The nuclear Overhauser effect from a quantitative perspective

Protocol for converting assigned nuclear Overhauser enhancement spectroscopy series peaks into exact distance restraints using MATLAB- or CYANA-eNORA

In the exact nuclear Overhauser enhancement (eNOE) method, tight upper and lower interatomic distance restraints for structure calculations and comparison are extracted from NMR nuclear Overhauser enhancement spectroscopy (NOESY) spectra of biomolecules recorded with different mixing times. Here, we present a protocol for exporting the resonance assignments of NOESY spectra from CCPNmr (v.2) into nmrDraw to obtain peak intensities. We then detail procedures for converting them into distances using either the CYANA- or MATLAB-based "exact NOE by relaxation matrix analysis" (eNORA) program.

Molecular Shells and Range of Interactions in Ionic Liquids as a Function of Temperature

Room-temperature ionic liquids (RTILs) represent a versatile class of chemical systems composed entirely of oppositely charged species whose bulk properties can be fine-tuned by adjusting molecular structures and, consequently, intermolecular interactions. Understanding the intricate dynamics between ionic species can aid in the rational design of RTILs for specific applications in a range of fields, including catalysis and electrochemistry. Here, we investigate the temperature dependence of intermolecular interactions through magnetization transfer by means of 1H-19F heteronuclear Overhauser effect spectroscopy (HOESY) for two ionic liquids, namely, [BMIM][BF4] and [BMIM][PF6]. We find that the cross-relaxation rates vary significantly over a rather small temperature range, even changing sign. Molecular dynamics (MD) simulations on neat RTIL systems replicate this behavior well and further show that the dynamic properties rather than coordination changes of RTILs account for the observed temperature behavior. Furthermore, the investigation of different coordination shells highlights the change of interaction range with temperature even to the point where inner and outer coordination shells could be in distinct motional regimes with cross-relaxation rates of opposite sign. Since temperature changes lead primarily to dynamic changes rather than structural ones, these findings underscore the versatility and high thermal stability of ionic liquids.

Improving quantification accuracy of a nuclear Overhauser enhancement signal at -1.6 ppm at 4.7 T using a machine learning approach

Objective.A new nuclear Overhauser enhancement (NOE)-mediated saturation transfer MRI signal at -1.6 ppm, potentially from choline phospholipids and termed NOE(-1.6), has been reported in biological tissues at high magnetic fields. This signal shows promise for detecting brain tumors and strokes. However, its proximity to the water peak and low signal-to-noise ratio makes accurate quantification challenging, especially at low fields, due to the difficulty in separating it from direct water saturation and other confounding signals. This study proposes using a machine learning (ML) method to address this challenge.Approach.The ML model was trained on a partially synthetic chemical exchange saturation transfer dataset with a curriculum learning denoising approach. The accuracy of our method in quantifying NOE(-1.6) was validated using tissue-mimicking data from Bloch simulations providing ground truth, with subsequent application to an animal tumor model at 4.7 T. The predictions from the proposed ML method were compared with outcomes from traditional Lorentzian fit and ML models trained on other data types, including measured and fully simulated data.Main results.Our tissue-mimicking validation suggests that our method offers superior accuracy compared to all other methods. The results from animal experiments show that our method, despite variations in training data size or simulation models, produces predictions within a narrower range than the ML method trained on other data types.Significance.The ML method proposed in this work significantly enhances the accuracy and robustness of quantifying NOE(-1.6), thereby expanding the potential for applications of this novel molecular imaging mechanism in low-field environments.

Impact of Linker Composition on VHL PROTAC Cell Permeability

The discovery of cell permeable and orally bioavailable von Hippel-Lindau (VHL) proteolysis targeting chimeras (PROTACs) is challenging as their structures locates them at, or beyond, the outer limits of oral druggable space. We have designed a set of nine VHL PROTACs and found that the linker had a profound impact on passive cell permeability. Determination of the solution ensembles in a nonpolar solvent revealed that high permeability was correlated to the ability of the PROTACs to adopt folded conformations that have a low solvent accessible 3D polar surface area. Our results suggest that the design of cell permeable VHL PROTACs could focus on linkers that facilitate shielding of polar surface area in the VHL ligand in a nonpolar but not in a polar environment. In addition, we found that not only intramolecular hydrogen bonds, but also NH-π and π-π interactions contribute to the stabilization of low-polarity conformations, and thereby to high cell permeability.

Constructing artificial gap junctions to mediate intercellular signal and mass transport

Natural gap junctions are a type of channel protein responsible for intercellular signalling and mass communication. However, the scope of applications for these proteins is limited as they cannot be prepared at a large scale and are unable to spontaneously insert into cell membranes in vitro. The construction of artificial gap junctions may provide an alternative strategy for preparing analogues of the natural proteins and bottom-up building blocks necessary for the synthesis of artificial cells. Here we show the construction of artificial gap junction channels from unimolecular tubular molecules consisting of alternately arranged positively and negatively charged pillar[5]arene motifs. These molecules feature a hydrophobic-hydrophilic-hydrophobic triblock structure that allows them to efficiently insert into two adjacent plasma membranes and stretch across the gap between the two membranes to form gap junctions. Similar to natural gap junction channels, the synthetic channels could mediate intercellular signal coupling and reactive oxygen species transmission, leading to cellular activity.

NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function

Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.

Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability

The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.

Representing structures of the multiple conformational states of proteins

Biomolecules exhibit dynamic behavior that single-state models of their structures cannot fully capture. We review some recent advances for investigating multiple conformations of biomolecules, including experimental methods, molecular dynamics simulations, and machine learning. We also address the challenges associated with representing single- and multiple-state models in data archives, with a particular focus on NMR structures. Establishing standardized representations and annotations will facilitate effective communication and understanding of these complex models to the broader scientific community.

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.

Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems

Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. proteins without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence and nuclear magnetic resonance (NMR) spectroscopy are both exceptionally well suited to decipher and describe these states and their interconversion. Different time scales, from picoseconds to several milliseconds, can be addressed by both techniques. The length scales probed and the sample requirements (e.g. concentration, molecular weight, sample complexity) are, however, vastly different, making NMR and single molecule fluorescence an excellent combination for integrated studies. Here, we review recently undertaken approaches for the combined use of NMR and single molecule fluorescence to study protein dynamics.

NMR-Verified Dearomatization of 5,7-Substituted Pyrazolo[1,5-a]pyrimidines

Tetrahydropyrazolo[1,5-a]pyrimidine (THPP) is an attractive scaffold for designing biologically active compounds. The most obvious way to obtain such compounds is to reduce pyrazolopyrimidines with complex hydrides, because the pyrimidine ring is reduced in the preference over the pyrazole ring. The presence of substituents at positions five and seven of pyrazolo[1,5-a]pyrimidines complicates the set of reaction products but makes it more attractive for medicinal chemistry because four possible stereoisomers can be formed during reduction. However, the formation of only syn-isomers has been described in the literature. This article is the first report on the formation of anti-configured isomers along with syn-isomers in the reduction of model 5,7-dimethylpyrazolo[1,5-a]pyrimidine, which was confirmed by NMR. The bicyclic core in the syn-configuration was shown to be conformationally stable, which was used to estimate the long-range interproton distances using NOESY data. At the same time, long-range dipole-dipole interactions corresponding to a distance between protons of more than 6 Å were first registered and quantified. In turn, the bicyclic core in the trans-configuration represents a conformationally labile system. For these structures, an analysis of conformations observed in solutions was carried out. Our results indicate the significant potential of trans-configured tetrahydropyrazolo[1,5-a]pyrimidines for the development of active small molecules. While possessing structural lability due to the low energy of the conformational transition, they have the ability to adjust to the active site of the desired target.

Isolation of amide proton transfer effect and relayed nuclear Overhauser enhancement effect at -3.5ppm using CEST with double saturation powers

PURPOSE

Quantifications of amide proton transfer (APT) and nuclear Overhauser enhancement (rNOE(-3.5)) mediated saturation transfer with high specificity are challenging because their signals measured in a Z-spectrum are overlapped with confounding signals from direct water saturation (DS), semi-solid magnetization transfer (MT), and CEST of fast-exchange pools. In this study, based on two canonical CEST acquisitions with double saturation powers (DSP), a new data-postprocessing method is proposed to specifically quantify the effects of APT and rNOE.

METHODS

For CEST imaging with relatively low saturation powers (ω 1 2 $$ {\upomega}_1^2 $$ ), both the fast-exchange CEST effect and the semi-solid MT effect roughly depend onω 1 2 $$ {\upomega}_1^2 $$ , whereas the slow-exchange APT/rNOE(-3.5) effect do not, which is exploited to isolate a part of the APT and rNOE effects from the confounding signals in this study. After a mathematical derivation for the establishment of the proposed method, numerical simulations based on Bloch equations are then performed to demonstrate its specificity to detections of the APT and rNOE effects. Finally, an in vivo validation of the proposed method is conducted using an animal tumor model at a 4.7 T MRI scanner.

RESULTS

The simulations show that DSP-CEST can quantify the effects of APT and rNOE and substantially eliminate the confounding signals. The in vivo experiments demonstrate that the proposed DSP-CEST method is feasible for the imaging of tumors.

CONCLUSION

The data-postprocessing method proposed in this study can quantify the APT and rNOE effects with considerably increased specificities and a reduced cost of imaging time.

Evaluation of contributors to amide proton transfer-weighted imaging and nuclear Overhauser enhancement-weighted imaging contrast in tumors at a high magnetic field

PURPOSE

The purpose is to evaluate the relative contribution from confounding factors (T1 weighting and magnetization transfer) to the CEST ratio (CESTR)-quantified amide proton transfer (APT) and nuclear Overhauser enhancement (NOE) (-3.5) in tumors as well as whether the CESTR can reflect the distribution of the solute concentration (fs ).

METHODS

We first provided a signal model that shows the separate dependence of CESTR on these confounding factors and the clean CEST/NOE effects quantified by an apparent exchange-dependent relaxation (AREX) method. We then measured the change in these effects in the 9-L tumor model in rats, through which we calculated the relative contribution of each confounding factor. fs was also fitted, and its correlations with the CESTR and AREX were assessed to evaluate their capabilities to reflect fs .

RESULTS

The CESTR-quantified APT shows "positive" contrast in tumors, which arises primarily from R1w at low powers and both R1w and magnetization transfer at high powers. CESTR-quantified NOE (-3.5) shows no or weak contrast in tumors, which is due to the cancelation of R1w and NOE (-3.5), which have opposite contributions. CESTR-quantified APT has a stronger correlation with APT fs than AREX-quantified APT. CESTR-quantified NOE (-3.5) has a weaker correlation with NOE (-3.5) fs than AREX-quantified NOE (-3.5).

CONCLUSION

CESTR reflects a combined effect of T1 weighting and CEST/NOE. Both factors depend on fs , which contributes positively to the dependence of CESTR on fs in APT imaging and enhances its correlation with fs . In contrast, these factors have opposite contributions to its dependence on fs in NOE (-3.5) imaging, thereby weakening the correlation.

NMR-Based Method for Intramolecular 13C Distribution at Natural Abundance Adapted to Small Amounts of Glucose

Quantitative nuclear magnetic resonance (NMR) for isotopic measurements, known as irm-NMR (isotope ratio measured by NMR), is well suited for the quantitation of ¹³C-isotopomers in position-specific isotope analysis and thus for measuring the carbon isotope composition (δ¹³C, mUr) in C-atom positions. Irm-NMR has already been used with glucose after derivatization to study sugar metabolism in plants. However, up to now, irm-NMR has exploited a "single-pulse" sequence and requires a relatively large amount of material and long experimental time, precluding many applications with biological tissues or extracts. To reduce the required amount of sample, we investigated the use of 2D-NMR analysis. We adapted and optimized the NMR sequence so as to be able to analyze a small amount (10 mg) of a glucose derivative (diacetonide glucofuranose, DAGF) with a precision better than 1 mUr at each C-atom position. We also set up a method to correct raw data and express ¹³C abundance on the usual δ¹³C scale (δ-scale). In fact, due to the distortion associated with polarization transfer and spin manipulation during 2D-NMR analyses, raw ¹³C abundance is found to be on an unusual scale. This was compensated for by a correction factor obtained via comparative analysis of a reference material (commercial DAGF) using both previous (single-pulse) and new (2D) sequences. Glucose from different biological origins (CO₂ assimilation metabolisms of plants, namely, C₃, C₄, and CAM) was analyzed with the two sequences and compared. Validation criteria such as selectivity, limit of quantification, precision, trueness, and robustness are discussed, including in the framework of green analytical chemistry.

Conformational State of Fenamates at the Membrane Interface: A MAS NOESY Study

The present work analyzes the ¹H NOESY MAS NMR spectra of three fenamates (mefenamic, tolfenamic, and flufenamic acids) localized in the lipid-water interface of phosphatidyloleoylphosphatidylcholine (POPC) membranes. The observed cross-peaks in the two-dimensional NMR spectra characterized intramolecular proximities between the hydrogen atoms of the fenamates as well as intermolecular interactions between the fenamates and POPC molecules. The peak amplitude normalization for an improved cross-relaxation (PANIC) approach, the isolated spin-pair approximation (ISPA) model, and the two-position exchange model were used to calculate the interproton distances indicative of specific conformations of the fenamates. The results showed that the proportions of the A+C and B+D conformer groups of mefenamic and tolfenamic acids in the presence of POPC were comparable within the experimental error and amounted to 47.8%/52.2% and 47.7%/52.3%, respectively. In contrast, these proportions for the flufenamic acid conformers differed and amounted to 56.6%/43.4%. This allowed us to conclude that when they bind to the POPC model lipid membrane, fenamate molecules change their conformational equilibria.

Ensemble determination by NMR data deconvolution

Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.

New experimental evidence for pervasive dynamics in proteins

There is ample computational, but only sparse experimental data suggesting that pico-ns motions with 1 Å amplitude are pervasive in proteins in solution. Such motions, if present in reality, must deeply affect protein function and protein entropy. Several NMR relaxation experiments have provided insights into motions of proteins in solution, but they primarily report on azimuthal angle variations of vectors of covalently-linked atoms. As such, these measurements are not sensitive to distance fluctuations, and cannot but under-represent the dynamical properties of proteins. Here we analyze a novel NMR relaxation experiment to measure amide proton transverse relaxation rates in uniformly 15 N labeled proteins, and present results for protein domain GB1 at 283 and 303 K. These relaxation rates depend on fluctuations of dipolar interactions between 1 HN and many nearby protons on both the backbone and sidechains. Importantly, they also report on fluctuations in the distances between these protons. We obtained a large mismatch between rates computed from the crystal structure of GB1 and the experimental rates. But when the relaxation rates were calculated from a 200 ns molecular dynamics trajectory using a novel program suite, we obtained a substantial improvement in the correspondence of experimental and theoretical rates. As such, this work provides novel experimental evidence of widespread motions in proteins. Since the improvements are substantial, but not sufficient, this approach may also present a new benchmark to help improve the theoretical forcefields underlying the molecular dynamics calculations.

Water irradiation devoid pulses enhance the sensitivity of 1H,1H nuclear Overhauser effects

The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the structures of medium-to-large size biomolecules and characterize protein-protein, protein-RNA, protein-DNA, and protein-ligand interactions in aqueous solutions. Typical [1H,1H] NOESY pulse sequences incorporate water suppression schemes to reduce the water signal that dominates 1H-detected spectra and minimize NOE intensity losses due to unwanted polarization exchange between water and labile protons. However, at high- and ultra-high magnetic fields, the excitation of the water signal during the execution of the NOESY pulse sequences may cause significant attenuation of NOE cross-peak intensities. Using an evolutionary algorithm coupled with artificial intelligence, we recently designed high-fidelity pulses [Water irrAdiation DEvoid (WADE) pulses] that elude water excitation and irradiate broader bandwidths relative to commonly used pulses. Here, we demonstrate that WADE pulses, implemented into the 2D [1H,1H] NOESY experiments, increase the intensity of the NOE cross-peaks for labile and, to a lesser extent, non-exchangeable protons. We applied the new 2D [1H,1H] WADE-NOESY pulse sequence to two well-folded, medium-size proteins, i.e., the K48C mutant of ubiquitin and the Raf kinase inhibitor protein. We observed a net increase of the NOE intensities varying from 30 to 170% compared to the commonly used NOESY experiments. The new WADE pulses can be easily engineered into 2D and 3D homo- and hetero-nuclear NOESY pulse sequences to boost their sensitivity.

NOE-weighted imaging in tumors using low-duty-cycle 2π-CEST

PURPOSE

Nuclear Overhauser enhancement (NOE)-mediated CEST imaging at -3.5 ppm has shown clinical interest in diagnosing tumors. Multiple-pool Lorentzian fit has been used to quantify NOE, which, however, requires a long scan time. Asymmetric analysis of CEST signals could be a simple and fast method to quantify this NOE, but it has contamination from the amide proton transfer (APT) at 3.5 ppm. This work proposes a new method using an asymmetric analysis of a low-duty-cycle pulsed-CEST sequence with a flip angle of 360°, termed 2π-CEST, to reduce the contribution from APT.

METHODS

Simulations were used to evaluate the capability of the 2π-CEST to reduce APT. Experiments on animal tumor models were performed to show its advantages compared with the conventional asymmetric analysis. Samples of reconstituted phospholipids and proteins were used to evaluate the molecular origin of this NOE.

RESULTS

The 2π-CEST has reduced contribution from APT. In tumors where we show that the NOE is comparable to the APT effect, reducing the contamination from APT is crucial. The results show that the NOE signal obtained with 2π-CEST in tumor regions appears more homogeneous than that obtained with the conventional method. The phantom study showed that both phospholipids and proteins contribute to the NOE at -3.5 ppm.

CONCLUSION

The NOE at -3.5 ppm has a different contrast mechanism from APT and other CEST/NOE effects. The proposed 2π-CEST is more accurate than the conventional asymmetric analysis in detecting NOE, and requires much less scan time than the multiple-pool Lorentzian fit.

Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields

D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D ¹H,¹H-NOESY and 1D ¹H,¹H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly ¹³C-isotope labeled α-D-[1,2-¹³C₂]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on ¹³C,¹³C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.

Metabolomics and NMR

The purpose of this manuscript will be to convince the reader to dive deeper into NMR spectroscopy and prevent the technique from being just another "black-box" in the lab. We will try to concisely highlight interesting topics and supply additional references for further exploration at each stage. The advantages of delving into the technique will be shown. The secondary objective, i.e., avoiding common problems before starting, will hopefully then become clear. Lastly, we will emphasize the spectrometer information needed for manuscript reporting to allow reproduction of results and confirm findings.

Atomic resolution protein allostery from the multi-state structure of a PDZ domain

Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally and dynamically correlated protein sites at atomic resolution. This is demonstrated in the present work for the well-studied PDZ2 domain of protein human tyrosine phosphatase 1E for which protein allostery had been predicted. Two-state protein structures were calculated for both the free form and in complex with the RA-GEF2 peptide using the exact nuclear Overhauser effect (eNOE) method. In the apo protein, an allosteric conformational selection step comprising almost 60% of the domain was detected with an "open" ligand welcoming state and a "closed" state that obstructs the binding site by changing the distance between the β-sheet 2, α-helix 2, and sidechains of residues Lys38 and Lys72. The observed induced fit-type apo-holo structural rearrangements are in line with the previously published evolution-based analysis covering ~25% of the domain with only a partial overlap with the protein allostery of the open form. These presented structural studies highlight the presence of a dedicated highly optimized and complex dynamic interplay of the PDZ2 domain owed by the structure-dynamics landscape.

Advances in the exact nuclear Overhauser effect 2018-2022

The introduction of the exact nuclear Overhauser enhancement (eNOE) methodology to solution-state nuclear magnetic resonance (NMR) spectroscopy results in tighter distance restraints from NOEs than in convention analysis. These improved restraints allow for higher resolution in structure calculation and even the disentanglement of different conformations of macromolecules. While initial work primarily focused on technical development of the eNOE, structural studies aimed at the elucidation of spatial sampling in proteins and nucleic acids were published in parallel prior to 2018. The period of 2018-2022 saw a continued series of technical innovation, but also major applications addressing biological questions. Here, we review both aspects, covering topics from the implementation of non-uniform sampling of NOESY buildups, novel pulse sequences, adaption of the eNOE to solid-state NMR, advances in eNOE data analysis, and innovations in structural ensemble calculation, to applications to protein, RNA, and DNA structure elucidation.

Linker-Dependent Folding Rationalizes PROTAC Cell Permeability

Proteolysis-targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and molecular dynamics (MD) simulations independently to gain insights into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with a low solvent-accessible 3D polar surface area in an apolar environment is correlated to high cell permeability. The chemical nature and the flexibility of the linker were essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, π-π interactions, and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs.

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

An improved, time-efficient approach to extract accurate distance restraints for NMR2 structure calculation

Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged 1 H-1 H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (N MR2 ) to determine the structure of the protein-ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.1 Å because of the asymmetrical nature of the filtered nuclear Overhauser enhancement spectroscopy (NOESY) experiment used in N MR2 . This error is further propagated to the eNOE equations used to fit and extract the distance restraints. In this work, a new analysis method is proposed to obtain inter-molecular distance restraints from the filtered NOESY spectrum more accurately and intuitively by dividing the NOE cross peak by the corresponding diagonal peak of the ligand. The method termed diagonal-normalised eNOEs was tested on the data acquired by on the complex of PIN1 and a small, weak-binding phenylimidazole fragment. N MR2 calculations performed using the distances derived from diagonal-normalised eNOEs yielded the right orientation of the fragment in the binding pocket and produced a structure that more closely resembles the benchmark X-ray structure (2XP6) with an average heavy-atom root-mean-square deviation (RMSD) of 1.681 Å with respect to it, when compared to the one produced with traditional N MR2 with an average heavy atom RMSD of 3.628 Å. This is attributed to the higher precision of the evaluated distance restraints.

Core packing of well-defined X-ray and NMR structures is the same

Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by X-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared with those of high-resolution X-ray crystal structures. Our current work investigates this result in more detail and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and sidechain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by X-ray crystallography at high resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and X-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments.

NMR-Based Configurational Assignments of Natural Products: How Floating Chirality Distance Geometry Calculations Simplify Gambling with 2N-1 Diastereomers

Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the probability of configurational assignments to judge the quality of structural elucidations using Bayesian inference in combination with floating-chirality distance geometry simulations. Based on reference-free NOE/ROE data, residual dipolar couplings (RDCs), and residual quadrupolar couplings (RQCs) in various combinations, we demonstrate how the relative configurations of three natural compounds, namely, jatrohemiketal (1), artemisinin (2), and Taxol (3), can be unambiguously established without the necessity to carry out time-consuming DFT-based configurational and conformational analyses. Our results quantitatively describe how reliably molecular geometries can be inferred from experimental NMR data, thereby unequivocally unveiling remaining assignment ambiguities. The methodology presented here will dramatically reduce the risk of incorrect structural assignments based on the overinterpretation of incomplete data and DFT-based structure models in chemistry.

Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes

Structures of protein–ligand complexes provide critical information for drug design. Most protein–ligand complex structures are determined using X-ray crystallography, but where crystallography is not able to generate a structure for a complex, NMR is often the best alternative. However, the available tools to enable rapid and robust structure determination of protein–ligand complexes by NMR are currently limited. This leads to situations where projects are either discontinued or pursued without structural data, rendering the task more difficult. We previously reported the NMR Molecular Replacement (NMR²) approach that allows the structure of a protein–ligand complex to be determined without requiring the cumbersome task of protein resonance assignment. Herein, we describe the NMR² approach to determine the binding pose of a small molecule in a weak protein–ligand complex by collecting sparse protein methyl-to-ligand NOEs from a selectively labeled protein sample and an unlabeled ligand. In the selective labeling scheme all methyl containing residues of the protein are protonated in an otherwise deuterated background. This allows measurement of intermolecular NOEs with greater sensitivity using standard NOESY pulse sequences instead of isotope-filtered NMR experiments. This labelling approach is well suited to the NMR² approach and extends its utility to include larger protein–ligand complexes.

On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins

Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.

Motional clustering in supra-τc conformational exchange influences NOE cross-relaxation rate

Biomolecular spin relaxation processes, such as the NOE, are commonly modeled by rotational τ_c-tumbling combined with fast motions on the sub-τ_c timescale. Motions on the supra-τ_c timescale, in contrast, are considered to be completely decorrelated to the molecular tumbling and therefore invisible. Here, we show how supra-τ_c dynamics can nonetheless influence the NOE build-up between methyl groups. This effect arises because supra-τ_c motions can cluster the fast-motion ensembles into discrete states, affecting distance averaging as well as the fast-motion order parameter and hence the cross-relaxation rate. We present a computational approach to estimate methyl-methyl cross-relaxation rates from extensive (>100×τ_c) all-atom molecular dynamics (MD) trajectories on the example of the 723-residue protein Malate Synthase G. The approach uses Markov state models (MSMs) to resolve transitions between metastable states and thus to discriminate between sub-τ_c and supra-τ_c conformational exchange. We find that supra-τ_c exchange typically increases NOESY cross-peak intensities. The methods described in this work extend the theory of modeling sub-μs dynamics in spin relaxation and thus contribute to a quantitative estimation of NOE cross-relaxation rates from MD simulations, eventually leading to increased precision in structural and functional studies of large proteins.

A B-factor for NOEs?

Nuclear Overhauser effects (NOEs) are influenced by motion. Here, we derive exact, analytical results for a model of isotropic, harmonic fluctuations of atom positions that corresponds to the one underlying crystallographic B-factors. The model includes steric repulsion and yields closed-form expressions for the expected value of general invertible functions of the distance between two atoms, with the special case r^-6 for NOEs. We discuss the implications for the definition of an NOE-based B-factor in solution NMR.

Statistical evaluation of simulated NMR data of flexible molecules

A new probability score-named χ-probability-is introduced for evaluating the fit of mixed NMR datasets to calculate molecular model ensembles, in order to answer challenging structural questions such as the determination of stereochemical configurations. Similar to the DP4 parameter, the χ-probability is based on Bayes theorem and expresses the probability that an experimental NMR dataset fits to a given individual within a finite set of candidate structures or configurations. Here, the χ-probability is applied to single out the correct configuration in four example cases, with increasing complexity and conformational mobility. The NMR data (which include RDCs, NOE distances and ³J couplings) are calculated from MDOC (Molecular Dynamics with Orientational Constraints) trajectories and are investigated against experimentally measured data. It is demonstrated that this approach singles out the correct stereochemical configuration with probabilities more than 98%, even for highly mobile molecules. In more demanding cases, a decisive χ-probability test requires that the datasets include high-quality NOE distances in addition to RDC values.

Poly(arylisocyanides) as Versatile, Enantiodiscriminating Alignment Media for Small Molecules

Lyotropic liquid crystalline (LLC) phases of amino acid derived polyarylisocyanides were employed as chiral alignment media for the measurement of residual dipolar couplings (RDCs) of small chiral organic molecules. Anisotropic samples in CDCl3 displayed quadrupolar splittings of the deuterium signal in the range of several hundreds of Hertz. The LLC phases showed excellent orienting properties for a broad range of analytes bearing various functional groups. The precise extraction of RDCs in the range of up to ±40 Hertz from F2-coupled HSQC spectra was possible. Additionally, the chiral environment offers the opportunity for diastereomorphous interactions with the enantiomers of chiral analytes leading to two different sets of RDCs. This differential order effect was particularly pronounced with ketones and alcohols.

Contribution of blood to nuclear Overhauser effect at -1.6 ppm

PURPOSE

A relayed nuclear Overhauser enhancement (rNOE) saturation transfer effect at around -1.6 ppm from water, termed NOE(-1.6), was previously reported in rat and human brain, and some publications suggest that it may be related to blood. Here, we studied whether the NOE(-1.6) arises from blood through in vivo and ex vivo experiments.

METHODS

To evaluate the contribution from in vivo blood to NOE(-1.6), intravascular signals in rat brain were suppressed by two approaches: (1) signal acquisition with a diffusion-weighting of b = 400 s/mm2 ; (2) intravascular injection of 5 mg/kg monocrystalline iron oxide nanoparticle (MION). Ex vivo blood sample was also prepared. The signals were acquired using a chemical exchange saturation transfer (CEST) pulse sequence. Multiple-pool Lorentzian fitting of CEST Z-spectra was performed to quantify the NOE(-1.6) signal.

RESULTS

There are no significant variations in the fitted in vivo NOE(-1.6) signals when measured with or without diffusion-weighting, but significant signal decease does occur after injection of MION. The NOE(-1.6) signal from ex vivo blood is weaker than that from in vivo tissues.

CONCLUSION

Considering the relatively small volume of blood in brain, the in vivo experiments with diffusion weighting and the ex vivo experiments both suggest that the NOE(-1.6) is not mainly from blood. The mechanism for the in vivo experiments with MION are less clear. MION not only suppresses MR signals from intravascular space, but changes the susceptibility in the perivascular space. This result suggests that although the NOE(-1.6) is not mainly from blood, it may be vasculature dependent.

NMR-Based Configurational Assignments of Natural Products: Gibbs Sampling and Bayesian Inference Using Floating Chirality Distance Geometry Calculations

Floating chirality restrained distance geometry (fc-rDG) calculations are used to directly evolve structures from NMR data such as NOE-derived intramolecular distances or anisotropic residual dipolar couplings (RDCs). In contrast to evaluating pre-calculated structures against NMR restraints, multiple configurations (diastereomers) and conformations are generated automatically within the experimental limits. In this report, we show that the "unphysical" rDG pseudo energies defined from NMR violations bear statistical significance, which allows assigning probabilities to configurational assignments made that are fully compatible with the method of Bayesian inference. These "diastereomeric differentiabilities" then even become almost independent of the actual values of the force constants used to model the restraints originating from NOE or RDC data.

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.

Rotating-Frame Overhauser Transfer via Long-Lived Coherences

Solution-state distance restraints for protein structure determination with Ångström-level resolution rely on through-space transfer of magnetization between nuclear spins. Such magnetization transfers, named Overhauser effects, occur via dipolar magnetic couplings. We demonstrate improvements in magnetization transfer using long-lived coherences (LLCs)—singlet-triplet superpositions that are antisymmetric with respect to spin-permutation within pairs of coupled magnetic nuclei—as the magnetization source. Magnetization transfers in the presence of radio-frequency irradiation, known as ‘rotating-frame’ Overhauser effects (ROEs), are predicted by theory to improve by the use of LLCs; calculations are matched by preliminary experiments herein. The LLC-ROE transfers were compared to the transmission of magnetization via classical transverse routes. Long-lived coherences accumulate magnetization on an external third proton, K, with transfer rates that depended on the tumbling regime. I,S →K transfers in the LLC configuration for (I,S) are anticipated to match, and then overcome, the same transfer rates in the classical configuration as the molecular rotational correlation times increase. Experimentally, we measured the LLC-ROE transfer in dipeptide AlaGly between aliphatic protons in different residues K = Ala − Hα and (I,S) = Gly − Hα1,2 over a distance dK,I,S = 2.3 Å. Based on spin dynamics calculations, we anticipate that, for such distances, a superior transfer of magnetization occurs using LLC-ROE compared to classical ROE at correlation times above τC=10 ns. The LLC-ROE effect shows potential for improving structural studies of large proteins and offering constraints of increased precision for high-affinity protein-ligand complexes in slow tumbling in the liquid state.

Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation

Mutanobactin D is a non-ribosomal, cyclic peptide isolated from Streptococcus mutans and shows activity reducing yeast-to-hyphae transition as well as biofilm formation of the pathogenic yeast Candida albicans. We report the first total synthesis of this natural product, which relies on enantioselective, zinc-mediated 1,3-dipolar cycloaddition and a sequence of cascading reactions, providing the key lipidated γ-amino acid found in mutanobactin D. The synthesis enables configurational assignment, determination of the dominant solution-state structure, and studies to assess the stability of the lipopeptide substructure found in the natural product. The information stored in the fingerprint region of the IR spectra in combination with quantum chemical calculations proved key to distinguishing between epimers of the α-substituted β-keto amide. Synthetic mutanobactin D drives discovery and analysis of its effect on growth of other members of the human oral consortium. Our results showcase how total synthesis is central for elucidating the complex network of interspecies communications of human colonizers.

Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation

Among the numerous contributions of Geoffrey Bodenhausen to NMR spectroscopy, his developments in the field of spin-relaxation methodology and theory will definitely have a long lasting impact. Starting with his seminal contributions to the excitation of multiple-quantum coherences, he and his group thoroughly investigated the intricate relaxation properties of these "forbidden fruits" and developed experimental techniques to reveal the relevance of previously largely ignored cross-correlated relaxation (CCR) effects, as "the essential is invisible to the eyes". Here we consider CCR within the challenging context of intrinsically disordered proteins (IDPs) and emphasize its potential and relevance for the studies of structural dynamics of IDPs in the future years to come. Conventionally, dynamics of globularly folded proteins are modeled and understood as deviations from otherwise rigid structures tumbling in solution. However, with increasing protein flexibility, as observed for IDPs, this apparent dichotomy between structure and dynamics becomes blurred. Although complex dynamics and ensemble averaging might impair the extraction of mechanistic details even further, spin relaxation uniquely encodes a protein's structural memory. Due to significant methodological developments, such as high-dimensional non-uniform sampling techniques, spin relaxation in IDPs can now be monitored in unprecedented resolution. Not embedded within a rigid globular fold, conventional 15 N spin probes might not suffice to capture the inherently local nature of IDP dynamics. To better describe and understand possible segmental motions of IDPs, we propose an experimental approach to detect the signature of anisotropic segmental dynamics by quantifying cross-correlated spin relaxation of individual 15 N 1 H N and 13 C ' 13 C α spin pairs. By adapting Geoffrey Bodenhausen's symmetrical reconversion principle to obtain zero frequency spectral density values, we can define and demonstrate more sensitive means to characterize anisotropic dynamics in IDPs.

Non-uniform sampling for NOESY? A case study on spiramycin

To date, most nuclear magnetic resonance (NMR)-based 3-D structure determinations of both small molecules and of biopolymers utilize the nuclear Overhauser effect (NOE) via NOESY spectra. The acquisition of high-quality NOESY spectra is a prerequisite for quantitative analysis providing accurate interatomic distances. As the acquisition of NOE build-ups is time-consuming, acceleration of the process by the use of non-uniform sampling (NUS) may seem beneficial; however, the quantitativity of NOESY spectra acquired with NUS has not yet been validated. Herein, NOESY spectra with various extents of NUS have been recorded, artificial NUS spectra with two different sampling schemes created, and by using two different NUS reconstruction algorithms the influence of NUS on the data quality was evaluated. Using statistical analyses, NUS is demonstrated to influence the accuracy of quantitative NOE experiments. The NOE-based distances show an increased error as the sampling density decreases. Weak NOE signals are affected more severely by NUS than more intense ones. The application of NUS with NOESY comes at two major costs: the interatomic distances are determined with lower accuracy and long-range correlations are lost.

Model-Free Approach for the Configurational Analysis of Marine Natural Products

The NMR-based configurational analysis of complex marine natural products is still not a routine task. Different NMR parameters are used for the assignment of the relative configuration: NOE/ROE, homo- and heteronuclear J couplings as well as anisotropic parameters. The combined distance geometry (DG) and distance bounds driven dynamics (DDD) method allows a model-free approach for the determination of the relative configuration that is invariant to the choice of an initial starting structure and does not rely on comparisons with (DFT) calculated structures. Here, we will discuss the configurational analysis of five complex marine natural products or synthetic derivatives thereof: the cis-palau’amine derivatives 1a and 1b, tetrabromostyloguanidine (1c), plakilactone H (2), and manzamine A (3). The certainty of configurational assignments is evaluated in view of the accuracy of the NOE/ROE data available. These case studies will show the prospective breadth of application of the DG/DDD method.

Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems

Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories - no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.

Reducing the measurement time of exact NOEs by non-uniform sampling

We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10 days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4 kDa protein human Pin1, the 4.1 kDa WW domain of Pin1 (both in 3D), and a 4.6 kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.

Unique Usage of a Classical Selective Homodecoupling Sequence for High-Resolution Quantitative 1H NMR

Classical selective homodecoupling was used in a ¹H NMR purity assay to improve accuracy by overcoming spectral overlaps due to ¹H-¹H spin coupling. Dummy irradiation at a specific frequency was used in addition to irradiation at a ¹H resonance of the analyte to avoid irradiation bias. The method was validated in a ¹H NMR purity assay of high-purity diethyl phthalate (National Metrology Institute of Japan Certified Reference Material (NMIJ CRM), purity: 99.98%). The obtained purity value biases were 0.27% or less. The utility of the method was demonstrated in another ¹H NMR purity assay of dipropyl phthalate (NMIJ CRM, purity: 98.41%), which contained a tiny amount of the structurally similar compound methyl propyl phthalate as an impurity. An accurate assay was achieved with the method, giving a purity of 98.39%, whereas the conventional method gave a purity 99.13%.

Reference-free NOE NMR analysis

Nuclear Overhauser Effect (NOE) methods in NMR are an important tool for 3D structural analysis of small molecules. Quantitative NOE methods conventionally rely on reference distances, known distances that have to be spectrally separated and are not always available. Here we present a new method for evaluation and 3D structure selection that does not require a reference distance, instead utilizing structures optimized by molecular mechanics, enabling NOE evaluation even on molecules without suitable reference groups.

A quantitative Nuclear Overhauser Effect (NOE) analysis approach that avoids the use of and internal reference distance to perform molecular configuration selection.

The simulation of NMR data of flexible molecules: sagittamide A as an example for MD simulations with orientational constraints

The recently developed MDOC (Molecular Dynamics with Orientational Constraints) simulation is applied for the first time to a fully flexible molecule. MDOC simulations aim to single out the naturally existing configuration of molecules and to elucidate conformer populations. The performance of the method was first demonstrated on a well-studied test case, the five-membered ring lactone (α-methylene-γ-butyrolactone). In the case of sagittamide A, one-bond ¹H-¹³C residual dipolar couplings (RDC) are used as orientational constraints that reorient the molecule or parts of it. In addition, NOE distances and ³J scalar couplings are used as constraints. Five possible configurations of sagittamide A (labelled a to e) are considered. One experimental RDC value per flexible unit was available and this was not sufficient to single out one valid configuration. The problem could be solved by including NOE distances as well as ³J couplings as complementary constraints into the MDOC simulations. In accordance with former investigations, we confirmed the configuration a for the natural product. A detailed analysis of conformers of the central chain of 6 chiral carbon atoms could be given by inspecting the MDOC trajectory. The relative abundance of these conformers is crucial in fulfilling all three sets of constraints.