Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR

Ultrafast Nuclear Magnetic Resonance as a Tool to Detect Rapid Chemical Change in Solution

Ultrafast nuclear magnetic resonance (NMR) uses spatial encoding to record an entire two-dimensional data set in just a single scan. The approach can be applied to either Fourier-transform or Laplace-transform NMR. In both cases, acquisition times are significantly shorter than traditional 2D/Laplace NMR experiments, which allows them to be used to monitor rapid chemical transformations. This Perspective outlines the principles of ultrafast NMR and focuses on examples of its use to detect fast molecular conversions in situ with high temporal resolution. We discuss how this valuable tool can be applied in the future to study a much wider variety of novel reactivity.

The matrix pencil as a tunable filter

Despite inherent sensitivity constraints, nuclear magnetic resonance (NMR) plays an indispensable role in probing molecular structures and dynamics across scientific disciplines. Remarkably, while extensive efforts have targeted instrumental and experimental sensitivity improvements, comparatively little focus has been dedicated to sensitivity enhancement through signal analysis. Amidst this present gap, the matrix pencil method (MPM) has emerged as a versatile algorithm that offers tunable filtering and phasing capabilities. Extensive prior research has established the MPM as an adept fitting tool in signal analysis. Here, the efficacy of the MPM is investigated by precisely modeling noisy data to separate information-bearing signals from noise, thereby expanding its utility in various magnetic resonance applications. Simulated data is used to confirm the ability of the MPM to discern and separate signals from noise. Comparative analyses against standard Fourier-based filtering methods highlight the superior performance of the matrix pencil filter (MPF) in preserving signal fidelity without introducing aliasing artifacts. A variety of experimental data is then explored to demonstrate the proficiency of the MPF in characterizing signal components and correcting phase distortions. Collectively, these case studies underscore the filtering capacity of the MPM, portending its use for analytical sensitivity improvements in a wide range of NMR applications.

Hyperpolarized nuclear Overhauser enhancement of alanine methyl groups by doubly relayed proton exchange

Hyperpolarized water in dissolution dynamic nuclear polarization (dDNP) experiments has emerged as a promising method for enhancing nuclear magnetic resonance (NMR) signals, particularly in studies of proteins and peptides. Herein, we focus on the application of "proton exchange-doubly relayed" nuclear Overhauser effects (NOE) from hyperpolarized water to achieve positive signal enhancement of methyl groups in the side chain of an alanine-glycine peptide. In particular, we show a cascade hyperpolarization transfer. Initial proton exchange between solvent and amide introduces hyperpolarization into the peptide. Subsequently, intermolecular NOE relays the hyperpolarization first to Ala-Hα and then in a second step to the Ala-CH3 moiety. Both NOEs have negative signs. Hence, the twice-relayed NOE pathway leads to a positive signal enhancement of the methyl group with respect to the thermal equilibrium magnetization. This effect might indicate a way towards hyperpolarized water-based signal enhancement for methyl groups, which are often used for NMR studies of large proteins in solution.

Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry

Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.

Frémy's Salt as a Low-Persistence Hyperpolarization Agent: Efficient Dynamic Nuclear Polarization Plus Rapid Radical Scavenging

Nuclear magnetic resonance (NMR) spectroscopy is a key technique for molecular structure determination in solution. However, due to its low sensitivity, many efforts have been made to improve signal strengths and reduce the required substrate amounts. In this regard, dissolution dynamic nuclear polarization (DDNP) is a versatile approach as signal enhancements of over 10 000-fold are achievable. Samples are signal-enhanced ex situ by transferring electronic polarization from radicals to nuclear spins before dissolving and shuttling the boosted sample to an NMR spectrometer for detection. However, the applicability of DDNP suffers from one major drawback, namely, paramagnetic relaxation enhancements (PREs) that critically reduce relaxation times due to the codissolved radicals. PREs are the primary source of polarization losses canceling the signal improvements obtained by DNP. We solve this problem by using potassium nitrosodisulfonate (Frémy's salt) as polarization agent (PA), which provides high nuclear spin polarization and allows for rapid scavenging under mild reducing conditions. We demonstrate the potential of Frémy's salt, (i) showing that both 1H and 13C polarization of ∼30% can be achieved and (ii) describing a hybrid sample shuttling system (HySSS) that can be used with any DDNP/NMR combination to remove the PA before NMR detection. This gadget mixes the hyperpolarized solution with a radical scavenger and injects it into an NMR tube, providing, within a few seconds, quantitatively radical-free, highly polarized solutions. The cost efficiency and broad availability of Frémy's salt might facilitate the use of DDNP in many fields of research.

Nuclear Overhauser spectroscopy in hyperpolarized water - chemical vs. magnetic exchange

Dissolution dynamic nuclear polarization (dDNP) is a versatile hyperpolarization technique to boost signal intensities in nuclear magnetic resonance (NMR) spectroscopy. The possibility to dissolve biomolecules in a hyperpolarized aqueous buffer under mild conditions has recently widened the scope of NMR by dDNP. The water-to-target hyperpolarization transfer mechanisms remain yet unclear, not least due to an often-encountered dilemma of dDNP experiments: The strongly enhanced signal intensities are accompanied by limited structural information as data acquisition is restricted to short time series of only one-dimensional spectra or a single correlation spectrum. Tackling this challenge, we combine dDNP with molecular dynamics (MD) simulations and predictions of cross-relaxation rates to unravel the spin dynamics of magnetization flow in hyperpolarized solutions.

Interfacing Liquid State Hyperpolarization Methods with NMR Instrumentation

Advances in liquid state hyperpolarization methods have enabled new applications of high-resolution NMR spectroscopy. Utilizing strong signal enhancements from hyperpolarization allows performing NMR spectroscopy at low concentration, or with high time resolution. Making use of the high, but rapidly decaying hyperpolarization in the liquid state requires new techniques to interface hyperpolarization equipment with liquid state NMR spectrometers. This article highlights rapid injection, high resolution NMR spectroscopy with hyperpolarization produced by the techniques of dissolution dynamic nuclear polarization (D-DNP) and para-hydrogen induced polarization (PHIP). These are popular, albeit not the only methods to produce high polarization levels for liquid samples. Gas and liquid driven sample injection techniques are compatible with both of these hyperpolarization methods. The rapid sample injection techniques are combined with adapted NMR experiments working in a single, or small number of scans. They expand the application of liquid state hyperpolarization to spins with comparably short relaxation times, provide enhanced control over sample conditions, and allow for mixing experiments to study reactions in real time.

Hyperpolarized water as universal sensitivity booster in biomolecular NMR

NMR spectroscopy is the only method to access the structural dynamics of biomolecules at high (atomistic) resolution in their native solution state. However, this method's low sensitivity has two important consequences: (i) typically experiments have to be performed at high concentrations that increase sensitivity but are not physiological, and (ii) signals have to be accumulated over long periods, complicating the determination of interaction kinetics on the order of seconds and impeding studies of unstable systems. Both limitations are of equal, fundamental relevance: non-native conditions are of limited pharmacological relevance, and the function of proteins, enzymes and nucleic acids often relies on their interaction kinetics. To overcome these limitations, we have developed applications that involve 'hyperpolarized water' to boost signal intensities in NMR of proteins and nucleic acids. The technique includes four stages: (i) preparation of the biomolecule in partially deuterated buffers, (ii) preparation of 'hyperpolarized' water featuring enhanced ¹H NMR signals via cryogenic dynamic nuclear polarization, (iii) sudden melting of the cryogenic pellet and dissolution of the protein or nucleic acid in the hyperpolarized water (enabling spontaneous exchanges of protons between water and target) and (iv) recording signal-amplified NMR spectra targeting either labile ¹H or neighboring ¹⁵N/¹³C nuclei in the biomolecule. Water in the ensuing experiments is used as a universal 'hyperpolarization' agent, rendering the approach versatile and applicable to any biomolecule possessing labile hydrogens. Thus, questions can be addressed, ranging from protein and RNA folding problems to resolving structure-function relationships of intrinsically disordered proteins to investigating membrane interactions.

Heteronuclear transfers from labile protons in biomolecular NMR: Cross polarization, revisited

INEPT- and HMQC-based pulse sequences are widely used to transfer polarization between heteronuclei, particularly in biomolecular spectroscopy: they are easy to setup and involve low power deposition. Still, these short-pulse polarization transfers schemes are challenged by fast solvent chemical exchange. An alternative to improve these heteronuclear transfers is J-driven cross polarization (J-CP), which transfers polarization by spin-locking the coupled spins under Hartmann-Hahn conditions. J-CP provides certain immunity against chemical exchange and other T₂-like relaxation effects, a behavior that is here examined in depth by both Liouville-space numerical and analytical derivations describing the transfer efficiency. While superior to INEPT-based transfers, fast exchange may also slow down these J-CP transfers, hurting their efficiency. This study therefore explores the potential of repeated projective operations to improve ¹H→¹⁵N and ¹H→¹⁵N→¹³C J-CP transfers in the presence of fast solvent chemical exchanges. It is found that while repeating J-CP provides little ¹H→¹⁵N transfer advantages over a prolonged CP, multiple contacts that keep both the water and the labile protons effectively spin-locked can improve ¹H→¹⁵N→¹³C transfers in the presence of chemical exchange. The ensuing Looped, Concatenated Cross Polarization (L-CCP) compensates for single J-CP losses by relying on the ¹³C's longer lifetimes, leading to a kind of "algorithmic cooling" that can provide high polarization for the ¹⁵N as well as carbonyl and alpha ¹³Cs. This can facilitate certain experiments, as demonstrated with triple resonance experiments on intrinsically disordered proteins involving labile, chemically exchanging protons.

Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water

Nuclear magnetic resonance (NMR) spectroscopy is a powerful and popular technique for probing the molecular structures, dynamics and chemical properties. However the conventional NMR spectroscopy is bottlenecked by its low sensitivity. Dynamic nuclear polarization (DNP) boosts NMR sensitivity by orders of magnitude and resolves this limitation. In liquid-state this revolutionizing technique has been restricted to a few specific non-biological model molecules in organic solvents. Here we show that the carbon polarization in small biological molecules, including carbohydrates and amino acids, can be enhanced sizably by in situ Overhauser DNP (ODNP) in water at room temperature and at high magnetic field. An observed connection between ODNP 13C enhancement factor and paramagnetic 13C NMR shift has led to the exploration of biologically relevant heterocyclic compound indole. The QM/MM MD simulation underscores the dynamics of intermolecular hydrogen bonds as the driving force for the scalar ODNP in a long-living radical-substrate complex. Our work reconciles results obtained by DNP spectroscopy, paramagnetic NMR and computational chemistry and provides new mechanistic insights into the high-field scalar ODNP.

Residue-resolved monitoring of protein hyperpolarization at sub-second time resolution

Signal-enhancement techniques for NMR spectroscopy are important to amplify the weak resonances provided by nuclear spins. Recently, 'hyperpolarization' techniques have been intensively investigated. These provide nuclear spin states far from equilibrium yielding strong signal boosts up to four orders of magnitude. Here we propose a method for real-time NMR of 'hyperpolarized' proteins at residue resolution. The approach is based on dissolution dynamic nuclear polarization (d-DNP), which enables the use of hyperpolarized buffers that selectively boost NMR signals of solvent-exposed protein residues. The resulting spectral sparseness and signal enhancements enable recording of residue-resolved spectra at a 2 Hz sampling rate. Thus, we monitor the hyperpolarization level of different protein residues simultaneously under near-physiological conditions. We aim to address two points: 1) NMR experiments are often performed under conditions that increase sensitivity but are physiologically irrelevant; 2) long signal accumulation impedes fast real-time monitoring. Both limitations are of fundamental relevance to ascertain pharmacological relevance and study protein kinetics.

Characterization of protein-ligand interactions by SABRE

Nuclear spin hyperpolarization through signal amplification by reversible exchange (SABRE), the non-hydrogenative version of para-hydrogen induced polarization, is demonstrated to enhance sensitivity for the detection of biomacromolecular interactions. A target ligand for the enzyme trypsin includes the binding motif for the protein, and at a distant location a heterocyclic nitrogen atom for interacting with a SABRE polarization transfer catalyst. This molecule, 4-amidinopyridine, is hyperpolarized with 50% para-hydrogen to yield enhancement values ranging from −87 and −34 in the ortho and meta positions of the heterocyclic nitrogen, to −230 and −110, for different solution conditions. Ligand binding is identified by flow-NMR, in a two-step process that separately optimizes the polarization transfer in methanol while detecting the interaction in a predominantly aqueous medium. A single scan Carr–Purcell–Meiboom–Gill (CPMG) experiment identifies binding by the change in R₂ relaxation rate. The SABRE hyperpolarization technique provides a cost effective means to enhance NMR of biological systems, for the identification of protein–ligand interactions and other applications.

Protein–ligand binding interactions are characterized by the para-H₂ based hyperpolarization technique SABRE and flow-NMR. Binding to the protein is identified by R₂ change of a ligand first interacting with the Ir polarization transfer catalyst.

Multiplet analysis by strong-coupling-artifact-suppression 2D J-resolved NMR spectroscopy

Benefitting from the capability of recording scalar (J) couplings and bonding information, 2D J-resolved NMR spectroscopy constitutes an important tool for molecular structure analysis and mixture component identification. Unfortunately, conventional 2D J-resolved experiments generally encounter challenges of insufficient spectral resolution and strong coupling artifacts. In this study, a general NMR approach is exploited to record absorption-mode artifact-free 2D J-resolved spectra. This proposal adopts the advanced triple-spin-echo pure shift yielded by chirp excitation element to eliminate J coupling splittings and preserve chemical shifts along the F2 dimension, and it additionally utilizes the echo-train J acquisition to reveal the multiplet structure along the F1 dimension in accelerated experimental acquisition. Thus, it permits one to extract multiplet structure information from crowded spectral regions in one-shot experiments, with considerable resolution advantage resulting from completely decoupling F2 dimension and absorption-mode presentation, thus facilitating analysis on complex samples. More importantly, this method grants the superior performance on suppressing strong coupling artifacts, which have been affirmed by experiments on a series of chemical samples. As a consequence, this proposed method serves as a useful tool for J coupling measurements and multiplet structure analyses on complex samples that contain crowded NMR resonances and strong coupling spin systems, and it may exhibit broad application potentials in fields of physics, chemistry, and medical science, among others.

2D NMR spectroscopy of refolding RNase Sa using polarization transfer from hyperpolarized water

Polarization transfer from hyperpolarized water through proton exchange is used to enhance the NMR signals of amide protons of the Ribonuclease Sa protein. Spectra of the refolding protein are measured within 6 s after dilution of the denaturant urea, at urea-dependent folding rates adjusted in the range of 0.3-0.8 s^-1. Peak patterns including a mixture of folded and unfolded protein at different ratios are observed. The changes in the observed signals indicate that each spectrum accesses a different point in the partial completion of the folding. A comparison to simulated 2D NMR spectra suggests a lower polarization transfer efficiency from water when the protein folds slowly, which may result from the molecular motions in the unfolded protein and the absence of long-range contacts. The ability to acquire 2D NMR spectra under different refolding conditions may open a new avenue for residue specific characterization of the folding process.

Highly Efficient Determination of Complex NMR Multiplet Structures in Inhomogeneous Magnetic Fields

Proton-proton scalar (J) coupling plays an important role in disentangling molecular structures and spatial conformations. But it is challenging to extract J coupling networks from congested ¹H NMR spectra, especially in inhomogeneous magnetic fields. Herein, we propose a general liquid NMR protocol, named HR-G-SERF, to implement highly efficient determination of individual J couplings and corresponding coupling networks via simultaneously suppressing effects of spectral congestions and magnetic field inhomogeneity. This method records full-resolved 2D absorption-mode spectra to deliver great convenience for multipet analyses on complex samples. More meaningfully, it is capable of disentangling multiplet structures of biological samples, that is, grape sarcocarp, despite of its heterogeneous semisolid state and extensive compositions. In addition, a modification, named AH-G-SERF, is developed to compress experimental acquisition and subsequently improve unit-time SNR, while maintaining satisfactory spectral performance. This accelerated variant may further boost the applicability for rapid NMR detections and afford the possibility of adopting hyperpolarized substances to enhance the overall sensitivity. Therefore, this study provides a promising tool for molecular structure elucidations and composition analyses in chemistry, biochemistry, and metabonomics among others.

NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function

Biomolecules are in constant motion. To understand how they function, and why malfunctions can cause disease, it is necessary to describe their three-dimensional structures in terms of dynamic conformational ensembles. Here, we demonstrate how nuclear magnetic resonance (NMR) spectroscopy provides an essential, dynamic view of structural biology that captures biomolecular motions at atomic resolution. We focus on examples that emphasize the diversity of biomolecules and biochemical applications that are amenable to NMR, such as elucidating functional dynamics in large molecular machines, characterizing transient conformations implicated in the onset of disease, and obtaining atomic-level descriptions of intrinsically disordered regions that make weak interactions involved in liquid-liquid phase separation. Finally, we discuss the pivotal role that NMR has played in driving forward our understanding of the biomolecular dynamics-function paradigm.

Diffusion Analysis on Complex Mixtures under Adverse Magnetic Field Conditions by Spatially-Selective Pure Shift-Based DOSY

Diffusion-ordered NMR spectroscopy (DOSY) serves as a noninvasive spectroscopic method for studying intact mixtures and identifying individual components present in mixtures according to their diffusion behaviors. However, DOSY techniques generally fail to discriminate complex compositions which exhibit crowded or overlapped NMR signals, particularly under adverse magnetic field conditions. Herein, we exploit the spatially selective pure shift-based DOSY strategy to address this challenge by eliminating inhomogeneous line broadenings and extracting pure shift singlets, thereby expediting diffusion analyses on complex mixtures. More importantly, this strategy is further applied to observing and analyzing electro-oxidation processes of blended alcohols, suggesting its potential to monitoring in situ electrochemical reactions. This study demonstrates a meaningful NMR trial for diffusion analysis on complex mixtures under adverse experimental circumstances, and particularly, it provides a proof-of-concept technique for electrochemical studies and shows promising prospects for applications in chemistry, biology, energy, etc.