Leveraging relaxation-optimized H-C correlations in 4-F-phenylalanine as atomic beacons for probing structure and dynamics of large proteins.

NMR spectroscopy of biomolecules provides atomic level information into their structure, dynamics and interactions with their binding partners. However, signal attenuation from line broadening caused by fast relaxation and signal overlap often limits the application of NMR to large macromolecular systems. Here we leverage the slow relaxation properties of C nuclei attached to F in aromatic F-C spin pairs as well as the spin-spin coupling between the fluorinated C nucleus and the hydrogen atom at the meta-position to record two-dimensional H-C correlation spectra with transverse relaxation-optimized spectroscopy selection on C.

Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct.

Heat shock protein 70 (Hsp70) isoforms are key players in the regulation of protein homeostasis and cell death pathways and are therefore attractive targets in cancer research. Developing nucleotide-competitive inhibitors or allosteric modulators, however, has turned out to be very challenging for this protein family, and no Hsp70-directed therapeutics have so far become available. As the field could profit from alternative starting points for inhibitor development, we present the results of a fragment-based screening approach on a two-domain Hsp70 construct using in-solution NMR methods, together with X-ray-crystallographic investigations and mixed-solvent molecular dynamics simulations.

Enhanced TROSY Effect in [2- F, 2- C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution.

Large RNAs are central to cellular functions, but characterizing such RNAs remains challenging by solution NMR. We present two labeling technologies based on [2- F, 2- C]-adenosine, which allow the incorporation of aromatic F- C spin pairs. The labels when coupled with the transverse relaxation optimized spectroscopy (TROSY) enable us to probe RNAs comprising up to 124 nucleotides.

Teaching under lockdown: the change in the social practice of teaching.

Due to the unprecedented situation caused by a global pandemic, the traditional way of teaching that is reliant on face-to-face interaction between teachers and students has been dismantled. This article looks into university teachers' experiences of teaching under lockdown, with an intention to understand what the change meant in terms of social practice. The research follows a qualitative design, in which ten university teachers were interviewed using a semi-structured interview guide.

Time-resolved structural analysis of an RNA-cleaving DNA catalyst.

The 10-23 DNAzyme is one of the most prominent catalytically active DNA sequences. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential. However, the high expectations have not yet been met, a fact that coincides with the lack of high-resolution and time-resolved information about its mode of action.

Surviving but not thriving: Comparing primary, vocational and higher education teachers' experiences during the COVID-19 lockdown.

In this paper we examine the impacts of the global pandemic in 2020 on different levels of education system, particularly looking at the changes in teaching practice. The health emergency caused closure of schools, and online distance education became a temporary solution, creating discomfort for many teachers for whom this was the first time engaged with online education. In our research we investigated two important dimensions, namely, how technology was used and what the newfound distance meant in terms of the teacher-student relationship.

Efficient affinity ranking of fluorinated ligands by F NMR: CSAR and FastCSAR.

Fluorine NMR has recently gained high popularity in drug discovery as it allows efficient and sensitive screening of large numbers of ligands. However, the positive hits found in screening must subsequently be ranked according to their affinity in order to prioritize them for follow-up chemistry. Unfortunately, the primary read-out from the screening experiments, namely the increased relaxation rate upon binding, is not proportional to the affinity of the ligand, as it is polluted by effects such as exchange broadening.

Aromatic F-C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics.

Atomic-level information about the structure and dynamics of biomolecules is critical for an understanding of their function. Nuclear magnetic resonance (NMR) spectroscopy provides unique insights into the dynamic nature of biomolecules and their interactions, capturing transient conformers and their features. However, relaxation-induced line broadening and signal overlap make it challenging to apply NMR spectroscopy to large biological systems.

Parallel NMR spectroscopy with simultaneous detection of (1) H and (19) F nuclei.

Recording NMR signals of several nuclear species simultaneously by using parallel receivers provides more information from a single measurement and at the same time increases the measurement sensitivity per unit time. Here we present a comprehensive series of the most frequently used NMR experiments modified for simultaneous direct detection of two of the most sensitive NMR nuclei - (1) H and (19) F. We hope that the presented material will stimulate interest in and further development of this technique.

Direct ¹³C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.

In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange.

NMR structure analysis of uniformly 13C-labeled carbohydrates.

In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point.

Improved NMR experiments with ¹³C-isotropic mixing for assignment of aromatic and aliphatic side chains in labeled proteins.

Three improved ¹³C-spinlock experiments for side chain assignments of isotope labelled proteins in liquid state are presented. These are based on wide bandwidth spinlock techniques that have become possible with contemporary cryogenic probes. The first application, the H(C(ali)C(aro))H-TOCSY, is an HCCH-TOCSY in which all CHn moieties of a protein are detected in a single experiment, including the aromatic ones.

Probing water-protein contacts in a MMP-12/CGS27023A complex by nuclear magnetic resonance spectroscopy.

Using the case of the catalytic domain of MMP-12 in complex with the known inhibitor CGS27023A, a recently assembled 3D (15)N-edited/(14)N,(12)C-filtered ROESY experiment is used to monitor and distinguish protein amide protons in fast exchange with bulk water from amide protons close to water molecules with longer residence times, the latter possibly reflecting water molecules of structural or functional importance. The (15)N-edited/(14)N,(12)C-filtered ROESY spectra were compared to the original (15)N-edited/(14)N,(12)C-filtered NOESY and the conventional amide-water exchange experiment, CLEANEX. Three protein backbone amide protons experiencing direct dipolar cross relaxation with water in the (15)N-edited/(14)N,(12)C-filtered ROESY spectrum were assigned.

Synovial fluid metabolomics in different forms of arthritis assessed by nuclear magnetic resonance spectroscopy.

Objectives: Currently there are no reliable biomarkers in the synovial fluid available to differentiate between septic and non-septic arthritis or to predict the prognosis of osteoarthritis, respectively. Nuclear magnetic resonance (NMR) spectroscopy is an analytical technique that allows a rapid, high throughput metabolic profiling of biological fluids or tissues.

Methods: Proton (1H)-nuclear magnetic resonance (NMR) spectroscopy was performed in synovial fluid samples from patients with septic arthritis, crystal arthropathy, different forms of inflammatory arthritis or osteoarthritis (OA).

13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides.

We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures.

Metal ion-N7 coordination in a ribozyme branch domain by NMR.

The N7 of purine nucleotides presents one of the most dominant metal ion binding sites in nucleic acids. However, the interactions between kinetically labile metal ions like Mg(2+) and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct (15)N detection, here we have used (2)J-[(1)H,(15)N]-HSQC (Heteronuclear Single Quantum Coherence) NMR experiments as a fast and efficient method to specifically observe and characterize such interactions within larger RNA constructs.

Does a fast nuclear magnetic resonance spectroscopy- and X-ray crystallography hybrid approach provide reliable structural information of ligand-protein complexes? A case study of metalloproteinases.

A human matrix metalloproteinase (MMP) hydroxamic acid inhibitor (CGS27023A) was cross-docked into 15 MMP-12, MMP-13, MMP-9, and MMP-1 cocrystal structures. The aim was to validate a fast protocol for ligand binding conformation elucidation and to probe the feasibility of using inhibitor-protein NMR contacts to dock an inhibitor into related MMP crystal structures. Such an approach avoids full NMR structure elucidation, saving both spectrometer- and analysis time.

Three-dimensional 13C-detected CH3-TOCSY using selectively protonated proteins: facile methyl resonance assignment and protein structure determination.

Recent advances in instrumentation and isotope labeling methodology allow proteins up to 100 kDa in size to be studied in detail using NMR spectroscopy. Using 2H/13C/15N enrichment and selective methyl protonation, we show that newly developed 13C direct detection methods can be used to rapidly yield proton and carbon resonance assignments for the methyl groups of Val, Leu, and Ile residues. We present a highly sensitive 13C-detected CH3-TOCSY experiment that, in combination with standard 1H-detected backbone experiments, allows the full assignment of side chain resonances in methyl-protonated residues.

Simultaneous 1H- or 2H-, 15N- and multiple-band-selective 13C-decoupling during acquisition in 13C-detected experiments with proteins and oligonucleotides.

Significant resolution improvement in 13C,13C-TOCSY spectra of uniformly deuterated and 13C, 15N-labeled protein and 13C,15N-labeled RNA samples is achieved by introduction of multiple-band-selective 13C-homodecoupling applied simultaneously with 1H- or 2H- and 15N-decoupling at all stages of multidimensional experiments including signal acquisition period. The application of single, double or triple band-selective 13C-decoupling in 2D-[13C,13C]-TOCSY experiments during acquisition strongly simplifies the homonuclear splitting pattern. The technical aspects of complex multiple-band homonuclear decoupling and hardware requirements are discussed.

Optimization of 13C direct detection NMR methods.

(13)C-detected experiments are still limited by their inherently lower sensitivity, as compared to the equivalent (1)H-detected experiments. Improving the sensitivity of (13)C detection methods remains a significant area of NMR research that may provide better means for studying large macromolecular systems by NMR. In this communication, we show that (13)C-detected experiments are less sensitive to the salt concentration of the sample solution than (1)H-detected experiments.

Conformation and concerted dynamics of the integrin-binding site and the C-terminal region of echistatin revealed by homonuclear NMR.

Echistatin is a potent antagonist of the integrins alpha(v)beta3, alpha5beta1 and alpha(IIb)beta3. Its full inhibitory activity depends on an RGD (Arg-Gly-Asp) motif expressed at the tip of the integrin-binding loop and on its C-terminal tail. Previous NMR structures of echistatin showed a poorly defined integrin-recognition sequence and an incomplete C-terminal tail, which left the molecular basis of the functional synergy between the RGD loop and the C-terminal region unresolved.

Measurements of side-chain 13C-13C residual dipolar couplings in uniformly deuterated proteins.

13C-only spectroscopy was used to measure multiple residual (13)C-(13)C dipolar couplings (RDCs) in uniformly deuterated and (13)C-labeled proteins. We demonstrate that (13)C-start and (13)C-observe spectra can be routinely used to measure an extensive set of the side-chain residual (13)C-(13)C dipolar couplings upon partial alignment of human ubiquitin in the presence of bacteriophages Pf1. We establish that, among different broadband polarization transfer schemes, the FLOPSY family can be used to exchange magnetization between a J coupled network of spins while largely decoupling dipolar interactions between these spins.

Concerted motions of the integrin-binding loop and the C-terminal tail of the non-RGD disintegrin obtustatin.

Obtustatin is a potent and selective inhibitor of the alpha1beta1 integrin in vitro and of angiogenesis in vivo. It possesses an integrin recognition loop that harbors, in a lateral position, the inhibitory 21KTS23 motif. We report an analysis of the dynamics of the backbone and side-chain atoms of obtustatin by homonuclear NMR methods.

A novel strategy for the assignment of side-chain resonances in completely deuterated large proteins using 13C spectroscopy.

The assignment of the aliphatic (13)C resonances of trimeric Bacillus Subtilis chorismate mutase, a protein with a molecular mass of 44 kDa, consisting of three 127-residue monomers is presented by use of two-dimensional (2D) (13)C-start and (13)C-observe NMR experiments. These experiments start with (13)C excitation and end with (13)C observation while relying on the long transverse relaxation times of (13)C spins in uniformly deuterated and (13)C,(15)N-labeled large proteins. Gains in sensitivity are achieved by the use of a paramagnetic relaxation enhancement agent to reduce (13)C T(1) relaxation times with little effect on (13)C T(2) relaxation times.