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

Accurate measurement of sequential Ar desorption energies from the dispersion-dominated Ar1-3 complexes of aromatic molecules

We present experimental determination of the energies associated with the gradual desorption of Ar atoms from the aromatic molecular surface. Non-covalently bound 2,2'-pyridylbenzimidazole-Ar_1-3 complexes were produced in the gas phase and characterized using resonant two-photon ionization (R2PI) spectroscopy. The single Ar desorption from the PBI-Ar, PBI-Ar₂ and PBI-Ar₃ complexes were measured as 581 ± 18, 656 ± 30 and 537 ± 31 cm^-1, respectively. The energies were bracketed between the last observed band in the respective R2PI spectra and the disappeared intramolecular modes of PBI. The Ar_n dissociation energies in the S₁ state were measured as 581 ± 18, 1237 ± 48 and 1774 ± 79 cm^-1, respectively, for n = 1, 2 and 3. The calculated dissociation energies of the respective complexes, obtained using three computational methods, show excellent agreement with the experimental data. The ground state dissociation energies were estimated by subtracting the Δν shift of the origin band, and the respective values are 541 ± 18, 1160 ± 48 and 1634 ± 79 cm^-1. Overall, the calculated values resulted in scaling factors ranging from 0.956 to 1.017, which depict the predictive power of the methods to determine dispersion energies. The current investigation describes a unique methodology to accurately determine the dissociation and desorption energies of Ar atoms from the surfaces of bio-relevant aromatic molecules.

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.

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.

A combined spectroscopic and computational investigation on dispersion-controlled docking of Ar atoms on 2-(2'-pyridyl)benzimidazole

The dispersion-controlled docking of inert Ar atoms on the face of polycyclic 2-(2'-pyridyl)-benzimidazole (PBI) was studied experimentally aided by computational findings. The PBI-Ar_n (n = 1-3) complexes were produced in a supersonically jet-cooled molecular beam and probed using resonant two-photon ionization coupled with a time-of-flight mass spectrometric detection scheme and laser-induced fluorescence spectroscopy. The ground state vibrational frequencies were obtained from single vibronic level fluorescence spectroscopy. The formation of multiple isomers was verified using UV-UV hole-burning spectroscopy. The geometries of PBI-Ar_n (n = 1-3) complexes were derived by mutual agreement between experimental findings and computational results such as vibrational frequencies in the ground and excited electronic states, Franck-Condon factors and spectral shift of the S₁← S₀ transitions. All the above analyses provided good agreement between the experimental and simulated spectrum with the most stable PBI-Ar_n (n = 1-3) clusters. The highest intermolecular interaction between PBI and Ar was obtained with the Ar atom positioned above the imidazolyl ring. A second Ar atom was preferably docking on the other side of the imidazolyl ring than the pyridyl ring. The subsequent addition of the third Ar atom preferred the position above the pyridyl ring. The current investigation can be useful to investigate the preferential docking of dispersion-controlled interacting partners in multifunctional aromatic side chains present in biological systems.

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.