Exploring hydrophobic sites in proteins with xenon or krypton

Metal-Organic Frameworks Possessing Suitable Pores for Xe/Kr Separation

Adsorption separation of the Xe/Kr mixture remains a tough issue since Xe and Kr have an inert nature and similar sizes. Here we present a chlorinated metal-organic framework (MOF) [JXNU-19(Cl)] and its nonchlorinated analogue (JXNU-19) for Xe/Kr separation. The two isostructural MOFs constructed from the heptanuclear cobalt-hydroxyl clusters bridged by organic ligands are three-dimensional structures. Detailed contrast of the Xe/Kr adsorption separation properties of the MOF shows that significantly enhanced Xe uptakes and Xe/Kr adsorption selectivity (17.1) are observed for JXNU-19 as compared to JXNU-19(Cl). The main binding sites for Xe in the MOF revealed by computational simulations are far away from the chlorine sites, suggesting that the introduction of the chlorine groups results in the unfavorable Xe adsorption for JXNU-19(Cl). The optimal pores, high surface area, and multiple strong Xe-framework interactions facilitate the effective Xe/Kr separation for JXNU-19.

Are Protein Cavities and Pockets Commonly Used by Redox Active Signalling Molecules?

It has been well known for a long time that inert gases, such as xenon (Xe), have significant biological effects. As these atoms are extremely unlikely to partake in direct chemical reactions with biomolecules such as proteins, lipids, and nucleic acids, there must be some other mode of action to account for the effects reported. It has been shown that the topology of proteins allows for cavities and hydrophobic pockets, and it is via an interaction with such protein structures that inert gases are thought to have their action. Recently, it has been mooted that the relatively inert gas molecular hydrogen (H₂) may also have its effects via such a mechanism, influencing protein structures and actions. H₂ is thought to also act via interaction with redox active compounds, particularly the hydroxyl radical (^·OH) and peroxynitrite (ONOO^-), but not nitric oxide (NO^·), superoxide anions (O₂^·-) or hydrogen peroxide (H₂O₂). However, instead of having a direct interaction with H₂, is there any evidence that these redox compounds can also interact with Xe pockets and cavities in proteins, either having an independent effect on proteins or interfering with the action of inert gases? This suggestion will be explored here.

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.

Filling of a water-free void explains the allosteric regulation of the β1-adrenergic receptor by cholesterol

Recent high-pressure NMR results indicate that the preactive conformation of the β₁-adrenergic receptor (β₁AR) harbours completely empty cavities of ~100 ų volume, which disappear in the active conformation of the receptor. Here we have localized these cavities using X-ray crystallography of xenon-derivatized β₁AR crystals. One of the cavities is in direct contact with the cholesterol-binding pocket. Solution NMR shows that addition of the cholesterol analogue cholesteryl hemisuccinate impedes the formation of the active conformation of detergent-solubilized β₁AR by blocking conserved G protein-coupled receptor microswitches, concomitant with an affinity reduction of both isoprenaline and G protein-mimicking nanobody Nb80 for β₁AR detected by isothermal titration calorimetry. This wedge-like action explains the function of cholesterol as a negative allosteric modulator of β₁AR. A detailed understanding of G protein-coupled receptor regulation by cholesterol by filling of a dry void and the easy scouting for such voids by xenon may provide new routes for the development of allosteric drugs.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase

Carbon monoxide dehydrogenase (CODH) plays an important role in the processing of the one‑carbon gases carbon monoxide and carbon dioxide. In CODH enzymes, these gases are channeled to and from the Ni-Fe-S active sites using hydrophobic cavities. In this work, we investigate these gas channels in a monofunctional CODH from Desulfovibrio vulgaris, which is unusual among CODHs for its oxygen-tolerance. By pressurizing D. vulgaris CODH protein crystals with xenon and solving the structure to 2.10 Å resolution, we identify 12 xenon sites per CODH monomer, thereby elucidating hydrophobic gas channels. We find that D. vulgaris CODH has one gas channel that has not been experimentally validated previously in a CODH, and a second channel that is shared with Moorella thermoacetica carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). This experimental visualization of D. vulgaris CODH gas channels lays groundwork for further exploration of factors contributing to oxygen-tolerance in this CODH, as well as study of channels in other CODHs. We dedicate this publication to the memory of Dick Holm, whose early studies of the Ni-Fe-S clusters of CODH inspired us all.

High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action

In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia.

Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.

Dinuclear Nickel-Oxygen Cluster-Based Metal-Organic Frameworks with Octahedral Cages for Efficient Xe/Kr Separation

Xe/Kr separation is industrially important but remains a daunting issue in chemical separations. Herein, a fluorinated metal-organic framework (MOF), [Ni₂(μ₂-O)(TFBPDC)(tpt)₂]_n (named JXNU-13-F), built from 3,3',5,5'-tetrakis(fluoro)biphenyl-4,4'-dicarboxylic (TFBPDC^2-) and 2,4,6-tri(4-pyridinyl)-1,3,5-triazine (tpt) ligands is provided. JXNU-13-F displays a three-dimensional (3D) framework constructed from distorted octahedral cages and an impressive Xe capacity of 144 cm³ g^-1 at 273 K and 1 bar, ranking among top MOFs. The high Xe uptake and moderate Xe/Kr adsorption selectivity endow JXNU-13-F with efficient Xe/Kr separation demonstrated by experimental column breakthrough tests. The comparative studies of gas adsorption between isostructural JXNU-13-F and JXNU-13 (the nonfluorinated analogue ([Ni₂(μ₂-O)(BPDC))(tpt)₂]_n with biphenyl-4,4'-dicarboxylic (BPDC^2-)) revealed that the F groups serve as the innocent groups during the Xe and Kr adsorption in JXNU-13-F. Thus, a combination of highly hydrophobic and π-electron-rich pore surfaces made of aromatic rings with strong interactions with the Xe atom possessing large polarizability and appropriate pore sizes that match well Xe having a large atom diameter has resulted in high Xe uptake and effective Xe/Kr separation characteristics of JXNU-13-F.

Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability

The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low-throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein target discovery. Here, we report the application of stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5000 methionine-containing peptides and over 5000 semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins, respectively, in the yeast proteome, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified are tied to previously established modes of action related to xenon's anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions. The sample preparation protocols and analytical methodologies developed here for xenon are also generally applicable to the discovery of a wide range of other protein-gas interactions in complex biological mixtures, such as cell lysates.

Creating Optimal Pockets in a Clathrochelate-Based Metal-Organic Framework for Gas Adsorption and Separation: Experimental and Computational Studies

The rational design and synthesis of robust metal-organic frameworks (MOFs) based on novel organic building blocks are fundamental aspects of reticular chemistry. Beyond simply fabricating new organic linkers, however, it is important to elucidate structure-property relationships at the molecular level to develop high-performing materials. In this work, we successfully targeted a highly porous and robust cage-type MOF (NU-200) with an nbo-derived fof topology through the deliberate assembly of a cyclohexane-functionalized iron(II)-clathrochelate-based meta-benzenedicarboxylate linker with a Cu₂(CO₂)₄ secondary building unit (SBU). NU-200 exhibited an outstanding adsorption capacity of xenon and a high ideal adsorbed solution theory (IAST) predicted selectivity for a 20/80 v/v mixture of xenon (Xe)/krypton (Kr) at 298 K and 1.0 bar. Our extensive computational simulations with grand canonical Monte Carlo (GCMC) and density functional theory (DFT) on NU-200 indicated that the MOF's hierarchical bowl-shaped nanopockets surrounded by custom-designed cyclohexyl groups─instead of the conventionally believed open metal sites (OMSs)─played a crucial role in reinforcing Xe-binding affinity. The optimally sized pockets firmly trapped Xe through numerous supramolecular interactions including Xe···H, Xe···O, and Xe···π. Additionally, we validated the unique pocket confinement effect by experimentally and computationally employing the similarly sized probe, sulfur dioxide (SO₂), which provided significant insights into the molecular underpinnings of the high uptake of SO₂ (11.7 mmol g^-1), especially at a low pressure of 0.1 bar (8.5 mmol g^-1). This work therefore can facilitate the judicious design of organic building blocks, producing MOFs featuring tailor-made pockets to boost gas adsorption and separation performances.

Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families

Argon belongs to the group of chemically inert noble gases, which display a remarkable spectrum of clinically useful biological properties. In an attempt to better understand noble gases, notably argon's mechanism of action, we mined a massive noble gas modeling database which lists all possible noble gas binding sites in the proteins from the Protein Data Bank. We developed a method of analysis to identify among all predicted noble gas binding sites the potentially relevant ones within protein families which are likely to be modulated by Ar. Our method consists in determining within structurally aligned proteins the conserved binding sites whose shape, localization, hydrophobicity, and binding energies are to be further examined. This method was applied to the analysis of two protein families where crystallographic noble gas binding sites have been experimentally determined. Our findings indicate that among the most conserved binding sites, either the most hydrophobic one and/or the site which has the best binding energy corresponds to the crystallographic noble gas binding sites with the best occupancies, therefore the best affinity for the gas. This method will allow us to predict relevant noble gas binding sites that have potential pharmacological interest and thus potential Ar targets that will be prioritized for further studies including in vitro validation.

Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization

The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.

Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory

There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

Molecular Sensing with Host Systems for Hyperpolarized 129Xe

Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.

An Ultra-Microporous Metal-Organic Framework with Exceptional Xe Capacity

Molecular confinement plays a significant effect on trapped gas and solvent molecules. A fundamental understanding of gas adsorption within the porous confinement provides information necessary to design a material with improved selectivity. In this regard, metal-organic framework (MOF) adsorbents are ideal candidate materials to study confinement effects for weakly interacting gas molecules, such as noble gases. Among the noble gases, xenon (Xe) has practical applications in the medical, automotive and aerospace industries. In this Communication, we report an ultra-microporous nickel-isonicotinate MOF with exceptional Xe uptake and selectivity compared to all benchmark MOF and porous organic cage materials. The selectivity arises because of the near perfect fit of the atomic Xe inside the porous confinement. Notably, at low partial pressure, the Ni-MOF interacts very strongly with Xe compared to the closely related Krypton gas (Kr) and more polarizable CO₂ . Further ¹²⁹ Xe NMR suggests a broad isotropic chemical shift due to the reduced motion as a result of confinement.

Ab initio relativistic potential energy surfaces of benzene-Xe complex with application to intermolecular vibrations

The benzene-Xe (BXe) complex in its electronic ground state is studied using ab initio methods. Since this complex contains the heavy Xe atom, the relativistic effects cannot be neglected. We test two different approaches that describe the scalar relativistic effects in the framework of the coupled-cluster level of theory with single, double, and perturbative triple excitations, used for the interaction energy calculations. The first one is based on the small core pseudopotential (PP), and the second one is based on the explicit treatment of scalar relativistic effects using the Douglas-Kroll-Hess (DKH) Hamiltonian. A few basis sets are tested with the PP and DKH, and for each one, the analytical potential energy surface (PES) is constructed. It is shown that the difference between PESs determined with PP and DKH methods is small, if the orbitals of the 4d subshell in Xe are correlated. We select the most appropriate approach for the calculation of the potential energy surface of BXe, with respect to accuracy and computational cost. The optimal level of theory includes a small Dunning's basis set for the benzene monomer and a larger PP basis set for Xe supplemented by midbond functions. The PES obtained using such an approach provides a reasonable accuracy when compared to the empirical one derived from the microwave spectra of BXe. The empirical and the theoretical values of intermolecular vibrational energies agree within 0.5 cm^-1 up to second overtones. The vibrational energy level pattern of BXe is characterized by a distinct polyad structure.

Massive in Silico Study of Noble Gas Binding to the Structural Proteome

Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas-protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas-protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop "atomic drugs" that can fully exploit their considerable and relatively unexplored potential in medicine.

Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase from Streptomyces griseoflavus Ac-993

Laccases (EC 1.10.3.2) are multicopper oxidoreductases acting on diphenols and related substances. Laccases are highly important for biotechnology and environmental remediation. These enzymes contain mononuclear one T2 copper ion and two T3 copper ions (Cu3_α and Cu3_β), which form the so-called trinuclear center (TNC). Along with the typical three-domain laccases Bacteria produce two-domain (2D) enzymes, which are active at neutral and basic pH, thermostable, and resistant to inhibitors. In this work we present the comparative analysis of crystal structures and catalytic properties of recombinant 2D laccase from Streptomyces griseoflavus Ac-993 (SgfSL) and its four mutant forms with replacements of two amino acid residues, located at the narrowing of the presumable T3-solvent tunnels. We obtained inactive enzymes with substitutions of His165, with Phe, and Ile170 with Ala or Phe. His165Ala variant was more active than the wild type. We suggest that His165 is a “gateway” at the O₂-tunnel leading from solvent to the Cu3_β of the enzyme. The side chain of Ile170 could be indirectly involved in the coordination of copper ions at the T3 center by maintaining the position of the imidazole ring of His157 that belongs to the first coordination sphere of Cu3_α.

Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design

Modulating protein activity with small-molecules binding to cryptic pockets offers great opportunities to overcome hurdles in drug design. Cryptic sites are atypical binding sites in proteins that are closed in the absence of a stabilizing ligand and are thus inherently difficult to identify. Many studies have proposed methods to predict cryptic sites. However, a general approach to prospectively sample open conformations of these sites and to identify cryptic pockets in an unbiased manner suitable for structure-based drug design remains elusive. Here, we describe an all-atom, explicit cosolvent, molecular dynamics (MD) simulations-based workflow to sample the open states of cryptic sites and identify opened pockets, in a manner that does not require a priori knowledge about these sites. Furthermore, the workflow relies on a target-independent parametrization that only distinguishes between binding pockets for peptides or small molecules. We validated our approach on a diverse test set of seven proteins with crystallographically determined cryptic sites. The known cryptic sites were found among the three highest-ranked predicted cryptic sites, and an open site conformation was sampled and selected for most of the systems. Crystallographic ligand poses were well reproduced by docking into these identified open conformations for five of the systems. When the fully open state could not be reproduced, we were still able to predict the location of the cryptic site, or identify other cryptic sites that could be retrospectively validated with knowledge of the protein target. These characteristics render our approach valuable for investigating novel protein targets without any prior information.

Acceleration of the autoxidation of nitric oxide by proteins

Lipoproteins and lipid membranes accelerate ^•NO autoxidation by increasing local concentration of ^•NO and O₂. Although the idea that proteins could also accelerate this reaction was presented some time ago, it was largely criticized and dismissed. Herein the effect of proteins on ^•NO autoxidation rates was studied following ^•NO disappearance with a selective electrode. It was found that human serum albumin (HSA) accelerated ^•NO autoxidation by a factor of 9 per g/mL of protein, much less than previously suggested. The acceleration by HSA was sensitive to pH and significantly decreased at pH lower than 4.5 coincident with the acid structure transition of HSA to a partially unfolded and rigid conformation. Other proteins with different surface hydrophobicity also accelerated ^•NO autoxidation and it was found to depend mostly on the protein size and dynamics. Mathematical simulations were performed to assess the physiological importance of this acceleration. It was calculated that in plasma the autoxidation of ^•NO is accelerated 1.38 times by HSA relative to water alone, but this becomes of little relevance when whole blood is simulated because of the rapid rate of ^•NO consumption by red blood cells.

Directly Functionalized Cucurbit[7]uril as a Biosensor for the Selective Detection of Protein Interactions by 129 Xe hyperCEST NMR

Advancement of hyperpolarized ¹²⁹ Xe MRI technology toward clinical settings demonstrates the considerable interest in this modality for diagnostic imaging. The number of contrast agents, termed biosensors, for ¹²⁹ Xe MRI that respond to specific biological targets, has grown and diversified. Directly functionalized xenon-carrying macrocycles, such as the large family of cryptophane-based biosensors, are good for localization-based imaging and provide contrast before and after binding events occur. Noncovalently functionalized constructs, such as cucurbituril- and cyclodextrin-based biosensors, benefit from commercial availability and optimal exchange dynamics for CEST imaging. In this work, we report the first directly functionalized cucurbituril used as a xenon biosensor. Biotinylated cucurbit[7]uril (btCB7) gives rise to a ¹²⁹ Xe hyperCEST response at the unusual shift of δ=28 ppm when bound to its protein target with substantial CEST contrast. We posit that the observed chemical shift is due to the deformation of btCB7 upon binding to avidin, caused by proximity to the protein surface. Conformational searches and molecular dynamics (MD) simulations support this hypothesis. This construct combines the strengths of both families of biosensors, enables a multitude of biological targets through avidin conjugation, and demonstrates the advantages of functionalized cucurbituril-based biosensors.

Computational Exploration of IRMOFs for Xenon Separation from Air

Metal-organic frameworks (MOFs) found their well-deserved position in the field of gas adsorption and separation because of their unique properties. The separation of xenon from different gas mixtures containing this valuable and essential noble gas is also benefited from the exciting nature of MOFs. In this research, we chose a series of isoreticular MOFs as our study models to apply advanced molecular simulation techniques in the context of xenon separation from air. We investigated the separation performance of our model set through simulation of ternary gas adsorption isotherms and consequent calculation of separation performance descriptors, finding out that IRMOF-7 shows better recovering capabilities compared to the other studied MOFs. We benefited from visualization of xenon energy landscape within MOFs to obtain valuable information on possible reasoning behind our observations. We also examined temperature-based separation performance boosting strategy. Additionally, we noted that although promising candidates are present among the studied MOFs for xenon recovery from air, they are not suitable for xenon recovery from exhaled anesthetic gas mixture.

Decoding the Rich Biological Properties of Noble Gases: How Well Can We Predict Noble Gas Binding to Diverse Proteins?

The chemically inert noble gases display a surprisingly rich spectrum of useful biological properties. Relatively little is known about the molecular mechanisms behind these effects. It is clearly not feasible to conduct large numbers of pharmacological experiments on noble gases to identify activity. Computational studies of the binding of noble gases and proteins can address this paucity of information and provide insight into mechanisms of action. We used bespoke computational grid calculations to predict the positions of energy minima in the interactions of noble gases with diverse proteins. The method was validated by quantifying how well simulations could predict binding positions in 131 diverse protein X-ray structures containing 399 Xe and Kr atoms. We found excellent agreement between calculated and experimental binding positions of noble gases. 94 % of all crystallographic xenon atoms were within 1 Xe van der Waals (vdW) diameter of a predicted binding site, and 97 % lay within 2 vdW diameters. 100 % of crystallographic krypton atoms were within 1 Kr vdW diameter of a predicted binding site. We showed the feasibility of large-scale computational screening of all ≈60 000 unique structures in the Protein Data Bank. This will elucidate biochemical mechanisms by which these novel 'atomic drugs' elicit their valuable biochemical properties and identify new medical uses.

A Structural Basis for 129 Xe Hyper-CEST Signal in TEM-1 β-Lactamase

Genetically encoded (GE) contrast agents detectable by magnetic resonance imaging (MRI) enable non-invasive visualization of gene expression and cell proliferation at virtually unlimited penetration depths. Using hyperpolarized ¹²⁹ Xe in combination with chemical exchange saturation transfer, an MR contrast approach known as hyper-CEST, enables ultrasensitive protein detection and biomolecular imaging. GE MRI contrast agents developed to date include nanoscale proteinaceous gas vesicles as well as the monomeric bacterial proteins TEM-1 β-lactamase (bla) and maltose binding protein (MBP). To improve understanding of hyper-CEST NMR with proteins, structural and computational studies were performed to further characterize the Xe-bla interaction. X-ray crystallography validated the location of a high-occupancy Xe binding site predicted by MD simulations, and mutagenesis experiments confirmed this Xe site as the origin of the observed CEST contrast. Structural studies and MD simulations with representative bla mutants offered additional insight regarding the relationship between local protein structure and CEST contrast.

Xenon-inhibition of the MscL mechano-sensitive channel and the CopB copper ATPase under different conditions suggests direct effects on these proteins

Xenon is frequently used as a general anesthetic in humans, but the mechanism remains an issue of debate. While for some membrane proteins, a direct interaction of xenon with the protein has been shown to be the inhibitory mechanism, other membrane protein functions could be affected by changes of membrane properties due to partitioning of the gas into the lipid bilayer. Here, the effect of xenon on a mechanosensitive ion channel and a copper ion-translocating ATPase was compared under different conditions. Xenon inhibited spontaneous gating of the Escherichia coli mechano-sensitive mutant channel MscL-G22E, as shown by patch-clamp recording techniques. Under high hydrostatic pressure, MscL-inhibition was reversed. Similarly, the activity of the Enterococcus hirae CopB copper ATPase, reconstituted into proteoliposomes, was inhibited by xenon. However, the CopB ATPase activity was also inhibited by xenon when CopB was in a solubilized state. These findings suggest that xenon acts by directly interacting with these proteins, rather than via indirect effects by altering membrane properties. Also, inhibition of copper transport may be a novel effect of xenon that contributes to anesthesia.

Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR

The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for ¹²⁹Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.

Many Ways to Derivatize Macromolecules and Their Crystals for Phasing

Due to the availability of many macromolecular models in the Protein Data Bank, the majority of crystal structures are currently solved by molecular replacement. However, truly novel structures can only be solved by one of the versions of the special-atom method. The special atoms such as sulfur, phosphorus or metals could be naturally present in the macromolecules, or could be intentionally introduced in a derivatization process. The isomorphous and/or anomalous scattering of X-rays by these special atoms is then utilized for phasing. There are many ways to obtain potentially useful derivatives, ranging from the introduction of special atoms to proteins or nucleic acids by genetic engineering or by chemical synthesis, to soaking native crystals in solutions of appropriate compounds with heavy and/or anomalously scattering atoms. No approach guarantees the ultimate success and derivatization remains largely a trial-and-error process. In practice, however, there is a very good chance that one of a wide variety of the available procedures will lead to successful structure solution.

Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure

Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.

Biomolecular MRI reporters: Evolution of new mechanisms

Magnetic resonance imaging (MRI) is a powerful technique for observing the function of specific cells and molecules inside living organisms. However, compared to optical microscopy, in which fluorescent protein reporters are available to visualize hundreds of cellular functions ranging from gene expression and chemical signaling to biomechanics, to date relatively few such reporters are available for MRI. Efforts to develop MRI-detectable biomolecules have mainly focused on proteins transporting paramagnetic metals for T1 and T2 relaxation enhancement or containing large numbers of exchangeable protons for chemical exchange saturation transfer. While these pioneering developments established several key uses of biomolecular MRI, such as imaging of gene expression and functional biosensing, they also revealed that low molecular sensitivity poses a major challenge for broader adoption in biology and medicine. Recently, new classes of biomolecular reporters have been developed based on alternative contrast mechanisms, including enhancement of spin diffusivity, interactions with hyperpolarized nuclei, and modulation of blood flow. These novel reporters promise to improve sensitivity and enable new forms of multiplexed and functional imaging.

Xenon for tunnelling analysis of the efflux pump component OprN

Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.

Inert Gas Deactivates Protein Activity by Aggregation

Biologically inert gases play important roles in the biological functionality of proteins. However, researchers lack a full understanding of the effects of these gases since they are very chemically stable only weakly absorbed by biological tissues. By combining X-ray fluorescence, particle sizing and molecular dynamics (MD) simulations, this work shows that the aggregation of these inert gases near the hydrophobic active cavity of pepsin should lead to protein deactivation. Micro X-ray fluorescence spectra show that a pepsin solution can contain a high concentration of Xe or Kr after gassing, and that the gas concentrations decrease quickly with degassing time. Biological activity experiments indicate a reversible deactivation of the protein during this gassing and degassing. Meanwhile, the nanoparticle size measurements reveal a higher number of “nanoparticles” in gas-containing pepsin solution, also supporting the possible interaction between inert gases and the protein. Further, MD simulations indicate that gas molecules can aggregate into a tiny bubble shape near the hydrophobic active cavity of pepsin, suggesting a mechanism for reducing their biological function.

Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography

Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.

NMR Hyperpolarization Techniques of Gases

Nuclear spin polarization can be significantly increased through the process of hyperpolarization, leading to an increase in the sensitivity of nuclear magnetic resonance (NMR) experiments by 4-8 orders of magnitude. Hyperpolarized gases, unlike liquids and solids, can often be readily separated and purified from the compounds used to mediate the hyperpolarization processes. These pure hyperpolarized gases enabled many novel MRI applications including the visualization of void spaces, imaging of lung function, and remote detection. Additionally, hyperpolarized gases can be dissolved in liquids and can be used as sensitive molecular probes and reporters. This Minireview covers the fundamentals of the preparation of hyperpolarized gases and focuses on selected applications of interest to biomedicine and materials science.

Gas chromatography/mass spectrometry measurement of xenon in gas-loaded liposomes for neuroprotective applications

RATIONALE

We have produced a liposomal formulation of xenon (Xe-ELIP) as a neuroprotectant for inhibition of brain damage in stroke patients. This mandates development of a reliable assay to measure the amount of dissolved xenon released from Xe-ELIP in water and blood samples.

METHODS

Gas chromatography/mass spectrometry (GC/MS) was used to quantify xenon gas released into the headspace of vials containing Xe-ELIP samples in water or blood. In order to determine blood concentration of xenon in vivo after Xe-ELIP administration, 6 mg of Xe-ELIP lipid was infused intravenously into rats. Blood samples were drawn directly from a catheterized right carotid artery. After introduction of the samples, each vial was allowed to equilibrate to 37°C in a water bath, followed by 20 minutes of sonication prior to headspace sampling. Xenon concentrations were calculated from a gas dose-response curve and normalized using the published xenon water-gas solubility coefficient.

RESULTS

The mean corrected percent of xenon from Xe-ELIP released into water was 3.87 ± 0.56% (SD, n = 8), corresponding to 19.3 ± 2.8 μL/mg lipid, which is consistent with previous independent Xe-ELIP measurements. The corresponding xenon content of Xe-ELIP in rat blood was 23.38 ± 7.36 μL/mg lipid (n = 8). Mean rat blood xenon concentration after intravenous administration of Xe-ELIP was 14 ± 10 μM, which is approximately 15% of the estimated neuroprotective level.

CONCLUSIONS

Using this approach, we have established a reproducible method for measuring dissolved xenon in fluids. These measurements have established that neuroprotective effects can be elicited by less than 20% of the calculated neuroprotective xenon blood concentration. More work will have to be done to establish the protective xenon pharmacokinetic range. Copyright © 2016 John Wiley & Sons, Ltd.

Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures

Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be inserted into protein crystals in the form of selenourea (SeC(NH₂)₂), by adding the crystalline powder of selenourea into mother liquor or cryo-solution with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as donors. Selenourea has different chemical properties than heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules.

Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology

Molecular oxygen (O2) is a key player in many fundamental biological processes. However, the combination of the labile nature and poor affinity of O2 often makes this substrate difficult to introduce into crystals at sufficient concentrations to enable protein/O2 interactions to be deciphered in sufficient detail. To overcome this problem, a gas pressure cell has been developed specifically for the `soak-and-freeze' preparation of crystals of O2-dependent biological molecules. The `soak-and-freeze' method uses high pressure to introduce oxygen molecules or krypton atoms (O2 mimics) into crystals which, still under high pressure, are then cryocooled for X-ray data collection. Here, a proof of principle of the gas pressure cell and the methodology developed is demonstrated with crystals of enzymes (lysozyme, thermolysin and urate oxidase) that are known to absorb and bind molecular oxygen and/or krypton. The successful results of these experiments lead to the suggestion that the soak-and-freeze method could be extended to studies involving a wide range of gases of biological, medical and/or environmental interest, including carbon monoxide, ethylene, methane and many others.

A Genetically Encoded β-Lactamase Reporter for Ultrasensitive (129) Xe NMR in Mammalian Cells

Molecular imaging holds considerable promise for elucidating biological processes in normal physiology as well as disease states, but requires noninvasive methods for identifying analytes at sub-micromolar concentrations. Particularly useful are genetically encoded, single-protein reporters that harness the power of molecular biology to visualize specific molecular processes, but such reporters have been conspicuously lacking for in vivo magnetic resonance imaging (MRI). Herein, we report TEM-1 β-lactamase (bla) as a single-protein reporter for hyperpolarized (HP) (129) Xe NMR, with significant saturation contrast at 0.1 μm. Xenon chemical exchange saturation transfer (CEST) interactions with the primary allosteric site in bla give rise to a unique saturation peak at 255 ppm, well removed (≈60 ppm downfield) from the (129) Xe-H2 O peak. Useful saturation contrast was also observed for bla expressed in bacterial cells and mammalian cells.

Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel

GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.

Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation

Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.