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

Detection of 15N-labeled metabolites in microbial extracts using AI-designed broadband pulses for 1H, 15N heteronuclear NMR spectroscopy

Approximately 40% of bacterial and mammalian metabolites contain nitrogen-based chemical moieties such as amides, amines, and imines. The identification and quantification of these groups via 2D 1H,15N heteronuclear NMR spectroscopy have broadened the catalog of NMR-detected metabolites. However, these NMR experiments necessitate broadband radiofrequency (RF) pulses for inversion and refocusing operations to encompass the full range of 15N chemical shifts, a challenge that becomes increasingly apparent at high and ultra-high magnetic fields. Here, we show that a newly AI-designed broadband 15N universal 180° pulse for both inversion and refocusing incorporated in the 2D 1H, 15N heteronuclear single quantum coherence (2D 1H-15N BB-HSQC) experiment significantly enhances spectral sensitivity. We demonstrate the advantage of the new technique by analyzing the crude extract of Micromonospora sp. WMMC264, a microbial strain that produces siderophores for iron absorption from the environment. The implementation of the AI-designed pulse in the 2D 1H-15N BB-HSQC experiment will contribute to advancing the analysis of nitrogen-containing metabolites in biological fluids and cell extracts.

Detection of Exchangeable Protons in NMR Metabolomic Analysis Using AI-Designed Water Irradiation Devoid Pulses

1H NMR spectroscopy has enabled the quantitative profiling of metabolites in various biofluids, emerging as a possible diagnostic tool for metabolic disorders and other diseases. To boost the signal-to-noise ratio and detect proton resonances near the water signal, current 1H NMR experiments require solvent suppression schemes (e.g., presaturation, jump-and-return, WATERGATE, excitation sculpting, etc.). Unfortunately, these techniques affect the quantitative assessment of analytes containing exchangeable protons. To address this issue, we introduce two new one-dimensional (1D) 1H NMR techniques that eliminate the water signal, preserving the intensities of exchangeable protons. Using GENETICS-AI, a software that combines an evolutionary algorithm and artificial intelligence, we tailored new water irradiation devoid (WADE) pulses and optimized the 1D 1H NOESY sequence for metabolomic analysis. When applied to human urine samples, kidney tissue extract, and plasma, the WADE technique allowed for accurate measurement of typical metabolites and direct quantification of urea, which is usually challenging to measure using standard NMR experiments. We anticipate that these new NMR techniques will significantly improve the accuracy and reliability of metabolite quantitative assessment for a wide range of biological fluids.

Toward Absolute Quantification of Soluble Proteins via Proton Nuclear Magnetic Resonance Spectroscopy: Total Protein Concentration in Blood Plasma

For absolute protein quantification using nuclear magnetic resonance (NMR) spectroscopy, we considered proteins as homopolymers and effective amino acid (AA) residues (AAREff) as monomer units. For diverse classes of proteins, we determined the AAREff molecular weight as 111.5 ± 3.2 Da and the number of hydrogens per AA as 7.8 ± 0.2. Their ratio of 14.3 ± 0.3 (g/LP)/(mol/LH) remains constant across various protein classes and is equivalent to Kjeldahl's nitrogen-to-protein conversion constant of 5.78 ± 0.29 gN/gP. By analogy to the Kjeldahl method, we suggest that the total integral of a 1H NMR solution protein spectrum could be used for total protein quantification. We synthesized low-resolution protein spectra from the weighted sums of individual AA spectra and compared them with experimental spectra. In the methyl region, the ratio of the protein mass to the total number of protons in the synthetic spectra (corrected for the chemical shift mismatch) was ∼1 (mg/mL)/mM, which agrees with an earlier reported experimental ratio for urine (1.05 ± 0.06 (mg/mL)/mM). For human blood plasma, in the methyl region, we found empirical ratios of 1.115 ± 0.006 (mg/mL)/mM (using 96 patient samples) and 1.121 ± 0.011 (mg/mL)/mM for the NIST plasma standard. This numerical agreement points to universal conversion constants, i.e., protein mixtures with unknown compositions could be quantified without the need for calibration standards by measuring the millimolar proton concentration within the methyl region of the NMR spectrum using the same conversion constant.

Slice through the water-Exploring the fundamental challenge of water suppression for benchtop NMR systems

Benchtop NMR provides improved accessibility in terms of cost, space, and technical expertise. In turn, this encourages new users into the field of NMR spectroscopy. Unfortunately, many interesting samples in education and research, from beer to whole blood, contain significant amounts of water that require suppression in 1H NMR in order to recover sample information. However, due to the significant reduction in chemical shift dispersion in benchtop NMR systems, the sample signals are much closer to the water resonance compared to those in a corresponding high-field NMR spectrum. Therefore, simply translating solvent suppression experiments intended for high-field NMR instruments to benchtop NMR systems without careful consideration can be problematic. In this study, the effectiveness of several popular water suppression schemes was evaluated for benchtop NMR applications. Emphasis is placed on pulse sequences with no, or few, adjustable parameters making them easy to implement. These fall into two main categories: (1) those based on Pre-SAT including Pre-SAT, PURGE, NOESY-PR, and g-NOESY-PR and (2) those based on binomial inversion including JRS and W5-WATERGATE. Among these schemes, solvent suppression sequences based on Pre-SAT offer a general approach for easy solvent suppression for samples with higher analyte concentrations (sucrose standard and Redbull™). However, for human urine, binomial-like sequences were required. In summary, it is demonstrated that highly efficient water suppression approaches can be implemented on benchtop NMR systems in a simple manner, despite the limited spectral dispersion, further illustrating the potential for widespread implementation of these approaches in education and research.

AI-designed RF pulses enable fast pulsing heteronuclear multiple quantum coherence NMR experiment at high and ultra-high magnetic fields

We present a new AI-optimized 2D heteronuclear multiple quantum coherence (RAPID-HMQC) pulse sequence for NMR spectroscopy. RAPID-HMQC is a longitudinal 1H relaxation-optimized experiment with new AI-designed band-selective pulses to accelerate the analysis of organic compounds, metabolites, biopolymers, and real-time monitoring of dynamic processes at high- and ultra-high magnetic fields.