Effects of Xylanase A double mutation on substrate specificity and structural dynamics.

While protein activity is traditionally studied with a major focus on the active site, the activity of enzymes has been hypothesized to be linked to the flexibility of adjacent regions, warranting more exploration into how the dynamics in these regions affects catalytic turnover. One such enzyme is Xylanase A (XylA), which cleaves hemicellulose xylan polymers by hydrolysis at internal ß-1,4-xylosidic linkages. It contains a "thumb" region whose flexibility has been suggested to affect the activity. The double mutation D11F/R122D was previously found to affect activity and potentially bias the thumb region to a more open conformation. We find that the D11F/R122D double mutation shows substrate-dependent effects, increasing activity on the non-native substrate ONPX2 but decreasing activity on its native xylan substrate. To characterize how the double mutant causes these kinetics changes, nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were used to probe structural and flexibility changes. NMR chemical shift perturbations revealed structural changes in the double mutant relative to the wild-type, specifically in the thumb and fingers regions. Increased slow-timescale dynamics in the fingers region was observed as intermediate-exchange line broadening. Lipari-Szabo order parameters show negligible changes in flexibility in the thumb region in the presence of the double mutation. To help understand if there is increased energetic accessibility to the open state upon mutation, alchemical free energy simulations were employed that indicated thumb opening is more favorable in the double mutant. These studies aid in further characterizing how flexibility in adjacent regions affects the function of XylA.

NMR Studies of the Interactions between Sialyllactoses and the Polysialytransferase Domain for Polysialylation Inhibition.

It is known that sialyllactose (SL) in mammalians is a major source of sialic acid (Sia), which can further form cytidine monophosphate sialic acid (CMP-Sia), and the final product is polysialic acid (polySia) using polysialyltransferases (polySTs) on the neural cell adhesion molecule (NCAM). This process is called NCAM polysialylation. The overexpression of polysialylation is strongly related to cancer cell migration, invasion, and metastasis. In order to inhibit the overexpression of polysialylation, in this study, SL was selected as an inhibitor to test whether polysialylation could be inhibited. Our results suggest that the interactions between the polysialyltransferase domain (PSTD) in polyST and CMP-Siaand the PSTD and polySia could be inhibited when the 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL) concentration is about 0.5 mM or 6'-SL and 3 mM, respectively. The results also show that SLs (particularly for 3'-SL) are the ideal inhibitors compared with another two inhibitors, low-molecular-weight heparin (LMWH) and cytidine monophosphate (CMP), because 3'-SL can not only be used to inhibit NCAM polysialylation, but is also one of the best supplements for infant formula and the gut health system.

Prevalence of TERT Promoter Mutations in Orbital Solitary Fibrous Tumors.

The orbital manifestation of a solitary fibrous tumor (SFT) is exceptionally rare and poses specific challenges in diagnosis and treatment. Its rather exceptional behavior among all SFTs comprises a high tendency towards local recurrence, but it rarely culminates in metastatic disease. This raises the question of prognostic factors in orbital SFTs (oSFTs). Telomerase reverse transcriptase (TERT)-promoter mutations have previously been linked to an unfavorable prognosis in SFTs of other locations. We analyzed the prevalence of TERT promoter mutations of SFTs in the orbital compartment. We performed a retrospective, descriptive clinico-histopathological analysis of nine cases of oSFTs between the years of 2017 and 2021. A TERT promoter mutation was present in one case, which was classified with intermediate metastatic risk. Local recurrence or progress occurred in six cases after primary resection; no distant metastases were reported. Multimodal imaging repeatedly showed particular morphologic patterns, including tubular vascular structures and ADC reduction. The prevalence of the TERT promoter mutation in oSFT was 11%, which is similar to the prevalence of extra-meningeal SFTs of the head and neck and lower than that in other extra-meningeal compartments. In the present study, the TERT promoter mutation in oSFT manifested in a case with an unfavorable prognosis, comprising aggressive local tumor growth, local recurrence, and eye loss.

Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals.

We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.

Distortion-free water-fat separated diffusion-weighted imaging using spatiotemporal joint reconstruction.

PURPOSE: Diffusion-weighted imaging (DWI) suffers from geometric distortion and chemical shift artifacts due to the commonly used Echo Planar Imaging (EPI) trajectory. Even with fat suppression in DWI, severe B0 and B1 variations can result in residual fat, which becomes both a source of image artifacts and a confounding factor in diffusion-weighted contrast in distinguishing benign and malignant tissues. This work presents a method for acquiring distortion-free diffusion-weighted images using spatiotemporal acquisition and joint reconstruction. Water-fat separation is performed by chemical-shift encoding. METHODS: Spatiotemporal acquisition is employed to obtain distortion-free images at a series of echo times. Chemical-shift encoding is used for water-fat separation. Reconstruction and separation are performed jointly in the spat-spectral domain. To address the shot-to-shot motion-induced phase in DWI, an Fast Spin Echo (FSE)-based phase navigator is incorporated into the sequence to obtain distortion-free phase information. The proposed method was validated in phantoms and in vivo for the brain, head and neck, and breast. RESULTS: The proposed method enables the acquisition of distortion-free diffusion-weighted images in the presence of B0 field inhomogenieties commonly observed in the body. Water and fat components are separated with no obvious spectral leakage artifacts. The estimated Apparent Diffusion Coefficient (ADC) is comparable to that of multishot DW-EPI. CONCLUSION: Distortion-free, water-fat separated diffusion-weighted images in body can be obtained through the utilization of spatiotemporal acquisition and joint reconstruction methods.

Chemical shift-encoded multishot EPI for navigator-free prostate DWI.

PURPOSE: DWI is an important contrast for prostate MRI to enable early and accurate detection of cancer. This study introduces a Dixon 3-shot-EPI protocol with structured low-rank reconstruction for navigator-free DWI. The aim is to overcome the limitations of single-shot EPI (ssh-EPI), such as geometric distortions and fat signal interference, while addressing the motion-induced phase variations of multishot EPI and simultaneously allowing water/fat separation. METHODS: DWI data were acquired from 7 healthy volunteers using both Dixon 3-shot EPI and standard fat-suppressed ssh-EPI with similar scan times for comparison. Two readers evaluated image quality using a 5-point Likert scale regarding different aspects. The ADC values were quantitatively compared between protocols. To show feasibility in a clinical setting, the protocol was applied to two patients. RESULTS: From the reader scores, Dixon 3-shot EPI significantly reduced geometric distortion compared with ssh-EPI (p < 0.01), with no significant differences in edge definition, SNR, or overall image quality. There was no significant difference in ADC values between the two protocols. However, the Dixon multishot-EPI protocol offered advantages such as self-referenced B0 map-driven distortion correction, greater flexibility in imaging parameters, and superior fat suppression. In the patient data, the lesion could be clearly identified in both protocols and on the associated ADC maps. CONCLUSION: The proposed Dixon 3-shot-EPI protocol shows promise as an alternative to ssh-EPI for prostate DWI, providing reduced geometric distortions and improved fat suppression. It addresses common DWI issues based on EPI and enhances scanning flexibility, indicating potential for optimized imaging.

Feasibility of omega-3 fatty acid fraction mapping using chemical shift encoding-based imaging at 3 T.

PURPOSE: The aim of this work is to develop an ω-3 fatty acid fraction mapping method at 3 T based on a chemical shift encoding model, to assess its performance in a phantom and in vitro study, and to further demonstrate its feasibility in vivo. METHODS: A signal model was heuristically derived based on spectral appearance and theoretical considerations of the corresponding molecular structures to differentiate between ω-3 and non-ω-3 fatty acid substituents in triacylglycerols in addition to the number of double bonds (ndb), the number of methylene-interrupted double bonds (nmidb), and the mean fatty acid chain length (CL). First, the signal model was validated using single-voxel spectroscopy and a time-interleaved multi-echo gradient-echo (TIMGRE) sequence in gas chromatography-mass spectrometry (GC-MS)-calibrated oil phantoms. Second, the TIMGRE-based method was validated in vitro in 21 adipose tissue samples with corresponding GC-MS measurements. Third, an in vivo feasibility study was performed for the TIMGRE-based method in the gluteal region of two healthy volunteers. Phantom and in vitro data was analyzed using a Bland-Altman analysis. RESULTS: Compared with GC-MS, MRS showed in the phantom study significant correlations in estimating the ω-3 fraction (p < 0.001), ndb (p < 0.001), nmidb (p < 0.001), and CL (p = 0.001); MRI showed in the phantom study significant correlations (all p < 0.001) for the ω-3 fraction, ndb, and nmidb, but no correlation for CL. Also in the in vitro study, significant correlations (all p < 0.001) between MRI and GC-MS were observed for the ω-3 fraction, ndb, and nmidb, but not for CL. An exemplary ROI measurement in vivo in the gluteal subcutaneous adipose tissue yielded (mean ± standard deviation) 0.8% ± 1.9% ω-3 fraction. CONCLUSION: The present study demonstrated strong correlations between gradient-echo imaging-based ω-3 fatty acid fraction mapping and GC-MS in the phantom and in vitro study. Furthermore, feasibility was demonstrated for characterizing adipose tissue in vivo.

Fingerprints of Chalcogen Bonding Revealed Through 77Se-NMR.

77Se-NMR is used to characterise several chalcogen bonded complexes of derivatives of the organoselenium drug ebselen, exploring a range of electron demand. NMR titration experiments support the intuitive understanding that chalcogen bond donors bearing more electron withdrawing substituents give rise stronger chalcogen bonds. The chemical shift of the selenium nucleus is also shown to move upfield as it participates in a chalcogen bond. Solid-state NMR is used to explore chalcogen bonding in co-crystals. Due to the lack of molecular reorientation on the NMR timescale in the solid state, the shape of the chemical shift tensor can be determined using this technique. A range of co-crystals are shown to have extremely large chemical shift anisotropy, which suggests a strongly anisotropic electron density distribution around the selenium atom. A single crystal NMR experiment was conducted using one of the co-crystals, affording the absolute orientation of the chemical shift tensor within the crystal. This showed that the selenium nucleus is strongly shielded in the direction of the chalcogen bond (due to the approach of the lone pair of the Lewis base), and strongly deshielded in the perpendicular direction. The orientation of the deshielded axis is consistent with the presence of a second σ-hole which is not participating in a chalcogen bond, showing the profound effect of electron density anisotropy on the chemical shift.

Chemical Shift-Encoded MRI of the Lumbar Vertebral Bone Marrow for Detecting Osteoporosis With Low Trabecular Bone Quality in Patients With Breast Cancer Receiving Aromatase Inhibitors.

BACKGROUND: Osteoporosis with low trabecular bone quality (OLB) in patients with breast cancer receiving aromatase inhibitor (AI) therapy is associated with an increased risk of vertebral fractures. The capability of chemical shift-encoded MRI (CSE-MRI) in detecting OLB needs to be investigated. PURPOSE: To assess the diagnostic performance of proton density fat fraction (PDFF) and R2* measurements from CSE-MRI for detecting OLB in postmenopausal women with breast cancer undergoing AI therapy. STUDY TYPE: Prospective. POPULATION: 126 postmenopausal females (mean age: 69.5 ± 8.8 years) receiving AIs (average period: 41.6 ± 26.5 months) after breast cancer surgery. FIELD STRENGTH/SEQUENCE: 1.5-T, three-dimensional CSE-MRI (six echoes), T1-weighted Dixon, short tau inversion recovery, and diffusion-weighted images. ASSESSMENT: Both CSE-MRI and dual-energy x-ray absorptiometry were performed on the same day. Measurements included averaged PDFF, R2*, bone mineral density (BMD), and trabecular bone score (TBS) from L1 to L4 vertebrae. A T-score ≤ -2.5 from BMD measurements indicated osteoporosis, whereas T-scores of ≤ - 2.5 plus TBS ≤-3.7 indicated OLB. The diagnostic performance of PDFF, R2*, and the combination of PDFF and R2* for identifying osteoporosis or OLB was assessed. STATISTICAL TESTS: Student's t-test; Mann-Whitney U test; χ2 or Fisher exact tests; Pearson correlation; multivariate analysis; Receiver operating characteristic (ROC) analysis with the area under the curve (AUC); logistic regression model; intraclass correlation coefficient. A P-value <0.05 was considered statistically significant. RESULTS: For detecting osteoporosis, AUC values were 0.59 (PDFF), 0.66 (R2*), and 0.65 (combined PDFF and R2*). Significant mean differences were noted between patients with and without OLB for PDFF (66.11 ± 5.36 vs. 57.49 ± 6.43) and R2* (46.62 ± 9.24 vs. 63.36 ± 12.44). AUC values for detecting OLB were 0.75 (PDFF), 0.82 (R2*), and 0.84 (combined PDFF and R2*). DATA CONCLUSION: R2* may perform better than PDFF for identifying OLB in patients with breast cancer receiving AIs. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY: Stage 4.

Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution.

The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with limited information on protein flexibility. An experimentally verified structural model of the binding interface in the native solution-state would support medicinal chemists in their molecular design decisions. Here we demonstrate that protein-bound ligand 1 H NMR chemical shifts are highly sensitive and accurate probes for the immediate chemical environment of protein-ligand interfaces. By comparing the experimental ligand 1 H chemical shift values with those computed from the X-ray structure using quantum mechanics methodology, we identify significant disagreements for parts of the ligand between the two experimental techniques. We show that quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) ensembles can be used to refine initial X-ray co-crystal structures resulting in a better agreement with experimental 1 H ligand chemical shift values. Overall, our findings highlight the usefulness of ligand 1 H NMR chemical shift information in combination with a QM/MM MD workflow for generating protein-ligand ensembles that accurately reproduce solution structural data.

Aromaticity and Antiaromaticity Reversals between the Electronic Ground State and the Two Lowest Triplet States of Thiophene.

It is shown, by examining the variations in off-nucleus isotropic magnetic shielding around a molecule, that thiophene which is aromatic in its electronic ground state (S0) becomes antiaromatic in its lowest triplet state (T1) and then reverts to being aromatic in T2. Geometry relaxation has an opposite effect on the aromaticities of the ππ* vertical T1 and T2: The antiaromaticity of T1 is reduced whereas the aromaticity of T2 is enhanced. The shielding picture around T2 is found to closely resemble those around certain second singlet ππ* excited states (S2), for example, those of benzene and cyclooctatetraene, thought to be "strongly aromatic" because of their very negative nucleus-independent chemical shift (NICS) values. It is argued that while NICS values correctly follow the changes in aromaticity along the potential energy surface of a single electronic state, the use of NICS values for the purpose of quantitative comparisons between the aromaticities of different electronic states cannot be justified theoretically and should be avoided. "Strongly aromatic" S2 and T2 states should be referred to simply as "aromatic" because detailed comparisons between the properties of these states and those of the corresponding S0 states do not suggest higher levels of aromaticity.

Sensitivity Enhancement of Ultra-Wideline NMR by Progressive Saturation of the Proton Reservoir Under Magic-Angle Spinning.

Solid-state NMR of low-γ nuclides is often characterized by low sensitivity and by significant spectral broadenings induced by the quadrupolar and the chemical-shift anisotropy interactions. Herein, we introduce an indirect acquisition method, termed PROgressive Saturation of the Proton Reservoir Under Spinning (PROSPRUS), which could facilitate the acquisition of ultra-wideline NMR spectra under magic-angle spinning (MAS), in systems with a sufficiently long dipolar relaxation time, T1D. PROSPRUS NMR relies on the generation of so-called second-order dipolar order among abundant protons undergoing MAS, and on the subsequent depletion of this dipolar order by a series of looped cross-polarization events, transferring the proton order into polarization of the low-γ I-nuclei as a function of the latter's offsets. While the spin dynamics of the ensuing experiment is complex, particularly when dealing with narrow I spectral lines, it is shown that PROSPRUS can lead to faithful lineshapes for ultra-wideline spin-1/2 and spin-1 species, providing high sensitivity with extremely low RF power requirements. It is also shown that the ensuing 1H-detected PROSPRUS experiments can efficiently characterize I-spin lineshapes in excess of 1 MHz without having to retune electronics, while providing improvements in sensitivity per unit time over current broadband direct-detection methods by up to a factor of four.

Non-contrast spectral CT vs chemical-shift MRI in discriminating lipid-poor adrenal lesions.

OBJECTIVES: To compare the diagnostic performance of conventional non-contrast CT, dual-energy spectral CT, and chemical-shift MRI (CS-MRI) in discriminating lipid-poor adenomas (> 10-HU on non-contrast CT) from non-adenomas. METHODS: A total of 110 patients (69 men; 41 women; mean age 66.5 ± 13.4 years) with 80 lipid-poor adenomas and 30 non-adenomas who underwent non-contrast dual-layer spectral CT and CS-MRI were retrospectively identified. For each lesion, non-contrast attenuation on conventional 120-kVp images, ΔHU-index ([attenuation difference between virtual monoenergetic 140-keV and 40-keV images]/conventional attenuation × 100), and signal intensity index (SI-index) were quantified. Each parameter was compared between adenomas and non-adenomas using the Mann-Whitney U-test. The area under the receiver operating characteristic curve (AUC) and sensitivity to achieve > 95% specificity for adenoma diagnosis were determined. RESULTS: Conventional non-contrast attenuation was lower in adenomas than in non-adenomas (22.4 ± 8.6 HU vs 32.8 ± 48.5 HU), whereas ΔHU-index (148.0 ± 103.2 vs 19.4 ± 25.8) and SI-index (41.6 ± 19.6 vs 4.2 ± 10.2) were higher in adenomas (all, p < 0.001). ΔHU-index showed superior performance to conventional non-contrast attenuation (AUC: 0.919 [95% CI: 0.852-0.963] vs 0.791 [95% CI: 0.703-0.863]; sensitivity: 75.0% [60/80] vs 27.5% [22/80], both p < 0.001), and near equivalent to SI-index (AUC: 0.952 [95% CI: 0.894-0.984], sensitivity 85.0% [68/80], both p > 0.05). Both the ΔHU-index and SI-index provided a sensitivity of 96.0% (48/50) for hypoattenuating adenomas (≤ 25 HU). For hyperattenuating (> 25 HU) adenomas, SI-index showed higher sensitivity than ΔHU-index (66.7% [20/30] vs 40.0% [12/30], p = 0.022). CONCLUSIONS: Non-contrast spectral CT and CS-MRI outperformed conventional non-contrast CT in distinguishing lipid-poor adenomas from non-adenomas. While CS-MRI demonstrated superior sensitivity for adenomas measuring > 25 HU, non-contrast spectral CT provided high discriminative values for adenomas measuring ≤ 25 HU. CLINICAL RELEVANCE STATEMENT: Spectral attenuation analysis improves the diagnostic performance of non-contrast CT in discriminating lipid-poor adrenal adenomas, potentially serving as an alternative to CS-MRI and obviating the necessity for additional diagnostic workup in indeterminate adrenal incidentalomas, particularly for lesions measuring ≤ 25 HU. KEY POINTS: Incidental adrenal lesion detection has increased as abdominal CT use has become more frequent. Non-contrast spectral CT and CS-MRI differentiated lipid-poor adenomas from non-adenomas better than conventional non-contrast CT. For lesions measuring ≤ 25 HU, spectral CT may obviate the need for additional evaluation.

Accelerated Chemical Shift Encoded Cardiac MRI with Use of Resolution Enhancement Network.

BACKGROUND: Cardiovascular magnetic resonance (CMR) chemical shift encoding (CSE) enables myocardial fat imaging. We sought to develop a deep learning network (FastCSE) to accelerate CSE. METHODS: FastCSE was built on a super-resolution generative adversarial network extended to enhance complex-valued image sharpness. FastCSE enhances each echo image independently before water-fat separation. FastCSE was trained with retrospectively identified cines from 1519 patients (56 ± 16 years; 866 men) referred for clinical 3T CMR. In a prospective study of 16 participants (58 ± 19 years; 7 females) and 5 healthy individuals (32 ± 17 years; 5 females), dual-echo CSE images were collected with 1.5 × 1.5mm2, 2.5 × 1.5 mm2, and 3.8 × 1.9mm2 resolution using generalized autocalibrating partially parallel acquisition (GRAPPA). FastCSE was applied to images collected with resolution of 2.5 × 1.5mm2 and 3.8 × 1.9 mm2 to restore sharpness. Fat images obtained from two-point Dixon reconstruction were evaluated using a quantitative blur metric and analyzed with 5-way analysis of variance. RESULTS: FastCSE successfully reconstructed CSE images inline. FastCSE acquisition, with a resolution of 2.5 × 1.5mm² and 3.8 × 1.9 mm², reduced the number of breath-holds without impacting visualization of fat by approximately 1.5-fold and 3-fold compared to GRAPPA acquisition with a resolution of 1.5 × 1.5 mm², from 3.0 ± 0.8 breath-holds to 2.0 ± 0.2 and 1.1 ± 0.4 breath-holds, respectively. FastCSE improved image sharpness and removed ringing artifacts in GRAPPA fat images acquired with a resolution of 2.5 × 1.5 mm2 (0.31 ± 0.03 vs. 0.35 ± 0.04, P < 0.001) and 3.8 × 1.9 mm2 (0.31 ± 0.03 vs. 0.42 ± 0.06, P < 0.001). Blurring in FastCSE images was similar to blurring in images with 1.5 × 1.5 mm² resolution (0.32 ±0.03 vs. 0.31 ± 0.03, P = 0.78; 0.32 ± 0.03 vs. 0.31 ± 0.03, P = 0.90). CONCLUSION: We showed that a deep learning-accelerated CSE technique based on complex-valued resolution enhancement can reduce the number of breath-holds in CSE imaging without impacting the visualization of fat. FastCSE showed similar image sharpness compared to a standardized parallel imaging method.

Solid-state NMR spectra of amino acid enantiomers and their relative intensities.

Under normal experimental conditions in an achiral environment, NMR spectra of enantiomers have chemical shifts and J couplings which are not differentiable. In this work, the reproducibility of spectral intensities for pairs of amino acid enantiomers, as well as factors influencing these intensities, is assessed using 13C and 15N cross-polarization magic-angle spinning (CP/MAS) NMR spectroscopy. Prompted by a recent literature debate over a possible influence of the chirality-induced spin selectivity (CISS) effect on spectral intensities obtained in CP/MAS NMR experiments carried out on enantiomers, a number of control experiments were performed with recycle delays of at least 5T1. These included the analysis of proton-decoupled Bloch decay solid-state NMR spectra as well as solution NMR spectra where the cross polarization process is absent. Bloch decay and CP/MAS NMR spectra yield the same relative intensities for pairs of enantiomers while solution NMR spectra provide relative intensities closest to unity. Differences of plus-or-minus a few percent in the D/L spectral intensity ratios observed in all solid-state NMR experiments are due to sample preparation (i.e., grinding, particle size, partial amorphization) and limitations on sample purity. As previously described in the literature, more drastic intensity differences on the order of 50% are easily created by ball milling the samples. Finally, apodization is shown to invert the apparent D/L ratio in low signal-to-noise 15N CP/MAS NMR spectra of aspartic acid enantiomers. In summary, no spectral intensity differences attributable to enantiomerism are identified.

Unveiling the "invisible" druggable conformations of GDP-bound inactive Ras.

The prevalent view on whether Ras is druggable has gradually changed in the recent decade with the discovery of effective inhibitors binding to cryptic sites unseen in the native structures. Despite the promising advances, therapeutics development toward higher potency and specificity is challenged by the elusive nature of these binding pockets. Here we derive a conformational ensemble of guanosine diphosphate (GDP)-bound inactive Ras by integrating spin relaxation-validated atomistic simulation with NMR chemical shifts and residual dipolar couplings, which provides a quantitative delineation of the intrinsic dynamics up to the microsecond timescale. The experimentally informed ensemble unequivocally demonstrates the preformation of both surface-exposed and buried cryptic sites in Ras•GDP, advocating design of inhibition by targeting the transient druggable conformers that are invisible to conventional experimental methods. The viability of the ensemble-based rational design has been established by retrospective testing of the ability of the Ras•GDP ensemble to identify known ligands from decoys in virtual screening.

Distinguishing between COOH, COO- , and hydrogen disordered COOH sites in solids with 13 C chemical shift anisotropy and T1 measurements.

Since 1993, it has been known that 13 C chemical shift tensor (i.e., δ11 , δ22 , and δ33 ) provides information sufficient to distinguish between COOH and COO- sites. Herein, four previously unreported metrics are proposed for differentiating COOH/COO- moieties. A new relationship is also introduced that correlates the asymmetry (i.e., δ11 -δ22 ) of COOH sites to the proximity of hydrogen bond donating partners within 2.6 Å with high accuracy (±0.05 Å). Conversely, a limitation to all proposed metrics is that they fail to distinguish between COO- and hydrogen disordered COOH sites. To reconcile this omission, a new approach is proposed based on T1 measurements of both 1 H and 13 C. The 13 C T1 values are particularly sensitive with the T1 for hydrogen disordered COOH moieties found to be nearly six times smaller than T1 's from COO- sites.

Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds.

This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations.

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non α-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic 15 N chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable 15 N CS tensor data. The averaged dipolar 1 H-15 N couplings and the δzz tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ß-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA.

13 C NMR as an analytical tool for the detection of carbonic acid and pKa determination.

NMR spectroscopy has become a standard technique in studies both on carbon capture and storage. 13 C NMR allows the detection of two peaks for carbonated aqueous samples: one for CO2(aq) and another one for the species H2 CO3 , HCO3 - , and CO3 2- -herein collectively named Hx CO3 x-2 . The chemical shift of this second peak depends on the molar fraction of the three species in equilibrium and has been used to assess the equilibrium between HCO3 - and CO3 2- . The detection of H2 CO3 at low pH solutions is hindered, because of the concurrent liberation of CO2 when the medium is acidified. Herein, a valved NMR tube facilitates the detection of the Hx CO3 x-2 peak across a wide pH range, even at pH 1.8 where the dominant species is H2 CO3 . The method employed the formation of frozen layers of NaH13 CO3 and acid solutions within the tube, which are mixed as the tube reaches room temperature. At this point, the tube is already securely sealed, preventing any loss of CO2 to the atmosphere. A spectrophotometry approach allowed the measurement of the actual pH inside the pressurized NMR tube. The chemical shift for H2 CO3 was determined as 160.33 ± 0.03 ppm, which is in good agreement with value obtained by DFT calculations combined with Car-Parrinello molecular dynamics. The H2 CO3 pKa value determined by the present method was 3.41 ± 0.03, for 15% D2 O aqueous medium and 0.8 mol/L ionic strength. The proposed method can be extended to studies about analogs such as alkyl carbonic and carbamic acids.