Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin.

Nitrite binding to recombinant wild-type Sperm Whale myoglobin (SWMb) was studied using a combination of spectroscopic methods including room-temperature magnetic circular dichroism. These revealed that the reactive species is free nitrous acid and the product of the reaction contains a nitrite ion bound to the ferric heme iron in the nitrito- (O-bound) orientation. This exists in a thermal equilibrium with a low-spin ground state and a high-spin excited state and is spectroscopically distinct from the purely low-spin nitro- (N-bound) species observed in the H64V SWMb variant. Substitution of the proximal heme ligand, histidine-93, with lysine yields a novel form of myoglobin (H93K) with enhanced reactivity towards nitrite. The nitrito-mode of binding to the ferric heme iron is retained in the H93K variant again as a thermal equilibrium of spin-states. This proximal substitution influences the heme distal pocket causing the pKa of the alkaline transition to be lowered relative to wild-type SWMb. This change in the environment of the distal pocket coupled with nitrito-binding is the most likely explanation for the 8-fold increase in the rate of nitrite reduction by H93K relative to WT SWMb.

A whale of a tale: A One Environmental Health approach to study metal pollution in the Sea of Cortez.

Marine metal pollution is an emerging concern for human, animal, and ecosystem health. We considered metal pollution in the Sea of Cortez, which is a relatively isolated sea rich in biodiversity. Here there are potentially significant anthropogenic inputs of pollution from agriculture and metal mining. We considered the levels of 23 heavy metals and selenium in seven distinct cetacean species found in the area. Our efforts considered two different periods of time: 1999 and 2016/17. We considered the metal levels in relation to (1) all species together across years, (2) differences between suborders Odontoceti and Mysticeti, (3) each species individually across years, and (4) gender differences for each of these comparisons. We further compared metal levels found in sperm whale skin samples collected during these voyages to a previous voyage in 1999, to assess changes in metal levels over a longer timescale. The metals Mg, Fe, Al, and Zn were found at the highest concentrations across all species and all years. For sperm whales, we observed decreased metal levels from 1999 to 2016/2017, except for iron (Fe), nickel (Ni), and chromium (Cr), which either increased or did not change during this time period. These results indicate a recent change in the metal input to the Sea of Cortez, which may indicate a decreased concern for human, animal, and ecosystem health for some metals, but raises concern for the genotoxic metals Cr and Ni. This work was supported by NIEHS grant ES016893 (J.P.W.) and numerous donors to the Wise Laboratory.

Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity.

Sperm whale myoglobin (Mb) functions as an oxygen-storage protein, but in the ferric state it possesses a weak peroxidase activity which enables it to carry out H2O2-dependent dehalogenation reactions. Hemoglobin/dehaloperoxidase from Amphitrite ornata (DHP) is a dual-function protein represented by two isoproteins DHP A and DHP B; its peroxidase activity is at least ten times stronger than that of Mb and plays a physiological role. The `DHP A-like' K42Y Mb mutant (K42Y) and the `DHP B-like' K42N mutant (K42N) were engineered in sperm whale Mb to mimic the extended heme environments of DHP A and DHP B, respectively. The peroxidase reaction rates increased ∼3.5-fold and ∼5.5-fold in K42Y and K42N versus Mb, respectively. The crystal structures of the K42Y and K42N mutants revealed that the substitutions at position 42 slightly elongate not only the distances between the distal His55 and the heme iron but also the hydrogen-bonding distances between His55 and the Fe-coordinated water. The enhanced peroxidase activity of K42Y and K42N thus might be attributed in part to the weaker binding of the axial water molecule that competes with hydrogen peroxide for the binding site at the heme in the ferric state. This is likely to be the mechanism by which the relationship `longer distal histidine to Fe distance - better peroxidase activity', which was previously proposed for heme proteins by Matsui et al. (1999) (J. Biol. Chem. 274, 2838-2844), works. Furthermore, positive cooperativity in K42N was observed when its dehaloperoxidase activity was measured as a function of the concentration of the substrate trichlorophenol. This serendipitously engineered cooperativity was rationalized by K42N dimerization through the formation of a dityrosine bond induced by excess H2O2.

Involvement of ferryl in the reaction between nitrite and the oxy forms of globins.

The reaction between nitrite and the oxy forms of globins has complex autocatalytic kinetics with several branching steps and evolves through chain reactions mediated by reactive species (including radicals) such as hydrogen peroxide, ferryl and nitrogen dioxide, starting with a lag phase, after which it proceeds onto an autocatalytic phase. Reported here are UV-Vis spectra collected upon stopped-flow mixing of myoglobin with a supraphysiological excess of nitrite. The best fit to the experimental data follows an A â†’ B â†’ C reaction scheme involving the formation of a short-lived intermediate identified as ferryl. This is consistent with a mechanism where nitrite binds to oxy myoglobin to generate an undetectable ferrous-peroxynitrate intermediate, whose decay leads to nitrate and ferryl. The ferryl is then reduced to met by the excess nitrite. DFT calculations reveal an essentially barrierless reaction between nitrite and the oxy heme, with a notable outer-sphere component; the resulting metastable ferrous-peroxynitrate adduct is found to feature a very low barrier towards nitrate liberation, with ferryl as a final product-in good agreement with experiment.

Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations.

Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O(2) partition constant measurement method in this study, we have examined the effects of these structural factors on the O(2) equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O(2) affinity and increasing catalytic activity along with the increase in the distal His N(ε)-heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O(2) affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O(2) affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O(2) carrier.

Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase.

A major barrier to understanding the mechanism of nitric oxide reductases (NORs) is the lack of a selective probe of NO binding to the nonheme FeB center. By replacing the heme in a biosynthetic model of NORs, which structurally and functionally mimics NORs, with isostructural ZnPP, the electronic structure and functional properties of the FeB nitrosyl complex was probed. This approach allowed observation of the first S=3/2 nonheme {FeNO}(7) complex in a protein-based model system of NOR. Detailed spectroscopic and computational studies show that the electronic state of the {FeNO}(7) complex is best described as a high spin ferrous iron (S=2) antiferromagnetically coupled to an NO radical (S=1/2) [Fe(2+)-NO(.)]. The radical nature of the FeB -bound NO would facilitate N-N bond formation by radical coupling with the heme-bound NO. This finding, therefore, supports the proposed trans mechanism of NO reduction by NORs.

Stabilization of myoglobin from different species (produced by cellular agriculture) using food-grade natural and synthetic antioxidants.

Cellular agriculture products, like myoglobin, are increasingly used by the food industry to provide desirable sensory properties to plant-based meat substitutes. This study elucidated the physicochemical properties and redox stability of myoglobin from both natural (equine) and cellular agriculture (bovine, sperm whale, and leopard) sources. The electrical characteristics and water-solubility of the different myoglobin samples were measured from pH 2.5 to 8.5. The isoelectric point of the myoglobin samples depended on the species, being pH 5.5 for equine, pH 4.5 for leopard and bovine, and pH 6.5 for sperm whale. All myoglobin samples had a solubility greater than 80% across the entire pH range studied. All myoglobin solutions appeared red and had two peaks in their UV-visible absorbance spectra after one day, which is consistent with oxymyoglobin formation. Equine myoglobin at pH 8 was selected to study its redox and color stability over time, where the oxymyoglobin oxidative status closely paralleled with the redness of the solutions. The effects of antioxidants (ascorbic acid, caffeic acid, catechin, gallic acid, quercetin, taxifolin, Trolox, and 4-methylcatechol) on the redox and color stability (redness) of the equine myoglobin (pH 8.0) was also studied. Antioxidants with low reduction potential values (ascorbic acid and quercetin) were particularly effective at enhancing the color stability of oxymyoglobin. The computational modeling study showed that amino acids on the myoglobin interacted with antioxidants through hydrogen bonds. The insights obtained may have important implications for the use of cellular agriculture to produce myoglobin for food applications.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Effect of artificial and natural phospholipid membranes on rate of sperm whale oxymyoglobin autooxidation.

We were the first to show that MbO2 deoxygenation in the cell occurs only upon interaction of myoglobin with mitochondrial membrane, which must be accompanied by changes in the heme cavity conformation of the protein and its affinity for the ligand. Under aerobic conditions, some changes in the equilibrium O2 dissociation constant (Kdis) can be detected by changes of the rate of MbO2 autooxidation, i.e. spontaneous turning it into metMb (kox), as far as a direct correlation between Kdis and kox is experimentally shown. In this work, we studied the effect on MbO2 autooxidation rate of phospholipid liposomes from neutral soybean phosphatidylcholine (lecithin) and from negatively charged 1-palmitoyl-2-oleylphosphatidylglycerol (POPG) at various phospholipid/MbO2 ratios from 25 : 1 to 100 : 1, and also the effect of rat liver mitochondria at concentration of 1 and 2 mg/ml mitochondrial protein (at 22 and 37°C). In all cases, kox was found to increase due to interaction of the protein with phospholipid membranes. The effect of negatively charged liposomes from POPG on kox is significantly greater than that of neutral lecithin liposomes. At the POPG/MbO2 molar ratio of 25 : 1, MbO2 autooxidation rate is almost 25-fold increased compared to the control, whereas in the presence of 50-fold molar excess of lecithin, kox is only ~10 times higher (10 mM buffer, pH 7.2, 22°C). With the same phospholipid/MbO2 ratio of 100 : 1, kox is 7 times higher for the POPG than for lecithin liposomes. In the presence of mitochondria inhibited by antimycin A, kox grows proportionally to their concentration (about 10-fold per 1 mg/ml of mitochondrial protein), and practically does not change after adding superoxide dismutase in the reaction mixture. The kox value decreases markedly at high ionic strength, thus suggesting an important role of coulombic electrostatics in the myoglobin-mitochondrial interaction. The increase in the autooxidation rate of MbO2 (and hence its Kdis) due to the interaction with phospholipid membranes points to decreasing affinity of myoglobin for oxygen, which facilitates O2 detachment from MbO2 at physiological p02 values.

Complex of myoglobin with phenol bound in a proximal cavity.

Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with Cß and Cγ of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water.

Water-protein interactions play a direct role in protein folding. The chain collapse that accompanies protein folding involves extrusion of water from the nonpolar core. For many proteins, including apomyoglobin (apoMb), hydrophobic interactions drive an initial collapse to an intermediate state before folding to the final structure. However, the debate continues as to whether the core of the collapsed intermediate state is hydrated and, if so, what the dynamic nature of this water is. A key challenge is that protein hydration dynamics is significantly heterogeneous, yet suitable experimental techniques for measuring hydration dynamics with site-specificity are lacking. Here, we introduce Overhauser dynamic nuclear polarization at 0.35 T via site-specific nitroxide spin labels as a unique tool to probe internal and surface protein hydration dynamics with site-specific resolution in the molten globular, native, and unfolded protein states. The (1)H NMR signal enhancement of water carries information about the local dynamics of the solvent within ∼10 Šof a spin label. EPR is used synergistically to gain insights on local polarity and mobility of the spin-labeled protein. Several buried and solvent-exposed sites of apoMb are examined, each bearing a covalently bound nitroxide spin label. We find that the nonpoloar core of the apoMb molten globule is hydrated with water bearing significant translational dynamics, only 4-6-fold slower than that of bulk water. The hydration dynamics of the native state is heterogeneous, while the acid-unfolded state bears fast-diffusing hydration water. This study provides a high-resolution glimpse at the folding-dependent nature of protein hydration dynamics.

Alkylamine-ligated H93G myoglobin cavity mutant: a model system for endogenous lysine and terminal amine ligation in heme proteins such as nitrite reductase and cytochrome f.

His93Gly sperm whale myoglobin (H93G Mb) has the proximal histidine ligand removed to create a cavity for exogenous ligand binding, providing a remarkably versatile template for the preparation of model heme complexes. The investigation of model heme adducts is an important way to probe the relationship between coordination structure and catalytic function in heme enzymes. In this study, we have successfully generated and spectroscopically characterized the H93G Mb cavity mutant ligated with less common alkylamine ligands (models for Lys or the amine group of N-terminal amino acids) in numerous heme iron states. All complexes have been characterized by electronic absorption and magnetic circular dichroism spectroscopy in comparison with data for parallel imidazole-ligated H93G heme iron moieties. This is the first systematic spectral study of models for alkylamine- or terminal amine-ligated heme centers in proteins. High-spin mono- and low-spin bis-amine-ligated ferrous and ferric H93G Mb adducts have been prepared together with mixed-ligand ferric heme complexes with alkylamine trans to nitrite or imidazole as heme coordination models for cytochrome c nitrite reductase or cytochrome f, respectively. Six-coordinate ferrous H93G Mb derivatives with CO, NO, and O(2) trans to the alkylamine have also been successfully formed, the latter for the first time. Finally, a novel high-valent ferryl species has been generated. The data in this study represent the first thorough investigation of the spectroscopic properties of alkylamine-ligated heme iron systems as models for naturally occurring heme proteins ligated by Lys or terminal amines.

Biosynthesis of ambrein in ambergris: evidence from isotopic data and identification of possible intermediates.

Ambrein is found in ambergris, a coprolith occurring in the rectum of the sperm whale. In vitro, ambrein is produced by enzymatic cyclisation of squalene, via a monocyclic intermediate. However, little is known of the in vivo process. In order to find evidence for the reaction in vivo, a comparison was made of the δ13C relative isotopic ratios of ambrein in ambergris with those of co-occurring sterols. A statistically significant difference was noted. This suggests that ambrein originates via a different biosynthetic mechanism from that of the sterols. Examination of the minor constituents of a hydrogenolysed extract of ambergris revealed compounds with a bicyclic polypodane nucleus, rather than those with monocyclic structures. It is hypothesised that in vivo biosynthesis of ambrein proceeds, at least in some cases, via bacterial production of bicyclic polypodenols. The latter are known products of non-concerted squalene (or squalene oxide) cyclisations in other organisms.

The main role of inner histidines in the molecular mechanism of myoglobin oxidation catalyzed by copper compounds.

In the presence of Cu(2+) and Cu(Gly)(2), the oxidation of two native MbO(2)'s (Mb = myoglobin), from the sperm whale and horse, and also two chemically modified sperm whale MbO(2)'s alkylated at solvent-accessible histidines by sodium bromoacetate (CM-MbO(2)) and by iodoacetamide (CA-MbO(2)) have been studied at different pH's, ionic strengths, and concentrations of the copper reagent. The influence of competitive redox-inactive zinc ions on the reaction rate is investigated as well. Localization of Cu(Gly)(2) in sperm whale met-Mb and CM-met-Mb has been examined using the high-resolution NMR method. The obtained data suggest that binding of copper compounds to the surface histidines (all of them are 1.8-2.7 nm apart from the heme) has only a minor, no more than 35%, contribution to the overall reaction rate, in particular under a large excess of the reagent (more than 8-10-fold). The noticeable contribution of His113(116), His48, and His81, which have the greatest affinity to copper according to NMR data, is revealed only at small concentrations of copper, less than a 5-fold excess relative to the protein. The main contribution to the reaction rate must be from the binding of copper to the inner histidines, His97 (0.62 nm from the heme), and possibly to the distal His64. Both are inaccessible to the modification by alkylating reagents and have much lower affinity to copper than all surface histidines, because they are hydrogen-bonded, the former with the carboxyl group of the heme propionate and the second with the liganded O(2).

Construction of an artificial system for ambrein biosynthesis and investigation of some biological activities of ambrein.

Ambergris, a sperm whale metabolite, has long been used as a fragrance and traditional medication, but it is now rarely available. The odor components of ambergris result from the photooxidative degradation of the major component, ambrein. The pharmacological activities of ambergris have also been attributed to ambrein. However, efficient production of ambrein and odor compounds has not been achieved. Here, we constructed a system for the synthesis of ambrein and odor components. First, we created a new triterpene synthase, "ambrein synthase," for mass production of ambrein by redesigning a bacterial enzyme. The ambrein yields were approximately 20 times greater than those reported previously. Next, an efficient photooxidative conversion system from ambrein to a range of volatiles of ambergris was established. The yield of volatiles was 8-15%. Finally, two biological activities, promotion of osteoclast differentiation and prevention of amyloid ß-induced apoptosis, were discovered using the synthesized ambrein.

Peroxynitrite scavenging by ferryl sperm whale myoglobin and human hemoglobin.

Globins protect from the oxidative and nitrosative cell damage. Here, kinetics of peroxynitrite scavenging by ferryl sperm whale myoglobin (MbFe(IV)O) and human hemoglobin (HbFe(IV)O), between pH 5.8 and 8.3 at 20.0 degrees C, are reported. In the absence of CO(2), values of the second-order rate constant for peroxynitrite scavenging by MbFe(IV)O and HbFe(IV)O (i.e., for MbFe(III) and HbFe(III) formation; k(on)) are 4.6 x 10(4)M(-1)s(-1) and 3.3 x 10(4)M(-1)s(-1), respectively, at pH 7.1. Values of k(on) increase on decreasing pH with pK(a) values of 6.9 and 6.7, this suggests that the ONOOH species reacts preferentially with MbFe(IV)O and HbFe(IV)O. In the presence of CO(2) (=1.2 x 10(-3)M), values of k(on) for peroxynitrite scavenging by MbFe(IV)O and HbFe(IV)O are essentially pH-independent, the average k(on) values are 7.1 x 10(4)M(-1)s(-1) and 1.2 x 10(5)M(-1)s(-1), respectively. As a whole, MbFe(IV)O and HbFe(IV)O, obtained by treatment with H(2)O(2), undertake within the same cycle H(2)O(2) and peroxynitrite detoxification.

Tissue distribution of organic contaminants in stranded pregnant sperm whale (Physeter microcephalus) from the Huizhou coast of the South China Sea.

Twelve persistent organic pollutants (POPs) were measured in 11 tissue samples from a pregnant sperm whale stranded on the Huizhou coast of the South China Sea, China, in March 2017. POPs were found to be more concentrated in the irrigated tissues such as placenta, ovary, mammary gland, and liver than the less irrigated tissues such as epidermis. High POP levels detected in the placenta might result in abnormal hormone secretion in the placenta, which would affect the unborn offspring. We hypothesized that ovary is potentially vulnerable to the exposure of higher contaminant levels. The PAH concentrations were higher in the lung than in other tissues, which suggest that PAH levels in the lung were breath-dependent in the sperm whale. The concentrations of POPs except PAHs in the sperm whale blubber were lower than those in the same species in the Northern Hemisphere and were comparable to or lower than those in the same species in the Southern Hemisphere.

Stable isotope ratios of carbon, nitrogen and sulphur and mercury concentrations as descriptors of trophic ecology and contamination sources of Mediterranean whales.

The Mediterranean Sea remains a complex system for mercury (Hg) cycling and accumulation in marine vertebrates. The extremely high levels these animals present demand for an urgent understanding of such processes and the development of new analytical techniques that go beyond the simple contamination monitoring. It was often proposed that prey selection or habitat use may affect Hg contamination in animals; however, it was never possible to measure which factor influences more rates and pathways of contamination. In this paper, we directly integrate toxicological information (Hg levels) and ecological tracers (stable isotopes of C, N and S) into a common data analysis framework (isotopic niches), with the aim of quantifying the influence of species' trophic behaviour on Hg contamination. The analysis was conducted on skin biopsies of fin whales Balaenoptera physalus, long-finned pilot whales Globicephala melas and sperm whales Physeter microcephalus. Their different trophic modes and residency in the area make them model species for the analysis of Hg accumulation along NWMS food webs. We measured Total Hg (T-Hg) concentrations through absorbance spectrometry with the DMA80 Milestone. Carbon, nitrogen and sulphur isotope compositions were measured via mass spectrometry in an IRMS coupled to an Elemental Analyser (EA) Isoprime. Comparison of ecological and contamination niches allowed to explain Hg accumulation in Mediterranean marine predators. Factors such as food web complexity, trophic position, hunting distribution or habitat use (e.g., foraging depth) did not influence Hg exposure. It is rather the selection of prey type, which determines the range of potential Hg sources and as a consequence the rates of accumulation in whales' tissues. A generalist piscivorous species such as the pilot whales will bioaccumulate more Hg than specialised sperm whales feeding mostly on cephalopods.

Ingestion of macroplastics by odontocetes of the Greek Seas, Eastern Mediterranean: Often deadly!

Plastic pollution is an omnipresent problem that threatens marine animals through ingestion and entanglement. Marine mammals are no exception to this rule but their interaction with plastic remains understudied in the Mediterranean Sea. Here we highlight this problem by analyzing the stomach contents of 34 individuals from seven odontocete species stranded in Greece. Macroplastic (>5 mm) was found in the stomachs of nine individuals from four species (harbour porpoise Phocoena phocoena, Risso's dolphin Grampus griseus, Cuvier's beaked whale Ziphius cavirostris and sperm whale Physeter macrocephalus) with the highest frequency of occurrence in sperm whales (60%). Gastric blockage from plastic was presumably lethal in three cases, with plastic bags being the most common finding (46%). Plastic ingestion is of particular conservation concern for the endangered Mediterranean sperm whales. A regular examination of stranded cetaceans with a standardised protocol is critical for allowing spatiotemporal comparisons within and across species.

The effect of heme on the conformational stability of micro-myoglobin.

Micro-myoglobin, the isolated heme-binding subdomain of myoglobin, is a valuable model system for the investigation of heme recognition and binding by proteins, and provides an example of protein folding induced by cofactor binding. Theoretical studies by molecular dynamics simulations on apo- and holo-micro-myoglobin show that, by contrast with the case of the full-length wild-type protein and in agreement with earlier experimental evidence, the apo-protein is not stably folded in a native-like conformation. With the cofactor bound, however, the protein fragment maintains its folded conformation over 1.5 ns in molecular dynamics simulations. Further inspection of the model structures reveals that the role of heme in stabilizing the folded state is not only a result of its direct interactions with binding residues (His93, Arg45 and Lys96), but also derives from its shielding effect on a long-range electrostatic interaction between Arg45 and Asp60, which, in the molecular dynamics simulations, apparently triggers the unfolding process of apo-micro-myoglobin.