between labile and nonlabile protons. This study explores two scenarios where similar sensitivity enhancements can be achieved in the absence of solvent exchange: the first one involves biomolecular paramagnetic systems, while the other involves small organic molecules in natural abundance.

Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility.

RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV).

Cross-Polarization Schemes for Improved Heteronuclear Transfers Involving Labile Protons in Biomolecular Solution NMR.

INEPT-based experiments are widely used for H→ N transfers, but often fail when involving labile protons due to solvent exchanges. J-based cross polarization (CP) strategies offer a more efficient alternative to perform such transfers, particularly when leveraging the H H exchange process to boost the H→ N transfer process. This leveraging, however, demands the simultaneous spin-locking of both H and H protons by a strong H RF field, while fulfilling the γ B =γ B Hartmann-Hahn matching condition.

A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2.

The pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein.

A denoising method for multidimensional magnetic resonance spectroscopy and imaging based on compressed sensing.

Both in spectroscopy and imaging, t-noise arising from instabilities such as temperature alterations, field-related frequency drifts, electronic and sample-spinning instabilities, or motions in in vivo experiments, affects many 2D Magnetic Resonance experiments. This work introduces a post-processing method that aims to attenuate t-noise, by suitably averaging multiple signals/representations that have been reconstructed from the sampled data. The ensuing Compressed Sensing Multiplicative (CoSeM) denoising starts from a fully sampled 2D MR data set, discards random indirect-domain points, and makes up for these missing, masked data, by a compressed sensing reconstruction of the now incompletely sampled 2D data set.

HORRENDOUS NMR: Establishing correlations in solution-state NMR by reinstating non-secular J-coupling terms.

Homonuclear isotropic mixing modules allow J-coupled spins to exchange magnetization even when separated by chemical shift offsets that exceed their couplings. This is exploited in TOtal Correlation SpectroscopY (TOCSY) experiments and its variants, which facilitate these homonuclear polarization exchanges by applying broadband RF pulses. These then establish an effective Hamiltonian in which chemical shift offsets are erased, while J-coupling terms -including flip-flop components- remain active.

H, C and N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2.

The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses.

On the potential of Fourier-encoded saturation transfers for sensitizing solid-state magic-angle spinning NMR experiments.

Chemical exchange saturation transfer (CEST) is widely used for enhancing the solution nuclear magnetic resonance (NMR) signatures of magnetically dilute spin pools, in particular, species at low concentrations undergoing chemical exchanges with an abundant spin pool. CEST's main feature involves encoding and then detecting weak NMR signals of the magnetically dilute spin pools on a magnetically abundant spin pool of much easier detection, for instance, the protons of HO. Inspired by this method, we propose and exemplify a methodology to enhance the sensitivity of magic-angle spinning (MAS) solid-state NMR spectra.

The Extended Hadamard Transform: Sensitivity-Enhanced NMR Experiments Among Labile and Non-Labile Hs of SARS-CoV-2-derived RNAs.

Hadamard encoded saturation transfer can significantly improve the efficiency of NOE-based NMR correlations from labile protons in proteins, glycans and RNAs, increasing the sensitivity of cross-peaks by an order of magnitude and shortening experimental times by ≥100-fold. These schemes, however, fail when tackling correlations within a pool of labile protons - for instance imino-imino correlations in RNAs or amide-amide correlations in proteins. Here we analyze the origin of the artifacts appearing in these experiments and propose a way to obtain artifact-free correlations both within the labile pool as well as between labile and non-labile Hs, while still enjoying the gains arising from Hadamard encoding and solvent repolarizations.

Heteronuclear transfers from labile protons in biomolecular NMR: Cross polarization, revisited.

INEPT- and HMQC-based pulse sequences are widely used to transfer polarization between heteronuclei, particularly in biomolecular spectroscopy: they are easy to setup and involve low power deposition. Still, these short-pulse polarization transfers schemes are challenged by fast solvent chemical exchange. An alternative to improve these heteronuclear transfers is J-driven cross polarization (J-CP), which transfers polarization by spin-locking the coupled spins under Hartmann-Hahn conditions.

Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs.

2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent-driven exchanges to enhance NOE correlations between exchangeable and non-exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons.

The Incorporation of Labile Protons into Multidimensional NMR Analyses: Glycan Structures Revisited.

Glycan structures are often stabilized by a repertoire of hydrogen-bonded donor/acceptor groups, revealing longer-lived structures that could represent biologically relevant conformations. NMR provides unique data on these hydrogen-bonded networks from multidimensional experiments detecting cross-peaks resulting from through-bond (TOCSY) or through-space (NOESY) interactions. However, fast OH/HO exchange, and the spectral proximity among these NMR resonances, hamper the use of glycans' labile protons in such analyses; consequently, studies are often restricted to aprotic solvents or supercooled aqueous solutions.

3D Heteronuclear Magnetization Transfers for the Establishment of Secondary Structures in SARS-CoV-2-Derived RNAs.

Multidimensional NOESY experiments targeting correlations between exchangeable imino and amino protons provide valuable information about base pairing in nucleic acids. It has been recently shown that the sensitivity of homonuclear correlations involving RNA's labile imino protons can be significantly enhanced, by exploiting the repolarization brought about by solvent exchanges. Homonuclear correlations, however, are of limited spectral resolution, and usually incapable of tackling relatively large homopolymers with repeating structures like RNAs.

Magnetization Transfer to Enhance NOE Cross-Peaks among Labile Protons: Applications to Imino-Imino Sequential Walks in SARS-CoV-2-Derived RNAs.

2D NOESY plays a central role in structural NMR spectroscopy. We have recently discussed methods that rely on solvent-driven exchanges to enhance NOE correlations between exchangeable and non-exchangeable protons in nucleic acids. Such methods, however, fail when trying to establish connectivities within pools of labile protons.

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.

The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets.

Sensitivity enhancement of homonuclear multidimensional NMR correlations for labile sites in proteins, polysaccharides, and nucleic acids.

Multidimensional TOCSY and NOESY are central experiments in chemical and biophysical NMR. Limited efficiencies are an intrinsic downside of these methods, particularly when targeting labile sites. This study demonstrates that the decoherence imparted on these protons through solvent exchanges can, when suitably manipulated, lead to dramatic sensitivity gains per unit time in the acquisition of these experiments.

Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR.

Hyperpolarized water can be a valuable aid in protein NMR, leading to amide group H polarizations that are orders of magnitude larger than their thermal counterparts. Suitable procedures can exploit this to deliver 2D H-N correlations with good resolution and enhanced sensitivity. These enhancements depend on the exchange rates between the amides and the water, thereby yielding diagnostic information about solvent accessibility.

A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR.

NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the H NMR signals of exchangeable sites by orders of magnitude over their thermal counterparts, while providing insight into chemical exchange and solvent accessibility at a site-resolved level. As HyperW's enhancements are achieved by exploiting fast solvent exchanges associated with minimal interscan delays, possibilities for the rapid monitoring of chemical reactions and biomolecular (re)folding are opened.

Enhanced hyperpolarized chemical shift imaging based on a priori segmented information.

Purpose: The purpose of the study was to develop an approach for improving the resolution and sensitivity of hyperpolarized C MRSI based on a priori anatomical information derived from featured, water-based H images.

Methods: A reconstruction algorithm exploiting H MRI for the redefinition of the C MRSI anatomies was developed, based on a modification of the spectroscopy with linear algebraic modeling (SLAM) principle. To enhance C spatial resolution and reduce spillover effects without compromising SNR, this model was extended by endowing it with a search allowing smooth variations in the C MR intensity within the targeted regions of interest.

Looped-PROjected SpectroscopY (L-PROSY): A simple approach to enhance backbone/sidechain cross-peaks in H NMR.

Cross-relaxation and isotropic mixing phenomena leading to the Nuclear Overhauser Effect (NOE) and to the TOCSY experiment, lie at the center of structural determinations by NMR. 2D TOCSY and NOESY exploit these polarization transfer effects to determine inter-site connectivities and molecular geometries under physiologically-relevant conditions. Among these sequences' drawback, particularly for the case of NOEs, are a lack of sensitivity arising from small structurally-relevant cross peaks.

Sensitivity-enhanced detection of non-labile proton and carbon NMR spectra on water resonances.

Chemical exchange saturation transfer (CEST) experiments enhance the NMR signals of labile protons by continuously transferring these protons' saturation to an abundant solvent pool like water. The present study expands these principles by fusing into these experiments homonuclear isotropic mixing sequences, enabling the water-enhanced detection of non-exchangeable species. Further opportunities are opened by the addition of coupling-mediated heteronuclear polarization transfers, which then impose on the water resonance a saturation stemming from non-labile heteronuclear species like C.

Heteronuclear 1D and 2D NMR Resonances Detected by Chemical Exchange Saturation Transfer to Water.

A method to detect NMR spectra from heteronuclei through the modulation that they impose on a water resonance is exemplified. The approach exploits chemical exchange saturation transfers, which can magnify the signal of labile protons through their influence on a water peak. To impose a heteronuclear modulation on water, an HMQC-type sequence was combined with the FLEX approach.