Dynamics of camel and human hemoglobin revealed by molecular simulations

Hemoglobin is one of the most widely studied proteins genetically, biochemically, and structurally. It is an oxygen carrying tetrameric protein that imparts the characteristic red color to blood. Each chain of hemoglobin harbors a heme group embedded in a hydrophobic pocket. Several studies have investigated structural variations present in mammalian hemoglobin and their functional implications. However, camel hemoglobin has not been thoroughly explored, especially from a structural perspective. Importantly, very little is known about how the heme group interacts with hemoglobin under varying conditions of osmolarity and temperature. Several experimental studies have indicated that the tense (T) state is more stable than the relaxed (R) state of hemoglobin under normal physiological conditions. Despite the fact that R state is less stable than the T state, no extensive structural dynamics studies have been performed to investigate global quaternary transitions of R state hemoglobin under normal physiological conditions. To evaluate this, several 500 ns all-atom molecular dynamics simulations were performed to get a deeper understanding of how camel hemoglobin behaves under stress, which it is normally exposed to, when compared to human hemoglobin. Notably, camel hemoglobin was more stable under physiological stress when compared to human hemoglobin. Additionally, when compared to camel hemoglobin, cofactor-binding regions of hemoglobin also exhibited more fluctuations in human hemoglobin under the conditions studied. Several differences were observed between the residues of camel and human hemoglobin that interacted with heme. Importantly, distal residues His58 of α hemoglobin and His63 of β hemoglobin formed more sustained interactions, especially at higher temperatures, in camel hemoglobin. These residues are important for oxygen binding to hemoglobin. Thus, this work provides insights into how camel and human hemoglobin differ in their interactions under stress.

Protective Effect of Dinitrosyl Iron Complexes Bound with Hemoglobin on Oxidative Modification by Peroxynitrite

Dinitrosyl iron complexes (DNICs) are a physiological form of nitric oxide (•NO) in an organism. They are able not only to deposit and transport •NO, but are also to act as antioxidant and antiradical agents. However, the mechanics of hemoglobin-bound DNICs (Hb-DNICs) protecting Hb against peroxynitrite-caused, mediated oxidative modification have not yet been scrutinized. Through EPR spectroscopy we show that Hb-DNICs are destroyed under the peroxynitrite action in a dose-dependent manner. At the same time, DNICs inhibit the oxidation of tryptophan and tyrosine residues and formation of carbonyl derivatives. They also prevent the formation of covalent crosslinks between Hb subunits and degradation of a heme group. These effects can arise from the oxoferryl heme form being reduced, and they can be connected with the ability of DNICs to directly intercept peroxynitrite and free radicals, which emerge due to its homolysis. These data show that DNICs may ensure protection from myocardial ischemia.

Sedimentary Cobalt Protoporphyrin as a Potential Precursor of Prosthetic Heme Group for Bacteria Inhabiting Fossil Organic Matter-Rich Shale Rock

This study hypothesizes that bacteria inhabiting shale rock affect the content of the sedimentary cobalt protoporphyrin present in it and can use it as a precursor for heme synthesis. To verify this hypothesis, we conducted qualitative and quantitative comparative analyses of cobalt protoporphyrin as well as heme, and heme iron in shale rock that were (i) inhabited by bacteria in the field, (ii) treated with bacteria in the laboratory, and with (iii) bacterial culture on synthetic cobalt protoporphyrin. Additionally, we examined the above-mentioned samples for the presence of enzymes involved in the heme biosynthesis and uptake as well as hemoproteins. We found depletion of cobalt protoporphyrin and a much higher heme concentration in the shale rock inhabited by bacteria in the field as well as the shale rock treated with bacteria in the laboratory. Similarly, we observed the accumulation of protoporphyrin in bacterial cells grown on synthetic cobalt protoporphyrin. We detected numerous hemoproteins in metaproteome of bacteria inhabited shale rock in the field and in proteomes of bacteria inhabited shale rock and synthetic cobalt protoporhyrin in the laboratory, but none of them had all the enzymes involved in the heme biosynthesis. However, proteins responsible for heme uptake, ferrochelatase and sirohydrochlorin cobaltochelatase/sirohydrochlorin cobalt-lyase were detected in all studied samples.

Assessment of Methaemoglobin in Haemoglobin Variants in Selected Ethnic Groups in Bayelsa State

Methaemoglobin (Met-Hb) is a type of the oxygen-carrying metalloproteinhemoglobin. The heme group iron exists as ferric (Fe3+) iron, rather than the ferrous (Fe2+) iron of typical hemoglobin. Met-Hb is unable to perform the function of binding to oxygen like oxyhaemoglobin does. The aim of this study was to compare methaemoglobin levels between AA and AS haemoglobin variants among the Ijaw, Igbo and Yoruba ethnic groups residing in Bayelsa State, Nigeria. A total of 150 subjects were enrolled for the study. One hundred and sixteen subjects constituted the Ijaws; 21 Igbos and 13 Yorubas. For each subject, 4mls of blood sample collected in EDTA bottle was assayed for methaemoglobin using a spectrophotometric method. Results revealed there was no significant difference in the methaemoglobin mean levels between the AA and AS haemoglobin variants (P-value>0.05) of the ethnic groups except the Igbo ethnic group (P-value <0.05). However, comparing the methaemoglobin mean levels among the ethnic groups showed a significant mean difference of methaemoglobin (P-value <0.05). All Post-hoc groups showed significant difference except the Igbo and Yorubo ethnic groups (P-value >0.05). In conclusion, this study has revealed that methaemoglobin levels changes significantly based on studied tribes but does not change based on studied haemoglobin variants.

In silico Discovery of a New Potent Inhibitor for Sterol 14-alpha Demethylase as a Promising Antifungal Drug against Aspergillus fumigatus Infection

Aspergillus fumigatus is a dangerous opportunistic pathogen that causes severe consequences for human beings when its conidia are inhaled. Several inhibitory drugs have recently been suggested to eradicate these fungi by inhibiting the cytochrome P450 sterol 14-alpha demethylase B (CYP51B). These drugs are designed to exhibit high specificity to the heme that is incorporated in the active site of this enzyme. Though effective binding with heme can be achieved, administration of these drugs can be accompanied by variable risks to the user’s health. Series of in silico screenings were conducted to find out more eligible drug-like compounds to inhibit CYP51B-heme with fewer side effects on patients. Using stringent ZINCPharmer restrictions, seventeen compounds were found to have efficient binding to the heme group of CYP51B. Their effectiveness against CYP51B was tested using molecular docking, drug-likeness prediction, and molecular dynamics (MD) simulation. One compound (ZINC000015774018 or molecule-8) was found to inhibit the heme group with better drug-likeness than that found in the other sixteen drug-like compounds. MD simulations showed that this ligand introduced stabilized interactions with the targeted protein upon interacting with its heme and amino acid residues. Thus it may be used as a potent antifungal inhibitor against A. fumigatus.

Hemoglobin-mediated lipid oxidation of herring filleting co-products during ensilaging and its inhibition by pre-incubation in antioxidant solutions

The aims of this study were to investigate the role of hemoglobin (Hb) in lipid oxidation development during ensilaging of herring filleting co-products, and, to inhibit this reaction by pre-incubating the co-products in water or physiological salt, with/without different antioxidants. Results showed that both peroxide value (PV) and 2-thiobarbituric acid reactive substances (TBARS) gradually increased during 7 days of ensilaging at 22 °C in absence of antioxidants. The increase in TBARS was proportional to the Hb levels present, while PV was less affected. A Hb-fortified Tris-buffer model system adjusted to pH 3.50 confirmed that Hb changed immediately from its native oxyHb to the metHb state, which facilitated heme group release and thus probably explains the increased PV and TBARS during ensilaging. Pre-incubating the co-products for 30 s in a solution containing 0.5% rosemary extract was the most promising strategy to inhibit lipid oxidation both in the co-products during pre-processing storage and during the actual ensilaging. The solution could be re-used up to ten times without losing its activity, illustrating that this methodology can be a scalable and cost-effective strategy to extend the oxidative stability of herring co-products allowing for further value adding e.g., into a high-quality silage.

In silico Characterization of the Heme Oxygenase 1 From Bottlenose Dolphin (Tursiops truncatus): Evidence of Changes in the Active Site and Purifying Selection

Cetacea is a clade well-adapted to the aquatic lifestyle, with diverse adaptations and physiological responses, as well as a robust antioxidant defense system. Serious injuries caused by boats and fishing nets are common in bottlenose dolphins (Tursiops truncatus); however, these animals do not show signs of serious infections. Evidence suggests an adaptive response to tissue damage and associated infections in cetaceans. Heme oxygenase (HO) is a cytoprotective protein that participates in the anti-inflammatory response. HO catalyzes the first step in the oxidative degradation of the heme group. Various stimuli, including inflammatory mediators, regulate the inducible HO-1 isoform. This study aims to characterize HO-1 of the bottlenose dolphin in silico and compare its structure to the terrestrial mammal protein. Upstream HO-1 sequence of the bottlenose dolphin was obtained from NCBI and Ensemble databases, and the gene structure was determined using bioinformatics tools. Five exons and four introns were identified, and proximal regulatory elements were detected in the upstream region. The presence of 10 α-helices, three 310 helices, the heme group lodged between the proximal and distal helices, and a histidine-25 in the proximal helix serving as a ligand to the heme group were inferred for T. truncatus. Amino acid sequence alignment suggests HO-1 is a conserved protein. The HO-1 “fingerprint” and histidine-25 appear to be fully conserved among all species analyzed. Evidence of positive selection within an α-helix configuration without changes in protein configuration and evidence of purifying selection were found, indicating evolutionary conservation of the coding sequence structure.

High Pressure Treatment Modifies Rigid Structure of Myoglobin and Improves Its Digestibility

Objectives Myoglobin is a special globular protein composed of a polypeptides chain and a heme group. Our previous in vitro and in vivo studies have shown that myoglobin is less susceptible to digestion because of its rigid structure. High pressure treatment is gaining more and more popularity in meat industry. To improve the digestibility and nutritional value of myoglobin, the effects of high pressure treatment on the structural and nutritional properties of myoglobin were investigated. Methods Myoglobin was treated during 100–400 MPa for 20 min, spectroscopic techniques and an in vitro digestion model were performed. Results High pressure treatment induced unfolding of globin and dissociation of heme, with an increase in the absorbance of Soret band and a reduction in the intensity of intrinsic and synchronous fluorescence spectra. Some certain changes occurred in the dissociated heme group, as the content of heme and metmyoglobin decreased. The gastric and intestinal digestibility of myoglobin increased as the pressure rose. Conclusions The results indicated that high pressure treatment could be a promising technology to improve digestibility of myoglobin by modifying its structure to improve its nutritional value. Funding Sources This work was supported by the grants from NSFC (32072211).

Covid-19 and cardiovascular diseases: Breaking news

COVID-19 disease is associated with a high inflammatory load that can induce vascular inflammation, myocarditis, and cardiac arrhythmias. Mortality from COVID-19 disease in 2019 is strongly associated with cardiovascular disease, diabetes, and hypertension. These disorders share the underlying pathophysiology related to the renin-angiotensin system (SARS). Cardiovascular disease and SARS pharmacological inhibition increase ACE2 levels, which can increase coronavirus virulence in the lung and heart. On the other hand, there is evidence that coronavirus infection can decrease ACE2, leading to toxic over-accumulation of angiotensin II, which induces acute respiratory distress syndrome and fulminant myocarditis. In addition, there is scientific evidence that SARS-CoV-2 can bind chemically to the heme group of hemoglobin and thus cause the release of iron ions (Fe2+ and Fe3+) that can damage tissues, including the lungs and heart. Another important information is that the heme group is produced by mitochondria and, in this case, the oral or intramuscular use of Coenzyme Q10 (ubiquinone) is strongly recommended, as it stimulates the increase in mitochondrial production. Therefore, the use of chelators of iron ions is notorious, as well as the administration of Coenzyme Q10 as a treatment for patients infected with SARS-CoV-2.

HEMOGLOBIN-BOUND DYNITROSIL IRON COMPLEXES PROTECT IT FROM OXIDATIVE MODIFICATION

Under the action of peroxynitrite, DNICs associated with hemoglobin are dose-dependently destroyed, while inhibiting the oxidation of tryptophan and tyrosine residues, the formation of carbonyl derivatives, preventing the formation of covalent cross-links between subunits, and preventing the degradation of the heme group.