On the Pathways of Biologically Relevant Diatomic Gases through Proteins. Dioxygen and Heme Oxygenase from the Perspective of Molecular Dynamics

This work deals with dioxygen (O₂) binding sites and pathways through inducible human heme oxygenase (HO‐1). The experimentally known distal binding site 1, and sites 2–3 above it, could be reproduced by means of non‐deterministic random‐acceleration molecular‐dynamics (RAMD) simulations. In addition, RAMD revealed the proximal binding site 5, a deeply‐seated binding site 4, which lies behind heme, as well as a few gates communicating with the external medium. In getting from site 1 to the main gate, which lies on the protein front opposed to site 4, O₂ follows chiefly the shortest direct pathway. Less frequently, O₂ visits intermediate sites 2, 4, or 5 along longer pathways. A similarity between HO‐1, myoglobin, and cytoglobin in using, for diatomic gas delivery, the direct shortest pathway from the heme center to the surrounding medium, is emphasized. Otherwise, comparing other proteins and diatomic gases, each system reveals its peculiarities as to sites, gates, and pathways. Thus, relating these properties to the physiological functions of the proteins remains in general a challenge for future studies.     

On Dioxygen Permeation through a Dehydrogenase‐Pyrroloquinoline Quinone Complex. A Molecular‐Dynamics Investigation

In this work, an all atom model of the quinoprotein dehydrogenase PqqC in complex with the PQQ (=4,5‐dihydro‐4,5‐dioxo‐1H‐pyrrolo[2,3‐f]quinoline‐2,7,9‐tricarboxylic acid) cofactor and dioxygen (O₂), solvated with TIP3 water in periodic boxes, was subjected to random‐acceleration molecular dynamics (RAMD). It was found that O₂ leaves the active binding pocket, in front of PQQ, to get to the solvent, as easily as with a variety of other O₂‐activating enzymes, O₂ carriers, and gas‐sensing proteins. The shortest pathway, orthogonal to the center of the mean plane of PQQ, was largely preferred by O₂ over pathways slightly deviating from this line. These observations challenge the interpretation of an impermeable active binding pocket of PqqC‐PQQ, as drawn from both X‐ray diffraction data of the crystal at low temperature and physiological experimentation.     

On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation

It is reported here on random acceleration molecular dynamics (RAMD) simulations with the 2GF3 bacterial monomeric sarcosine oxidase (MSOX), O₂, and furoic acid in place of sarcosine, solvated by TIP3 H₂O in a periodic box. An external tiny force, acting randomly on O₂, accelerated its relocation, from the center of activation between residue K265 and the si face of the flavin ring of the flavin adenine dinucleotide cofactor, to the surrounding solvent. Only three of the four O₂ gates previously described for this system along a composite method technique were identified, while two more major O₂ gates were found. The RAMD simulations also revealed that the same gate can be reached by O₂ along different pathways, often involving traps for O₂. Both the residence time of O₂ in the traps, and the total trajectory time for O₂ getting to the solvent, could be evaluated. The new quick pathways discovered here suggest that O₂ exploits all nearby interstices created by the thermal fluctuations of the protein, not having necessarily to look for the permanent large channel used for uptake of the FADH cofactor. To this regard, MSOX resembles closely KijD3 N‐oxygenase. These observations solicit experimental substantiation, in a long term aim at discovering whether gates and pathways for the small gaseous ligands inside the proteins are under Darwinian functional evolution or merely stochastic control operates.     

Myoglobin discriminates between O2, NO, and CO by electrostatic interactions with the bound ligand

 Most biological substrates have distinctive sizes, shapes, and charge distributions which can be recognized specifically by proteins. In contrast, myoglobin must discriminate between the diatomic gases O₂, CO, and NO which are apolar and virtually the same size. Selectivity occurs at the level of the covalent Fe-ligand complexes, which exhibit markedly different bond strengths and electrostatic properties. By pulling a water molecule into the distal pocket, His64(E7)¹ inhibits the binding of all three ligands by a factor of ∼10 compared to that observed for protoheme-imidazole complexes in organic solvents. In the case of O₂ binding, this unfavorable effect is overcome by the formation of a strong hydrogen bond between His64(E7) and the highly polar FeO₂ complex. This favorable electrostatic interaction stabilizes the bound O₂ by a factor of ∼1000, and the net result is a 100-fold increase in overall affinity compared to model hemes or mutants with an apolar residue at position 64. Electrostatic interaction between FeCO and His64 is very weak, resulting in only a two- to three-fold stabilization of the bound state. In this case, the inhibitory effect of distal pocket water dominates, and a net fivefold reduction in K _CO is observed for the wild-type protein compared to mutants with an apolar residue at position 64. Bound NO is stabilized ∼tenfold by hydrogen bonding to His64. This favorable interaction with FeNO exactly compensates for the tenfold inhibition due to the presence of distal pocket water, and the net result is little change in K _NO when the distal histidine is replaced with apolar residues. Thus, it is the polarity of His64 which allows discrimination between the diatomic gases. Direct steric hindrance by this residue plays a minor role as judged by: (1) the independence of K _O2, K _CO, and K _NO on the size of apolar residues inserted at position 64, and (2) the observation of small decreases, not increases, in CO affinity when the mobility of the His64 side chain is increased. Val68(E11) does appear to hinder selectively the binding of CO. However, the extent is no more than a factor of 2–5, and much smaller than electrostatic stabilization of bound O₂ by the distal histidine. Received, accepted: 23 May 1997     

On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution

In a preliminary exploration of the dummy model for diiron proteins, random‐acceleration molecular dynamics (RAMD) revealed that a pure four‐helix bundle structure, like hemerythrin, constitutes an efficient cage for dioxygen (O₂), which can only leave from defined, albeit very broad, gates. However, this well ordered structure does not constitute an archetype on which to compare O₂ permeation of other diiron proteins, like the complex of soluble methane monooxygenase hydroxylase with the regulatory protein (sMMOH‐MMOB). The reason is that with this complex, unlike hemerythrin, the four helices of the four‐helix bundle are heavily bent, and RAMD showed that most traps for O₂ lie outside them. It was also observed that, in spite of a nearly identical van der Waals radius for O₂ and the natural substrate CH₄, the latter behaves under RAMD as a bulkier molecule than O₂, requiring a higher external force to be brought out of sMMOH‐MMOB along trajectories of viable length. All that determined with sMMOH‐MMOB multiple gates and multiple pathways to each of them through several binding pockets, for both O₂ and CH₄. Of the two equally preferred pathways for O₂, at right angle with one another, one proved to be in accordance with the Xe‐atom mapping for sMMOH. In contrast, none of the pathways identified for CH₄ proved to be in accordance with such mapping, CH₄ looking for more open avenues instead.     

On Dioxygen Permeation of MaL Laccase from the Thermophilic Fungus Melanocarpus albomyces: An all‐Atom Molecular Dynamics Investigation

In this article, biased molecular dynamics (MD) simulations of O₂ egress from the active center of MaL laccase toward the bulk solvent were described. Parameterization of the set of four Cu(II) ions, in the framework of CHARMM‐36 FF, was carried out on a recent dummy‐atom model that takes into account the Jahn–Teller effect. By carrying out a number of statistically relevant MD simulations, under a tiny randomly oriented external force applied to the molecule O₂, three preferred gates for O₂ egress from the enzyme and a few intermediate binding pockets (BPs) for O₂ were visible; all the gates and pockets were located on two of the three domains. This wide distribution of preferred gates notwithstanding the molecule O₂ was seen to follow specific pathways, exploiting consistently the interstices created by the enzyme thermal fluctuations. These are features that can be imagined to have evolved to make MaL laccase extremely efficient as catalysts in various reactions that require O₂.     

Generation of a hypoxia‐sensing mouse model

Oxygen (O₂) homeostasis is essential to the metazoan life. O₂‐sensing or hypoxia‐regulated molecular pathways are intimately involved in a wide range of critical cellular functions and cell survival from embryogenesis to adulthood. In this report, we have designed an innovative hypoxia sensor (O₂CreER) based on the O₂‐dependent degradation domain of the hypoxia‐inducible factor‐1α and Cre recombinase. We have further generated a hypoxia‐sensing mouse model, R26‐O₂CreER, by targeted insertion of the O₂CreER‐coding cassette in the ROSA26 locus. Using the ROSA^mTmG mouse strain as a reporter, we have found that this novel hypoxia‐sensing mouse model can specifically identify hypoxic cells under the pathological condition of hind‐limb ischemia in adult mice. This model can also label embryonic cells including vibrissal follicle cells in E13.5–E15.5 embryos. This novel mouse model offers a valuable genetic tool for the study of hypoxia and O₂ sensing in mammalian systems under both physiological and pathological conditions.     

Electron transfer function versus oxygen delivery: a comparative study for several hexacoordinated globins across the animal kingdom

Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O(2) and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O(2) as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O(2) actually binding to the iron atom, since the heme is oxidized by O(2) faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins.     

Use of carbon monoxide and hydrogen by a bacteria–animal symbiosis from seagrass sediments

The gutless marine worm Olavius algarvensis lives in symbiosis with chemosynthetic bacteria that provide nutrition by fixing carbon dioxide (CO₂) into biomass using reduced sulfur compounds as energy sources. A recent metaproteomic analysis of the O. algarvensis symbiosis indicated that carbon monoxide (CO) and hydrogen (H₂) might also be used as energy sources. We provide direct evidence that the O. algarvensis symbiosis consumes CO and H₂. Single cell imaging using nanoscale secondary ion mass spectrometry revealed that one of the symbionts, the γ3‐symbiont, uses the energy from CO oxidation to fix CO₂. Pore water analysis revealed considerable in‐situ concentrations of CO and H₂ in the O. algarvensis environment, Mediterranean seagrass sediments. Pore water H₂ concentrations (89–2147 nM) were up to two orders of magnitude higher than in seawater, and up to 36‐fold higher than previously known from shallow‐water marine sediments. Pore water CO concentrations (17–51 nM) were twice as high as in the overlying seawater (no literature data from other shallow‐water sediments are available for comparison). Ex‐situ incubation experiments showed that dead seagrass rhizomes produced large amounts of CO. CO production from decaying plant material could thus be a significant energy source for microbial primary production in seagrass sediments.     

Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2,4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4(1H)‐one. A Perspective from Molecular Dynamics Simulations

This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O₂) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O₂ in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O₂ moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O₂ from the protein, which can also be taken as gates for O₂ uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O₂. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.     

A computer-operated routine of gas exchange and optical measurements to diagnose photosynthetic apparatus in leaves

Photosynthesis is a complex process whose rate is affected by many biochemical and biophysical factors. Fortunately, it is possible to determine, or at least estimate, many of the most important parameters using a combination of optical methods and gas transient analyses. We describe here a computer‐operated routine that has been developed to make detailed assessments of photosynthesis at a comprehensive level. The routine comprised the following measurements: steady‐state light and CO₂ response curves of net CO₂ assimilation at 21 and 2 kPa O₂; transients from limiting to different saturating CO₂ concentrations at 2 kPa O₂; post‐illumination CO₂ fixation transient; dark–light induction of O₂ evolution; O₂ yield from one saturating single‐turnover flash; chlorophyll fluorescence F₀, F_s and F_m during the light and CO₂ response curves; leaf transmission at 820 nm (P700⁺) during the light and CO₂ response curves; post‐illumination re‐reduction time of P700⁺. The routine was executed on a two‐channel fast‐response gas exchange measurement system (A. Laisk and V. Oja: Dynamic Gas Exchange of Leaf Photosynthesis. CSIRO, Canberra, Australia). Thirty‐six intrinsic characteristics of the photosynthetic machinery were derived, including quantum yield of CO₂ fixation (Y_CO2), time constant of P700 re‐reduction (τ′), relative optical cross‐sections of PSII and PSI antennae (a_II, a_I), PSII and PSI density per leaf area unit, plastoquinone pool, total mesophyll resistance, mesophyll diffusion resistance, V_m, K_m(CO₂) and CO₂/O₂ specificity of Rubisco, RuBP pool at CO₂ limitation (assimilatory charge). An example of the routine and calculations are shown for one leaf and data are presented for leaves of 8‐year‐old‐trees of two birch clones growing in Suonenjoki Forest Research Station, Finland, during summer 2000. Parameters Y_CO2, basic τ′, a_II, a_I, K_m(CO₂) and K_s varied little in different leaves [relative standard deviation (RSD) < 7%], other parameters scattered widely (RSD typically 10–40%). It is concluded that the little scattered parameters are determined by basic physico‐chemical properties of the photosynthetic machinery whereas the widely scattered parameters are adjusting to growth conditions. The proposed non‐destructive routine is suitable for diagnosing the photosynthetic machinery of leaves and may be applied in plant ecophysiology and in genetic engineering of plants.     

Structural studies of constitutive nitric oxide synthases with diatomic ligands bound

Crystal structures are reported for the endothelial nitric oxide synthase (eNOS)–arginine–CO ternary complex as well as the neuronal nitric oxide synthase (nNOS) heme domain complexed with l-arginine and diatomic ligands, CO or NO, in the presence of the native cofactor, tetrahydrobiopterin, or its oxidized analogs, dihydrobiopterin and 4-aminobiopterin. The nature of the biopterin has no influence on the diatomic ligand binding. The binding geometries of diatomic ligands to nitric oxide synthase (NOS) follow the {MXY} ⁿ formalism developed from the inorganic diatomic–metal complexes. The structures reveal some subtle structural differences between eNOS and nNOS when CO is bound to the heme which correlate well with the differences in CO stretching frequencies observed by resonance Raman techniques. The detailed hydrogen-bonding geometries depicted in the active site of nNOS structures indicate that it is the ordered active-site water molecule rather than the substrate itself that would most likely serve as a direct proton donor to the diatomic ligands (CO, NO, as well as O₂) bound to the heme. This has important implications for the oxygen activation mechanism critical to NOS catalysis.     

Post‐illumination transient O2‐uptake is driven by photorespiration in tobacco leaves

This study aims to elucidate the molecular mechanism for the transient increase in the O₂‐uptake rate in tobacco (Nicotiana tabacum cv Xanthi) leaves after turning off actinic lights (ALs). The photosynthetic O₂ evolution rate reaches a maximum shortly after the onset of illumination with ALs and then decreases to zero in atmospheric CO₂/O₂ conditions. After turning off the ALs, tobacco leaves show a transient increase in the O₂‐uptake rate, the post‐illumination transient O₂‐uptake, and thereafter, the O₂‐uptake rate decreases to the level of the dark‐respiration rate. Photosynthetic linear electron flow, evaluated as the quantum yield of photosystem II [Y(II)], maintained a steady‐state value distinct from the photosynthetic O₂‐evolution rate. In high‐[CO₂] conditions, the photosynthetic O₂‐evolution rate and Y(II) showed a parallel behavior, and the post‐illumination transient O₂‐uptake was suppressed. On the other hand, in maize leaves (a C4 plant), even in atmospheric CO₂/O₂ conditions, Y(II) paralleled the photosynthetic O₂‐evolution rate and the post‐illumination transient O₂‐uptake was suppressed. Hypothesizing that the post‐illumination transient O₂‐uptake is driven by C3 plant photorespiration in tobacco leaves, we calculated both the ribulose 1,5‐bisphosphate carboxylase‐ and oxygenase‐rates (Vc and Vo) from photosynthetic O₂‐evolution and the post‐illumination transient O₂‐uptake rates. These values corresponded to those estimated from simultaneous chlorophyll fluorescence/O₂‐exchange analysis. Furthermore, the H⁺‐consumption rate for ATP synthesis in both photosynthesis and photorespiration, calculated from both Vc and Vo that were estimated from chlorophyll fluorescence/CO₂‐exchange analysis, showed a positive linear relationship with the dissipation rate of the electrochromic shift signal. Thus, these findings support our hypothesis.     

(S)‐(−)‐(2‐MeBu)N(Pr)2MeI Salt as Template in the Enantioselective Synthesis of the Enantiopure Two‐dimensional (S)‐(−)‐(2‐MeBu)N(Pr)2Me[ΛMnΔCr(C2O4)3] Ferromagnet

We describe herein the synthesis of (rac)‐ or enantiopure (S)‐(?)‐(2‐MeBu)N(Pr)₂MeI ammonium salts. These racemic and enantiopure ammonium salts were used as cationic templates to obtain new two‐dimensional (2D) ferromagnets [(rac)‐(2‐MeBu)N(Pr)₂Me][MnCr(C₂O₄)₃] and [(S)‐(?)‐(2‐MeBu)N(Pr)₂Me][ΔMnΛ nCr(C₂O₄)₃]. The absolute configuration of the hexacoordinated Cr(III) metallic ion in the enantiopure 2D network was determined by a circular dichroism measurement. The structure of [(2‐MeBu)N(Pr)₂Me][MnCr(C₂O₄)₃], established by single crystal X‐ray diffraction, belongs to the chiral P6₃ space group. According to direct current (dc) magnetic measurements, these compounds are ferrromagnets with a temperature Tc = 6°K. Chirality 25:444–448, 2013. © 2013 Wiley Periodicals, Inc.     

Differential carbon monoxide sensitivity of cytochrome C oxidase in the leaves of c(3) and c(4) plants

CO sensitivity of cytochrome a₃ in the leaves of a number of C₃ and C₄ plants was monitored by the nitrate reductase assay under differing CO to O₂ ratios. All the C₃ plants were relatively insensitive to CO and required a high CO to O₂ ratio of 40 to promote significant nitrate reductase activity. However, when treated with 2 millimolar 2,4-dinitrophenol, these leaves readily responded to CO even at low CO to O₂ ratios of 10 or less. On the other hand, the leaves of all C₄ plants tested, belonging to the three subgroups, were highly sensitive to CO, even at CO to O₂ ratios of 5 or less. In these leaves, the uncoupler was without any effect, probably because the mitochondria, either from mesophyll or bundle sheath cells or both, lacked tight respiratory control.     

Unveiling the Pathways of Dioxygen Through the C2 Component of the Environmentally Relevant Monooxygenase p‐Hydroxyphenylacetate Hydroxylase from Acinetobacter baumannii: A Molecular Dynamics Investigation

In this work, models of the homotetrameric C2 component of the monooxygenase p‐hydroxyphenylacetate hydroxylase from Acinetobacter baumannii, in complex with dioxygen (O₂) and, or not, the substrate p‐hydroxyphenylacetate (HPA) were built. Both models proved to be amenable to random‐acceleration molecular dynamics (RAMD) simulations, whereby a tiny randomly oriented external force, acting on O₂ at the active site in front of flavin mononucleotide (FMNH^?), accelerated displacement of O₂ toward the bulk solvent. This allowed us to carry out a sufficiently large number of RAMD simulations to be of statistical significance. The two systems behaved very similarly under RAMD, except for O₂ leaving the active site more easily in the absence of HPA, but then finding similar obstacles in getting to the gate as when the active site was sheltered by HPA. This challenges previous conclusions that HPA can only reach the active center after that the C4aOOH derivative of FMNH^? is formed, requiring uptake of O₂ at the active site before HPA. According to these RAMD simulations, O₂ could well get to FMNH^? also in the presence of the substrate at the active site.