129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration

RIBOsensor for FRET-based, real-time ribose measurements in live cells

d-Ribose is a building block of many essential biomolecules, including all nucleic acids, and its supplementation can enhance energy production, particularly under stress conditions such as ischemia and heart failure. The distribution, biosynthesis, and regulation of ribose in mammalian systems remain poorly understood. To explore intracellular ribose dynamics, we developed a genetically encoded fluorescence resonance energy transfer (FRET) sensor using ribose binding protein (RBP) and enhanced cyan and yellow fluorescent proteins (FPs). The RIBOsensor, which positions one FP near the active site of RBP, achieves the necessary sensitivity for cellular imaging by increasing the FRET signal upon ribose binding, compared to traditional N- and C-terminal FP orientations. This sensor rapidly, reversibly, and selectively detects labile ribose in live cells-enabling longitudinal studies-and can be employed for intracellular ribose quantitation, which provides a valuable tool for investigating ribose transport and metabolism in normal and disease states.

Continuous Delivery of Hyperpolarized Xenon-129 Gas Using a "Stopped-Flow" Clinical-Scale Cryogen-Free Hyperpolarizer

In 2022, the FDA approved hyperpolarized (HP) 129Xe gas as an inhalable contrast agent for functional lung imaging. For clinical imaging, HP 129Xe is usually given as a bolus inhalation. However, for preclinical applications (e.g., pulmonary imaging in small rodents), the continuous delivery of HP 129Xe is greatly desired to enable MRI scanning under conditions of physiological continuous animal breathing patterns. Moreover, HP 129Xe gas can be utilized for other applications including materials science and bioanalytical chemistry, where a continuous flow of hyperpolarized gas through an NMR sample over several minutes is also desired for sensing of 129Xe inside an NMR spectrometer. 129Xe is often hyperpolarized using continuous-flow spin-exchange optical pumping, which employs a lean (1-2%) mixture of Xe and a carrier gas (e.g., He and N2). The low Xe concentration in the produced output reduces the NMR detection sensitivity, and thus, Xe cryo-collection is typically employed to achieve near-100% pure gas-phase Xe before administration to the sample or subject. However, the need for cryo-collection undermines a key advantage of continuous-flow production, i.e., the continuous flowing in a hyperpolarizer HP 129Xe gas is trapped inside the hyperpolarizer, and the produced HP 129Xe gas is released at once when the production cycle (30-60 min) is completed. An alternative HP 129Xe production technology employs a "stopped-flow" approach, where a batch of HP gas is hyperpolarized over time and quickly released from a hyperpolarizer. Here, a clinical-scale "stopped-flow" 129Xe hyperpolarizer was employed to hyperpolarize a 1.3 L-atm batch of 50:50 Xe:N2 gas mixture inside a glass cell with an ultralong lifetime of the HP 129Xe state (T1 > 2 h). The produced HP 129Xe gas was slowly delivered into a 5 mm NMR tube via PEEK tubing under a wide range of gas flow rates: 3-180 standard cubic centimeters per minute (sccm). The polarization of the gas ejected from the hyperpolarizer was quantified using in situ low-field NMR polarimetry and additionally verified using a 0.35 T clinical MRI scanner. Continuous-flow delivery of HP 129Xe was demonstrated for up to 15 min with a gas flow rate of 45-150 sccm over a 2.5-m length of PEEK tubing, suffering only small losses in 129Xe polarization. These observations are additionally supported by 129Xe relaxation measurements inside the PEEK tubing employed for gas delivery and the 5 mm NMR tube employed for polarimetry. 129Xe polarization of 16-19% was obtained in the delivered gas, starting with an "in-polarizer" 129Xe polarization of 19%. We envision that this method can be employed for on-demand cryogen-free delivery of hyperpolarized gas using "stopped-flow" 129Xe hyperpolarizers for a broad range of applications, from preclinical imaging to biosensors, and to spectroscopy of materials surfaces.

Ultrasensitive 129Xe Magnetic Resonance Imaging: From Clinical Monitoring to Molecular Sensing

Magnetic resonance imaging (MRI) is a cornerstone technology in clinical diagnostics and in vivo research, offering unparalleled visualization capabilities. Despite significant advancements in the past century, traditional 1H MRI still faces sensitivity limitations that hinder its further development. To overcome this challenge, hyperpolarization methods have been introduced, disrupting the thermal equilibrium of nuclear spins and leading to an increased proportion of hyperpolarized spins, thereby enhancing sensitivity by hundreds to tens of thousands of times. Among these methods, hyperpolarized (HP) 129Xe MRI, also known as ultrasensitive 129Xe MRI, stands out for achieving the highest polarization enhancement and has recently received clinical approval. It effectively tackles the challenge of weak MRI signals from low proton density in the lungs. HP 129Xe MRI is valuable for assessing structural and functional changes in lung physiology during pulmonary disease progression, tracking cells, and detecting target molecules at pico-molar concentrations. This review summarizes recent developments in HP 129Xe MRI, including its physical principles, manufacturing methods, in vivo characteristics, and diverse applications in biomedical, chemical, and material sciences. In addition, it carefully discusses potential technical improvements and future prospects for enhancing its utility in these fields, further establishing HP 129Xe MRI's importance in advancing medical imaging and research.

D-ribose metabolic disorder and diabetes mellitus

D-ribose, an ubiquitous pentose compound found in all living cells, serves as a vital constituent of numerous essential biomolecules, including RNA, nucleotides, and riboflavin. It plays a crucial role in various fundamental life processes. Within the cellular milieu, exogenously supplied D-ribose can undergo phosphorylation to yield ribose-5-phosphate (R-5-P). This R-5-P compound serves a dual purpose: it not only contributes to adenosine triphosphate (ATP) production through the nonoxidative phase of the pentose phosphate pathway (PPP) but also participates in nucleotide synthesis. Consequently, D-ribose is employed both as a therapeutic agent for enhancing cardiac function in heart failure patients and as a remedy for post-exercise fatigue. Nevertheless, recent clinical studies have suggested a potential link between D-ribose metabolic disturbances and type 2 diabetes mellitus (T2DM) along with its associated complications. Additionally, certain in vitro experiments have indicated that exogenous D-ribose exposure could trigger apoptosis in specific cell lines. This article comprehensively reviews the current advancements in D-ribose's digestion, absorption, transmembrane transport, intracellular metabolic pathways, impact on cellular behaviour, and elevated levels in diabetes mellitus. It also identifies areas requiring further investigation.

Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme

Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe-protein interactions at the molecular level and inspire further biochemical investigations with noble gases.

Protein and peptide engineering for chemical exchange saturation transfer imaging in the age of synthetic biology

At the beginning of the millennium, the first chemical exchange saturation transfer (CEST) contrast agents were bio-organic molecules. However, later, metal-based CEST agents (paraCEST agents) took center stage. This did not last too long as paraCEST agents showed limited translational potential. By contrast, the CEST field gradually became dominated by metal-free CEST agents. One branch of research stemming from the original work by van Zijl and colleagues is the development of CEST agents based on polypeptides. Indeed, in the last 2 decades, tremendous progress has been achieved in this field. This includes the design of novel peptides as biosensors, genetically encoded recombinant as well as synthetic reporters. This was a result of extensive characterization and elucidation of the theoretical requirements for rational designing and engineering of such agents. Here, we provide an extensive overview of the evolution of more precise protein-based CEST agents, review the rationalization of enzyme-substrate pairs as CEST contrast enhancers, discuss the theoretical considerations to improve peptide selectivity, specificity and enhance CEST contrast. Moreover, we discuss the strong influence of synthetic biology on the development of the next generation of protein-based CEST contrast agents.

Nanomaterials for hyperpolarized nuclear magnetic resonance and magnetic resonance imaging

Nanomaterials play an important role in the development and application of hyperpolarized materials for magnetic resonance imaging (MRI). In this context they can not only act as hyperpolarized materials which are directly imaged but also play a role as carriers for hyperpolarized gases and catalysts for para-hydrogen induced polarization (PHIP) to generate hyperpolarized substrates for metabolic imaging. Those three application possibilities are discussed, focusing on carbon-based materials for the directly imaged particles. An overview over recent developments in all three fields is given, including the early developments in each field as well as important steps towards applications in MRI, such as making the initially developed methods more biocompatible and first imaging experiments with spatial resolution in either phantoms or in vivo studies. Focusing on the important features nanomaterials need to display to be applicable in the MRI context, a wide range of different approaches to that extent is covered, giving the reader a general idea of different possibilities as well as recent developments in those different fields of hyperpolarized magnetic resonance. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.

Programming xenon diffusion in maltose-binding protein

Protein interiors contain void space that can bind small gas molecules. Determination of gas pathways and kinetics in proteins has been an intriguing and challenging task. Here, we combined computational methods and the hyperpolarized xenon-129 chemical exchange saturation transfer (hyper-CEST) NMR technique to investigate xenon (Xe) exchange kinetics in maltose-binding protein (MBP). A salt bridge ∼9 Å from the Xe-binding site formed upon maltose binding and slowed the Xe exchange rate, leading to a hyper-CEST 129Xe signal from maltose-bound MBP. Xe dissociation occurred faster than dissociation of the salt bridge, as shown by 13C NMR spectroscopy and variable-B1 hyper-CEST experiments. "Xe flooding" molecular dynamics simulations identified a surface hydrophobic site, V23, that has good Xe binding affinity. Mutations at this site confirmed its role as a secondary exchange pathway in modulating Xe diffusion. This shows the possibility for site-specifically controlling xenon protein-solvent exchange. Analysis of the available MBP structures suggests a biological role of MBP's large hydrophobic cavity to accommodate structural changes associated with ligand binding and protein-protein interactions.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Cryptophane-xenon complexes for 129Xe MRI applications

The use of magnetic resonance imaging (MRI) and spectroscopy (MRS) in the clinical setting enables the acquisition of valuable anatomical information in a rapid, non-invasive fashion. However, MRI applications for identifying disease-related biomarkers are limited due to low sensitivity at clinical magnetic field strengths. The development of hyperpolarized (hp) ¹²⁹Xe MRI/MRS techniques as complements to traditional ¹H-based imaging has been a burgeoning area of research over the past two decades. Pioneering experiments have shown that hp ¹²⁹Xe can be encapsulated within host molecules to generate ultrasensitive biosensors. In particular, xenon has high affinity for cryptophanes, which are small organic cages that can be functionalized with affinity tags, fluorophores, solubilizing groups, and other moieties to identify biomedically relevant analytes. Cryptophane sensors designed for proteins, metal ions, nucleic acids, pH, and temperature have achieved nanomolar-to-femtomolar limits of detection via a combination of ¹²⁹Xe hyperpolarization and chemical exchange saturation transfer (CEST) techniques. This review aims to summarize the development of cryptophane biosensors for ¹²⁹Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of ¹²⁹Xe MRI.

This review aims to summarize the development of cryptophane biosensors for ¹²⁹Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of ¹²⁹Xe MRI.

Molecular Concentration Determination Using Long-Interval Chemical Exchange Inversion Transfer (CEIT) NMR Spectroscopy

Functionalized hyperpolarized xenon "cage" molecules have often been used for ultrasensitive detection of biomolecules and microenvironment properties. However, the rapid and accurate measurement of molecule concentration is still a challenge. Here, we report a molecule concentration measurement method using long-interval chemical exchange inversion transfer (CEIT) NMR spectroscopy. The molecule concentration can be quantitatively measured with only 2 scans, which shortens the acquisition time by about 10 times compared to conventional Hyper-CEST (chemical exchange saturation transfer) z-spectrum method. Moreover, we found that the accuracy of concentration determination would be the best when the CEIT effect is 1-1/e or close to it, and a relative deviation of CrA-(COOH)₆ less than ±1% has been achieved by only a one-step optimization of the number of cycles. The proposed method enables efficient and accurate determination of molecule concentration, which provides a potential way for rapid quantitative molecular imaging applications.