Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 25
Filtrar
1.
Nucleic Acids Res ; 51(9): 4555-4571, 2023 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-36928389

RESUMO

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. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further fragment expansion and drug development.


Assuntos
Tratamento Farmacológico da COVID-19 , COVID-19 , Proteínas do Nucleocapsídeo de Coronavírus , Desenvolvimento de Medicamentos , SARS-CoV-2 , Humanos , COVID-19/virologia , RNA Viral/metabolismo , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/metabolismo , Proteínas do Nucleocapsídeo de Coronavírus/antagonistas & inibidores , Proteínas do Nucleocapsídeo de Coronavírus/química , Proteínas do Nucleocapsídeo de Coronavírus/metabolismo , Ressonância Magnética Nuclear Biomolecular , Espectrometria de Massas , Fluxo de Trabalho , Ligação Proteica
2.
Anal Chem ; 95(49): 18091-18098, 2023 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-38008904

RESUMO

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. It is shown that, in both cases, the effects introduced by either differential paramagnetic shift and relaxation or by polarization sharing among networks of protons can provide a similar sensitivity boost, as previously discussed for solvent exchange. The origin and potential of the resulting enhancements are analyzed, and experiments that demonstrate them in protein and natural products are exemplified. Limitations and future improvements of these approaches are also briefly discussed.

3.
Proc Natl Acad Sci U S A ; 117(5): 2449-2455, 2020 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-31949004

RESUMO

NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the 1H 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. HyperW NMR can also accommodate heteronuclear transfers, facilitating the rapid acquisition of 2-dimensional (2D) 15N-1H NMR correlations, and thereby combining an enhanced spectral resolution with speed and sensitivity. This work demonstrates how these qualities can come together for the study of nucleic acids. HyperW injections were used to target the guanine-sensing riboswitch aptamer domain (GSRapt) of the xpt-pbuX operon in Bacillus subtilis Unlike what had been observed in proteins, where residues benefited of HyperW NMR only if/when sufficiently exposed to water, these enhancements applied to every imino resonance throughout the RNA. The >300-fold enhancements observed in the resulting 1H NMR spectra allowed us to monitor in real time the changes that GSRapt undergoes upon binding hypoxanthine, a high-affinity interaction leading to conformational refolding on a ∼1-s timescale at 36 °C. Structural responses could be identified for several nucleotides by 1-dimensional (1D) imino 1H NMR as well as by 2D HyperW NMR spectra acquired upon simultaneous injection of hyperpolarized water and hypoxanthine. The folding landscape revealed by this HyperW strategy for GSRapt, is briefly discussed.


Assuntos
Iminoácidos/química , Ressonância Magnética Nuclear Biomolecular/métodos , RNA/química , Água/química , Aptâmeros de Nucleotídeos/química , Dobramento de RNA , Riboswitch
4.
Angew Chem Int Ed Engl ; 62(35): e202304900, 2023 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-37408374

RESUMO

INEPT-based experiments are widely used for 1 H→15 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 Hwater ↔ ${ \leftrightarrow }$ HN exchange process to boost the 1 H→15 N transfer process. This leveraging, however, demands the simultaneous spin-locking of both Hwater and HN protons by a strong 1 H RF field, while fulfilling the γH B1,H =γN B1,N Hartmann-Hahn matching condition. Given the low value of γN /γH , however, these demands are often incompatible-particularly when experiments are executed by the power-limited cryogenic probes used in contemporary high field NMR. The present manuscript discusses CP alternatives that can alleviate this limitation, and evaluates their performance on urea, amino acids, and intrinsically disordered proteins. These alternatives include new CP variants based on frequency-swept and phase-modulated pulses, designed to simultaneously fulfill the aforementioned conflicting conditions. Their performances vis-à-vis current options are theoretically analyzed with Liouville-space simulations, and experimentally tested with double and triple resonance transfer experiments.

5.
Chemphyschem ; 23(4): e202100704, 2022 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-34968005

RESUMO

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 1 Hs, while still enjoying the gains arising from Hadamard encoding and solvent repolarizations. The principles required for implementing what we define as the extended Hadamard scheme are derived, and its clean, artifact-free, sensitivity-enhancing performance is demonstrated on RNA fragments derived from the SARS-CoV-2 genome. Sensitivity gains per unit time approaching an order of magnitude are then achieved in both imino-imino and imino-amino/aromatic protons 2D correlations; similar artifact-free sensitivity gains can be observed when carrying out extended Hadamard encodings of 3D NOESY/HSQC-type experiments. The resulting spectra reveal significantly more correlations than their conventionally acquired counterparts, which can support the spectral assignment and secondary structure determination of structured RNA elements.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , Espectroscopia de Ressonância Magnética/métodos , Proteínas/química , RNA
6.
J Chem Phys ; 156(5): 054201, 2022 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-35135290

RESUMO

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 H2O. Inspired by this method, we propose and exemplify a methodology to enhance the sensitivity of magic-angle spinning (MAS) solid-state NMR spectra. Our proposal uses the abundant 1H reservoir arising in organic solids as the magnetically abundant spin pool and relies on proton spin diffusion in lieu of chemical exchange to mediate polarization transfer between a magnetically dilute spin pool and this magnetically abundant spin reporter. As an initial test of this idea, we target the spectroscopy of naturally abundant 13C and rely on a Fourier-encoded version of the CEST experiment for achieving broadbandness in coordination with both MAS and heteronuclear decoupling, features normally absent in CEST. Arbitrary evolutions of multiple 13C sites can, thus, be imprinted on the entire 1H reservoir, which is subsequently detected. Theoretical predictions suggest that orders-of-magnitude signal enhancements should be achievable in this manner, on the order of the ratio between the 13C and the 1H reservoirs' abundances. Experiments carried out under magic-angle spinning conditions evidenced 5-10× gains in signal amplitudes. Further opportunities and challenges arising in this Fourier-encoded saturation transfer MAS NMR approach are briefly discussed.

7.
Nucleic Acids Res ; 48(22): 12415-12435, 2020 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-33167030

RESUMO

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. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.


Assuntos
COVID-19/prevenção & controle , Espectroscopia de Ressonância Magnética/métodos , Conformação de Ácido Nucleico , RNA Viral/química , SARS-CoV-2/genética , Regiões 3' não Traduzidas/genética , Sequência de Bases , COVID-19/epidemiologia , COVID-19/virologia , Mudança da Fase de Leitura do Gene Ribossômico/genética , Genoma Viral/genética , Humanos , Modelos Moleculares , Pandemias , SARS-CoV-2/fisiologia
8.
J Am Chem Soc ; 143(23): 8935-8948, 2021 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-34085814

RESUMO

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/H2O 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. These nonphysiological conditions may lead to unrepresentative structures or to probing a small subset of accessible conformations that may miss "active" glycan conformations. Looped, projected spectroscopy (L-PROSY) has been recently shown to substantially enhance protein NOESY and TOCSY cross-peaks, for 1Hs that undergo fast exchange with water. This study shows that even larger enhancements can be obtained for rapidly exchanging OHs in saccharides, leading to the retrieval of previously undetectable 2D TOCSY/NOESY cross-peaks with nonlabile protons. After demonstrating ≥300% signal enhancements on model monosaccharides, these experiments were applied at 1 GHz to elucidate the structural network adopted by a sialic acid homotetramer, used as a model for α,2-8 linked polysaccharides. High-field L-PROSY NMR enabled these studies at higher temperatures and provided insight previously unavailable from lower-field NMR investigations on supercooled samples, involving mostly nonlabile nuclei. Using L-PROSY's NOEs and other restraints, a revised structural model for the homotetramer was obtained combining rigid motifs and flexible segments, that is well represented by conformations derived from 40 µs molecular dynamics simulations.

9.
J Am Chem Soc ; 143(13): 4942-4948, 2021 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-33783202

RESUMO

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. This study presents a heteronuclear-resolved version of those NOESY experiments, in which magnetization transfers between the aqueous solvent and the nucleic acid protons are controlled by selecting specific chemical shift combinations of a coupled 1H-15N spin pair. This selective control effectively leads to a pseudo-3D version of HSQC-NOESY, but with cross-peaks enhanced by ∼2-5× as compared with conventional 2D NOESY counterparts. The enhanced signal sensitivity as well as access to both 15N-1H and 1H-1H NOESY dimensions can greatly facilitate RNA assignments and secondary structure determinations, as demonstrated here with the analysis of genome fragments derived from the SARS-CoV-2 virus.


Assuntos
Fenômenos Magnéticos , Espectroscopia de Ressonância Magnética , RNA Viral/química , SARS-CoV-2/genética , Temperatura
10.
Angew Chem Int Ed Engl ; 60(21): 11884-11891, 2021 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-33683819

RESUMO

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. This study introduces an alternative that also enhances NOEs between such labile sites, based on encoding a priori selected peaks by selective saturations. The resulting selective magnetization transfer (SMT) experiment proves particularly useful for enhancing the imino-imino cross-peaks in RNAs, which is a first step in the NMR resolution of these structures. The origins of these enhancements are discussed, and their potential is demonstrated on RNA fragments derived from the genome of SARS-CoV-2, recorded with better sensitivity and an order of magnitude faster than conventional 2D counterparts.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , Prótons , RNA Viral/análise , SARS-CoV-2/química , Fenômenos Magnéticos , RNA Viral/química
11.
J Am Chem Soc ; 142(20): 9267-9284, 2020 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-32338002

RESUMO

Hyperpolarized water can be a valuable aid in protein NMR, leading to amide group 1H polarizations that are orders of magnitude larger than their thermal counterparts. Suitable procedures can exploit this to deliver 2D 1H-15N 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. This study applied this "HyperW" method to four proteins exhibiting a gamut of exchange behaviors: PhoA(350-471), an unfolded 122-residue fragment; barstar, a fully folded ribonuclease inhibitor; R17, a 13.3 kDa system possessing folded and unfolded forms under slow interconversion; and drkN SH3, a protein domain whose folded and unfolded forms interchange rapidly and with temperature-dependent population ratios. For PhoA4(350-471) HyperW sensitivity enhancements were ≥300×, as expected for an unfolded protein sequence. Though fully folded, barstar also exhibited substantial enhancements; these, however, were not uniform and, according to CLEANEX experiments, reflected the solvent-exposed residues. R17 showed the expected superposition of ≥100-fold enhancements for its unfolded form, coexisting with more modest enhancements for their folded counterparts. Unexpected, however, was the behavior of drkN SH3, for which HyperW enhanced the unfolded but, surprisingly, enhanced even more certain folded protein sites. These preferential enhancements were repeatedly and reproducibly observed. A number of explanations-including three-site exchange magnetization transfers between water and the unfolded and folded states; cross-correlated relaxation processes from hyperpolarized "structural" waters and labile side-chain protons; and the possibility that faster solvent exchange rates characterize certain folded sites over their unfolded counterparts-are considered to account for them.


Assuntos
Fosfatase Alcalina/química , Proteínas de Escherichia coli/química , Ressonância Magnética Nuclear Biomolecular , Dobramento de Proteína , Desdobramento de Proteína , Água/química
12.
Magn Reson Med ; 81(5): 3080-3093, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30652358

RESUMO

PURPOSE: The purpose of the study was to develop an approach for improving the resolution and sensitivity of hyperpolarized 13 C MRSI based on a priori anatomical information derived from featured, water-based 1 H images. METHODS: A reconstruction algorithm exploiting 1 H MRI for the redefinition of the 13 C MRSI anatomies was developed, based on a modification of the spectroscopy with linear algebraic modeling (SLAM) principle. To enhance 13 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 13 C MR intensity within the targeted regions of interest. RESULTS: Experiments were performed in vitro on enzymatic solutions and in vivo on rodents, based on the administration of 13 C-enriched hyperpolarized pyruvate and urea. The spectral images reconstructed for these substrates and from metabolic products based on predefined 1 H anatomical compartments using the new algorithm, compared favorably with those arising from conventional Fourier-based analyses of the same data. The new approach also delivered reliable kinetic 13 C results, for the kind of processes and timescales usually targeted by hyperpolarized MRSI. CONCLUSION: A simple, flexible strategy is introduced to boost the sensitivity and resolution provided by hyperpolarized 13 C MRSI, based on readily available 1 H MR information.


Assuntos
Processamento de Imagem Assistida por Computador/métodos , Imageamento por Ressonância Magnética/métodos , Algoritmos , Animais , Isótopos de Carbono/química , Feminino , Análise de Fourier , Cinética , Modelos Lineares , Masculino , Modelos Estatísticos , Imagens de Fantasmas , Prótons , Ácido Pirúvico/metabolismo , Ratos , Ratos Wistar , Razão Sinal-Ruído , Ureia/metabolismo
14.
Phys Chem Chem Phys ; 20(1): 56-62, 2017 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-29171604

RESUMO

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 13C. To multiplex the ensuing experiments, these relayed approaches are combined with time-domain schemes involving multiple Ramsey-labeling experiments imparting the frequencies of the non-labile sites on the water resonance, via chemical exchange. 13C and 1H NMR spectra were detected in this fashion with about two-fold SNR amplification vis-à-vis conventionally detected spectroscopies. When combined with non-uniform sampling principles, this methodology thus becomes a sensitive alternative to detect non-exchangeable species in biomolecules. Still, multiple parameters including the scalar couplings and solvent exchange rates, will affect the efficiency and consequently the practicality of the overall experiment.

15.
Angew Chem Int Ed Engl ; 56(13): 3521-3525, 2017 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-28240443

RESUMO

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. 1D 15 N NMR spectra of exchanging sites could thus be detected, with about tenfold amplifications over the 15 N modulations afforded by conventionally detected HMQC NMR spectroscopy. Extensions of this approach enable 2D heteronuclear acquisitions on directly bonded 1 H-15 N spin pairs, also with significant signal amplification. Despite the interesting limits of detection that these signal enhancements could open in NMR spectroscopy, these gains are constrained by the rates of solvent exchange of the targeted heteronuclear pairs, as well as by spectrometer instabilities affecting the intense water resonances detected in these experiments.

16.
Mol Biol Cell ; 35(5): ar73, 2024 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-38568799

RESUMO

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. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/fisiologia , RNA , Separação de Fases , Nucleocapsídeo , Concentração de Íons de Hidrogênio , Aminoácidos
17.
Sci Adv ; 10(10): eadm7435, 2024 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-38446881

RESUMO

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). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.


Assuntos
Condensados Biomoleculares , Preservação Biológica , Separação de Fases , RNA , Ribonucleoproteínas
18.
Nat Commun ; 14(1): 6429, 2023 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-37833274

RESUMO

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). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.


Assuntos
Sítios Internos de Entrada Ribossomal , Proteínas de Ligação a RNA , Proteínas de Ligação a RNA/metabolismo , Vírus da Encefalomiocardite/genética , RNA Viral/metabolismo , Conformação de Ácido Nucleico , Biossíntese de Proteínas
19.
J Magn Reson ; 337: 107176, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35272112

RESUMO

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. The polarization that these non-secular terms will transfer among systems of chemically inequivalent sites over the course of a mixing period, are widely used modules in 1D and in multidimensional liquid-state NMR. Homonuclear correlation experiments are also common in solids NMR, particularly among X = 13C or 15N nuclei. Solids NMR experiments are often challenged by high-power RF demands which have led to a family of homonuclear solid-state correlation experiments that avoid pulsing on the nuclei of interest, and focus instead on the 1Hs that are bonded to them. These solid experiments usually reintroduce/strengthen 1H-X dipolar couplings; these, in conjunction with assistance from rotational resonance effects, bring back the truncated X-X dipolar interactions and facilitate the generation of cross peaks. The present study explores whether a similar goal can be achieved for solution-state counterparts, based on the reintroduction of truncated flip-flop terms in the J-coupling Hamiltonian via the pulsing on other, heteronuclear species. A proposal to achieve this is derived, and the resulting HOmonucleaR Recoupling by hEteroNuclear DecOUplingS (HORRENDOUS) approach to provide correlations between like nuclei without pulsing on them, is demonstrated.


Assuntos
Imageamento por Ressonância Magnética , Espectroscopia de Ressonância Magnética/métodos
20.
J Magn Reson ; 338: 107187, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35292421

RESUMO

Both in spectroscopy and imaging, t1-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 t1-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. This procedure is repeated for multiple renditions of the masked data -some of which will have been more strongly affected by t1-noise than others. This leads to a large set of 2D NMR spectra/images compatible with the collected data; CoSeM chooses out of these those renditions that reduce the noise according to a suitable criterion, and then sums up their spectra/images leading to a reduction in t1-noise. The performance of the method was assessed in synthetic data, as well as in numerous different experiments: 2D solid and solution state NMR, 2D localized MRS of live brains, and 2D abdominal MRI. Throughout all these data, CoSeM processing evidenced 2-3 fold increases in SNR, without introducing biases, false peaks, or spectral/image blurring. CoSeM also retains a quantitative linearity in the information -allowing, for instance, reliable T1 inversion-recovery MRI mapping experiments.


Assuntos
Processamento de Imagem Assistida por Computador , Imageamento por Ressonância Magnética , Algoritmos , Processamento de Imagem Assistida por Computador/métodos , Imageamento por Ressonância Magnética/métodos , Espectroscopia de Ressonância Magnética , Movimento (Física) , Razão Sinal-Ruído
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA