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Oxygen
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Interaction of Oxygen and Other Gases with Haem Containing Proteins
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Interaction of Oxygen and Other Gases with Haem Containing Proteins

A special issue of Oxygen (ISSN 2673-9801).

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 4447

Special Issue Editor

Prof. Dr. John T. Hancock

E-Mail Website
Guest Editor
School of Applied Sciences, University of the West of England, Bristol, UK
Interests: redox signaling; reactive oxygen species; hydrogen sulfide; hydrogen gas; nitric oxide
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The interaction of molecular oxygen (O2) and haem-containing proteins has been known of for a long time. Oxygen is transiently bound by both haemoglobin and myoglobin in animals, as well as by globins, found in plants. Oxygen also binds to proteins with haem prosthetic groups which function as terminal electron acceptors, such as in the enzyme NADPH oxidase, which is instrumental in the generation of reactive oxygen species in animals and plants. Other gases, besides oxygen, interact with haem-containing proteins too. Carbon dioxide and carbon monoxide are two good examples, but several other gases are also known to cause similar effects. Inert gases, such as xenon (Xe), can bind to hydrophobic cavities and alter protein function, with the globin proteins being a good model system for the study of such effects. Nitric oxide (NO) is known to affect haem proteins, such as haemoglobin and guanylyl cyclase. More recently, molecular hydrogen (H2) has been found to cause significant biological effects, partly mediated by the removal of hydroxyl radicals. One mechanism suggested is the interaction of H2 with protein haem groups. Therefore, along with oxygen, several gases which are likely to be present in cells at the same time are able to interact with a range of proteins which contain haem, and their interplay and how they affect cellular function will no doubt be an area of interest in the foreseeable future.

Prof. Dr. John T. Hancock
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Oxygen is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • oxygen oxygen transport and movement
  • oxygen binding
  • gasotransmitters haem (Heme)
  • prosthetic groups
  • guanylyl cyclase (Guanylate cyclase)
  • NADPH oxidase
  • carbon monoxide
  • carbon dioxide
  • electron transfer
  • nitric oxide
  • nitric oxide synthase
  • xenon
  • argon
  • krypton
  • hydrogen
  • hydrogen sulfide
  • hydrophobic cavities and pockets
  • protein structure alterations

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Published Papers (3 papers)

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Research

Jump to: Review, Other

13 pages, 4291 KiB  
Article
Diffusion and Spectroscopy of H2 in Myoglobin
by Jiri Käser, Kai Töpfer and Markus Meuwly
Oxygen 2024, 4(4), 389-401; https://doi.org/10.3390/oxygen4040024 - 31 Oct 2024
Viewed by 380
Abstract
The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H2) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or inflammation. Here, the internal diffusion through the protein matrix was characterized, [...] Read more.
The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H2) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or inflammation. Here, the internal diffusion through the protein matrix was characterized, and the vibrational spectroscopy was investigated using conventional empirical energy functions and improved models able to describe higher-order electrostatic moments of the ligand. Depending on the energy function used, H2 can occupy the same internal defects as already found for Xe or CO (Xe1 to Xe4 and B-state). Furthermore, four additional sites were found, some of which had been discovered in earlier simulation studies. Simulations using a model based on a Morse oscillator and distributed charges to correctly describe the molecular quadrupole moment of H2 indicate that the vibrational spectroscopy of the ligand depends on the docking site it occupies. This is consistent with the findings for CO in Mb from experiments and simulations. For H2, the maxima of the absorption spectra cover ∼20 cm−1 which are indicative of a pronounced Stark effect of the surrounding protein matrix on the vibrational spectroscopy of the ligand. Electronic structure calculations show that H2 forms a stable complex with the heme iron (stabilized by ∼−12 kcal/mol), but splitting of H2 is unlikely due to a high activation energy (∼50 kcal/mol). Full article
(This article belongs to the Special Issue Interaction of Oxygen and Other Gases with Haem Containing Proteins)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>Pocket representation in Mb. Shown is the secondary structure of Mb (eight helices) with the heme-unit in ball-and-stick representation together with the pockets determined for H<sub>2</sub> found in the present simulations. The pockets are Xe1 to Xe4, B-state, and pockets 6 to 9, which were found in addition to the experimentally known ligand-binding sites [<a href="#B13-oxygen-04-00024" class="html-bibr">13</a>,<a href="#B30-oxygen-04-00024" class="html-bibr">30</a>].</p> Full article ">Figure 2
<p>H<sub>2</sub> ESP fit. Panel (<b>A</b>): reference ESP contour plot of H<sub>2</sub> along the <math display="inline"><semantics> <mrow> <mo>(</mo> <mi>x</mi> <mo>,</mo> <mi>z</mi> <mo>)</mo> </mrow> </semantics></math>—plane going through the molecule. H<sub>2</sub> is at equilibrium bond length, and the ESP is only shown for for grid points with distances larger than <math display="inline"><semantics> <mrow> <mn>1.44</mn> </mrow> </semantics></math> Å of the closest hydrogen atom. Panel (<b>B</b>): ESP difference contour plot between reference and model ESP. The open black circles mark the positions of the hydrogen atoms.</p> Full article ">Figure 3
<p>PES scan of H<sub>2</sub> interacting with the Heme–Histidine active site of myoglobin. Calculations were carried out at the rPBE/def2-TZVP level of theory. The coordinate system for scanning this potential energy surface is shown in <a href="#app1-oxygen-04-00024" class="html-app">Figure S1</a>.</p> Full article ">Figure 4
<p>Pocket dynamics of H<sub>2</sub> in Mb. Panels (<b>A</b>,<b>B</b>) report the pocket occupied by H<sub>2</sub> as a function of the simulation time from simulations using the CGenFF and MDCM/Morse energy functions, respectively. Panels (<b>C</b>,<b>D</b>) show the separation between H<sub>2</sub> and each of the pocket centers (Xe1 to Xe4, B-state, and 6 to 9). For better visualization, only 1 ns out of the 5 ns trajectory is shown, specifically in panels (<b>A</b>,<b>B</b>). Each color corresponds to a particular separation between H<sub>2</sub> and the respective pocket center. In panel D, between 150 and 300 ps, the distance between H<sub>2</sub> and any other pocket is ∼5 Å, which points to one or several other uncharacterized docking sites. Simulations for panels (<b>A</b>–<b>D</b>) were started from identical initial structures, each with five H<sub>2</sub> molecules located at sites B-state (3) and Xe4 (2) to increase sampling. Results are reported for one out of the five H<sub>2</sub> molecules.</p> Full article ">Figure 5
<p>Vibrational spectra of H<sub>2</sub> in Mb from unconstrained MD simulations. Panel (<b>A</b>): simulations using CGenFF and Panel (<b>B</b>): simulations using the Morse potential and MDCM for H<sub>2</sub>. The black trace is the total spectrum as it would, for example, be measured from an experiment. Filled circles indicate the mean of each spectrum, the mean frequencies are given in the legend, and the simulated frequency of gas phase H<sub>2</sub> is shown as a vertical dashed line at (<b>A</b>) <math display="inline"><semantics> <mrow> <mn>4062.4</mn> </mrow> </semantics></math> cm<sup>−1</sup> and (<b>B</b>) <math display="inline"><semantics> <mrow> <mn>4465.4</mn> </mrow> </semantics></math> cm<sup>−1</sup>. The differences between panels (<b>A</b>,<b>B</b>) are both due to using a harmonic bond (<b>A</b>) versus a Morse oscillator (<b>B</b>) and a point charge description for H<sub>2</sub> (<b>A</b>) versus an MDCM model (<b>B</b>).</p> Full article ">Figure 6
<p>Vibrational spectra of H<sub>2</sub> in Mb from pocket-constrained MD simulations. Panel (<b>A</b>): simulations using the CGenFF energy function. Panel (<b>B</b>): using the MDCM model for H<sub>2</sub> but a conventional harmonic bond potential. Panel (<b>C</b>): using the MDCM model and the Morse potential for H<sub>2</sub>. The weighted average position of the maximum intensity (in cm<sup>−1</sup>) for each spectra is given in brackets in the legend. The vibrational frequency from the MD simulation of H<sub>2</sub> in the gas phase is marked as a vertical dashed line.</p> Full article ">

Review

Jump to: Research, Other

11 pages, 261 KiB  
Review
Noble Gases in Medicine: Current Status and Future Prospects
by David A. Winkler
Oxygen 2024, 4(4), 421-431; https://doi.org/10.3390/oxygen4040026 - 16 Nov 2024
Viewed by 397
Abstract
Noble gases are a valuable but overlooked source of effective and safe therapeutics. Being monoatomic and chemically inert, they nonetheless have a surprisingly wide range of biochemical and medically valuable properties. This mini review briefly summarizes these properties for the most widely used [...] Read more.
Noble gases are a valuable but overlooked source of effective and safe therapeutics. Being monoatomic and chemically inert, they nonetheless have a surprisingly wide range of biochemical and medically valuable properties. This mini review briefly summarizes these properties for the most widely used noble gases and focuses and research gaps and missed opportunities for wider use of these intriguing ‘atomic’ drugs. The main research gaps and opportunities lie firstly in the application of advanced computational modelling methods for noble gases and recent developments in accurate predictions of protein structures from sequence (AlphaFold), and secondly in the use of very efficient and selective drug delivery technologies to improve the solubility, efficacy, and delivery of noble gases to key targets, especially for the lighter, poorly soluble gases. Full article
(This article belongs to the Special Issue Interaction of Oxygen and Other Gases with Haem Containing Proteins)

Other

Jump to: Research, Review

16 pages, 1549 KiB  
Perspective
An Interplay of Gases: Oxygen and Hydrogen in Biological Systems
by Grace Russell, Jennifer May and John T. Hancock
Oxygen 2024, 4(1), 37-52; https://doi.org/10.3390/oxygen4010003 - 9 Feb 2024
Cited by 2 | Viewed by 3125
Abstract
Produced by photosynthesis, oxygen (O2) is a fundamentally important gas in biological systems, playing roles as a terminal electron receptor in respiration and in host defence through the creation of reactive oxygen species (ROS). Hydrogen (H2) plays a role [...] Read more.
Produced by photosynthesis, oxygen (O2) is a fundamentally important gas in biological systems, playing roles as a terminal electron receptor in respiration and in host defence through the creation of reactive oxygen species (ROS). Hydrogen (H2) plays a role in metabolism for some organisms, such as at thermal vents and in the gut environment, but has a role in controlling growth and development, and in disease states, both in plants and animals. It has been suggested as a medical therapy and for enhancing agriculture. However, the exact mode of action of H2 in biological systems is not fully established. Furthermore, there is an interrelationship between O2 and H2 in organisms. These gases may influence each other’s presence in solution, and may both interact with the same cellular components, such as haem prosthetic groups. It has also been suggested that H2 may affect the structures of some proteins, such as globins, with possible effects on O2 movement in organisms. Lastly, therapies may be based on supplying O2 and H2 together, such as with oxyhydrogen. Therefore, the relationship regarding how biological systems perceive and respond to both O2 and H2, and the interrelationship seen are worth considering, and will be discussed here. Full article
(This article belongs to the Special Issue Interaction of Oxygen and Other Gases with Haem Containing Proteins)
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Figure 1

Figure 1
<p>Oxygen can be reduced to reactive oxygen species (ROS), such as superoxide anions (O<sub>2</sub><sup>•−</sup>), hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and the hydroxyl radical (<sup>•</sup>OH). In mitochondrial respiration, O<sub>2</sub> is converted to water by a 4-electron reaction.</p> Full article ">Figure 2
<p>Estimation of the O<sub>2</sub> concentration in solution. On extrapolation, this gives the half-life of concentration elevation. The solution was bubbled with oxyhydrogen solution 450 mL/min for 30 min (HydroVitality™, Wakefield, UK). O<sub>2</sub> was measured with a Clark-type electrode (Hanna Instruments, Bedfordshire, UK. Cat. #H198198). The red dotted line is an extrapolation, whilst the horizonal line represents the half-way point of increase. The arrow indicates an approximate half-life. Data representative of 3 repeats +/− SEM.</p> Full article ">Figure 3
<p>Estimation of the H<sub>2</sub> concentration in solution after bubbling with oxyhydrogen gas 450 mL/min for 30 min (HydroVitality™, Wakefield, UK). H<sub>2</sub> was measured with a methylene blue-based assay system (H<sub>2</sub>Blue, H<sub>2</sub> Sciences Inc., Henderson, NV, USA). The horizontal dotted line is halfway between the maximal concentration measured and the minimal concentration expected when the solution is equilibrated with atmospheric air. The red dotted line is an extrapolation, whilst the horizonal line represents the half-way point of increase. The arrow indicates an approximate half-life Data representative of 3 repeats +/− SEM.</p> Full article ">Figure 4
<p>Concentration of O<sub>2</sub> and H<sub>2</sub> in solution. H<sub>2</sub> was produced using a magnesium-based tablet (Drink HRW, Oxnard, USA). The tablet was dropped into deionised water (15 MΩ∙cm<sup>2</sup>) in a non-sealed conical flask (500 mL). H<sub>2</sub> was measured with a methylene blue-based assay system (H<sub>2</sub>Blue, H<sub>2</sub> Sciences Inc., Henderson, NV, USA). O<sub>2</sub> was measured using a Clark-type electrode (Hanna Instruments, Bedfordshire, UK. Cat. #H198198). Data are mean 3 repeats +/− SEM.</p> Full article ">
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